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GEOCHEMISTRY ARTICLES – August 2019?Analytical ChemistryFerreiro, B., Andrade, J.M., Paz-Quintáns, C., López-Mahía, P., Muniategui-Lorenzo, S., Rey-Garrote, M., Vázquez-Padín, C., Vales, C., 2019. Improved sensitivity of natural gas infrared measurements using a filling gas. Energy & Fuels 33, 6929-6933.Hill, A.H., Fu, D., 2019. Cellular imaging using stimulated Raman scattering microscopy. Analytical Chemistry 91, 9333-9342.Lee, J., Jung, D., Park, K., 2019. Hydrophobic deep eutectic solvents for the extraction of organic and inorganic analytes from aqueous environments. TrAC Trends in Analytical Chemistry 118, 853-868.Raab, A., Feldmann, J., 2019. Biological sulphur-containing compounds – Analytical challenges. Analytica Chimica Acta 1079, 20-29.Rivera-Barrera, D., Rueda-Chacón, H., Molina V, D., 2019. Prediction of the total acid number (TAN) of Colombian crude oils via ATR–FTIR spectroscopy and chemometric methods. Talanta 206, 120186.Yeap, D., Hichwa, P.T., Rajapakse, M.Y., Peirano, D.J., McCartney, M.M., Kenyon, N.J., Davis, C.E., 2019. Machine vision methods, natural language processing, and machine learning algorithms for automated dispersion plot analysis and chemical identification from complex mixtures. Analytical Chemistry 91, 10509-10517.Gas Chromatography/GC×GC/GC-MSHatch, L.E., Jen, C.N., Kreisberg, N.M., Selimovic, V., Yokelson, R.J., Stamatis, C., York, R.A., Foster, D., Stephens, S.L., Goldstein, A.H., Barsanti, K.C., 2019. Highly speciated measurements of terpenoids emitted from laboratory and mixed-conifer forest prescribed fires. Environmental Science & Technology 53, 9418-9428.Nan, H., Kuroda, K., Takahashi, K., Anderson, J.L., 2019. Examining the unique retention behavior of volatile carboxylic acids in gas chromatography using zwitterionic liquid stationary phases. Journal of Chromatography A 1603, 288-296.Savareear, B., Escobar-Arnanz, J., Brokl, M., Saxton, M.J., Wright, C., Liu, C., Focant, J.-F., 2019. Non-targeted analysis of the particulate phase of heated tobacco product aerosol and cigarette mainstream tobacco smoke by thermal desorption comprehensive two-dimensional gas chromatography with dual flame ionisation and mass spectrometric detection. Journal of Chromatography A 1603, 327-337.Siriviboon, P., Tungkaburee, C., Weerawongphrom, N., Kulsing, C., 2019. Direct equations to retention time calculation and fast simulation approach for simultaneous material selection and experimental design in comprehensive two dimensional gas chromatography. Journal of Chromatography A 1602, 425-431.S?rensen, L., McCormack, P., Altin, D., Robson, W.J., Booth, A.M., Faksness, L.-G., Rowland, S.J., St?rseth, T.R., 2019. Establishing a link between composition and toxicity of offshore produced waters using comprehensive analysis techniques – A way forward for discharge monitoring? Science of The Total Environment 694, 133682.Sudol, P.E., Gough, D.V., Prebihalo, S.E., Synovec, R.E., 2020. Impact of data bin size on the classification of diesel fuels using comprehensive two-dimensional gas chromatography with principal component analysis. Talanta 206, 120239.Wallace, M.A.G., Pleil, J.D., Whitaker, D.A., Oliver, K.D., 2019. Recovery and reactivity of polycyclic aromatic hydrocarbons collected on selected sorbent tubes and analyzed by thermal desorption-gas chromatography/mass spectrometry. Journal of Chromatography A 1602, 19-29.Yang, X., Wang, C., Shao, H., Zheng, Q., 2019. Non-targeted screening and analysis of volatile organic compounds in drinking water by DLLME with GC–MS. Science of The Total Environment 694, 133494.Imaging: AFMGao, Y., Cai, X., Zhang, P., He, G., Gao, Q., Wan, J., 2019. Pore characteristics and evolution of Wufeng–Longmaxi Fms shale gas reservoirs in the basin-margin transition zone of SE Chongqing. Natural Gas Industry B 6, 323-332.Wang, C.-T., Jiang, B., Zhou, Y.-W., Jiang, T.-W., Liu, J.-H., Zhu, G.-D., Cai, W.-B., 2019. Exploiting the surface-enhanced IR absorption effect in the photothermally induced resonance AFM-IR technique toward nanoscale chemical analysis. Analytical Chemistry 91, 10541-10548.Zhang, Y., 2019. Similarities in diverse polycyclic aromatic hydrocarbons of asphaltenes and heavy oils revealed by noncontact atomic force microscopy: Aromaticity, bonding, and implications for reactivity, in: Rahimi, P., Ovalles, C., Zhang, Y., Adams, J.J. (Eds.), Chemistry Solutions to Challenges in the Petroleum Industry. American Chemical Society, Washington DC, pp. 39-65.Imaging: SEM, TEM, HIMBegum, M., Yassin, M.R., Dehghanpour, H., 2019. Effect of kerogen maturity on organic shale wettability: A Duvernay case study. Marine and Petroleum Geology 110, 483-496.Cornet, Y., Fran?ois, C., Compère, P., Callec, Y., Roberty, S., Plumier, J.C., Javaux, E.J., 2019. New insights on the paleobiology, biostratigraphy and paleogeography of the pre-Sturtian microfossil index taxon Cerebrosphaera. Precambrian Research 332, 105410.Fang, H., Sang, S., Liu, S., Du, Y., 2019. Methodology of three-dimensional visualization and quantitative characterization of nanopores in coal by using FIB-SEM and its application with anthracite in Qinshui basin. Journal of Petroleum Science and Engineering 182, 106285.Gao, Y., Cai, X., Zhang, P., He, G., Gao, Q., Wan, J., 2019. Pore characteristics and evolution of Wufeng–Longmaxi Fms shale gas reservoirs in the basin-margin transition zone of SE Chongqing. Natural Gas Industry B 6, 323-332.Gilbert, P.U.P.A., Porter, S.M., Sun, C.-Y., Xiao, S., Gibson, B.M., Shenkar, N., Knoll, A.H., 2019. Biomineralization by particle attachment in early animals. Proceedings of the National Academy of Sciences, 201902273.Guo, S., Mao, W., 2019. Division of diagenesis and pore evolution of a Permian Shanxi shale in the Ordos Basin, China. Journal of Petroleum Science and Engineering 182, 106351.Javaux, E.J., 2019. Challenges in evidencing the earliest traces of life. Nature 572, 451-460.Li, J., Zhang, P., Lu, S., Chen, C., Xue, H., Wang, S., Li, W., 2019. Scale-dependent nature of porosity and pore size distribution in lacustrine shales: An investigation by BIB-SEM and X-Ray CT methods. Journal of Earth Science 30, 823-833.Li, Z., Jiang, Z., Liang, Z., Yu, H., Yang, Y., 2019. Pore-structure characterisation of tectonically deformed shales: a case study of Wufeng-Longmaxi Formation in western Hunan Province, southern China. Australian Journal of Earth Sciences 66, 1075-1084.Li, Z., Liu, D., Cai, Y., Wang, Y., Teng, J., 2019. Adsorption pore structure and its fractal characteristics of coals by N2 adsorption/desorption and FESEM image analyses. Fuel 257, 116031.Liu, J., Sheng, J.J., Huang, W., 2019. Experimental investigation of microscopic mechanisms of surfactant-enhanced spontaneous imbibition in shale cores. Energy & Fuels 33, 7188-7199.Rangel-Alvarado, R.B., Willis, C.E., Kirk, J.L., St Louis, V.L., Amyot, M., Bélanger, D., Ariya, P.A., 2019. Athabasca oil sands region snow contains efficient micron and nano-sized ice nucleating particles. Environmental Pollution 252, 289-295.Ren, F., Zhu, Y., Liu, Q., Wu, H., 2019. Characteristics of morphology and mobility of iron species on iron-poisoned fluid catalytic cracking catalyst particles, in: Rahimi, P., Ovalles, C., Zhang, Y., Adams, J.J. (Eds.), Chemistry Solutions to Challenges in the Petroleum Industry. American Chemical Society, Washington DC, pp. 327-335.Singh, K., 2019. How hydraulic properties of organic matter control effective liquid permeability of mudrocks. Transport in Porous Media 129, 761-777.Vallalar, B., Meyer-Dombard, D.A.R., Cardace, D., Arcilla, C.A., 2019. Multimetal resistant, alkalitolerant bacteria isolated from serpentinizing fluid-associated sediments and acid mine drainage in the Zambales ophiolite, the Philippines. Geomicrobiology Journal 36, 792-809.Wang, M., Ma, R., Li, J., Lu, S., Li, C., Guo, Z., Li, Z., 2019. Occurrence mechanism of lacustrine shale oil in the Paleogene Shahejie Formation of Jiyang Depression, Bohai Bay Basin, China. Petroleum Exploration and Development 46, 833-846.Wei, M., Zhang, L., Xiong, Y., Peng, P.a., 2019. Main factors influencing the development of nanopores in over-mature, organic-rich shales. International Journal of Coal Geology 212, 103233.Yan, J., He, X., Zhang, S., Feng, C., Wang, J., Hu, Q., Cai, J., Wang, M., 2020. Sensitive parameters of NMR T2 spectrum and their application to pore structure characterization and evaluation in logging profile: A case study from Chang 7 in the Yanchang Formation, Heshui area, Ordos Basin, NW China. Marine and Petroleum Geology 111, 230-239.Zhang, W., Hu, W., Borjigin, T., Zhu, F., 2020. Pore characteristics of different organic matter in black shale: A case study of the Wufeng-Longmaxi Formation in the Southeast Sichuan Basin, China. Marine and Petroleum Geology 111, 33-43.Zhang, Y., Barber, T.J., Hu, Q., Bleuel, M., El-Sobky, H.F., 2019. Complementary neutron scattering, mercury intrusion and SEM imaging approaches to micro- and nano-pore structure characterization of tight rocks: A case study of the Bakken shale. International Journal of Coal Geology 212, 103252.Zhou, W., Jiang, Z., Qiu, H., Jin, X., Wang, R., Cen, W., Tang, X., Li, X., Wang, G., Cao, X., Sun, Y., 2019. Shale gas accumulation conditions and prediction of favorable areas for the Lower Carboniferous Luzhai Formation in Guizhong depression Acta Petrolei Sinica 40, 798-812.Imaging: Xray CTDing, H., Wang, Y., Shapoval, A., Zhao, Y., Rahman, S., 2019. Macro- and microscopic studies of “smart water” flooding in carbonate rocks: An image-based wettability examination. Energy & Fuels 33, 6961-6970.Gooya, R., Silvestri, A., Moaddel, A., Andersson, M.P., Stipp, S.L.S., S?rensen, H.O., 2019. Unstable, super critical CO2–water displacement in fine grained porous media under geologic carbon sequestration conditions. Scientific Reports 9, 11272.Li, J., Zhang, P., Lu, S., Chen, C., Xue, H., Wang, S., Li, W., 2019. Scale-dependent nature of porosity and pore size distribution in lacustrine shales: An investigation by BIB-SEM and X-Ray CT methods. Journal of Earth Science 30, 823-833.Li, Q., Jew, A.D., Kohli, A., Maher, K., Brown, G.E., Bargar, J.R., 2019. Thicknesses of chemically altered zones in shale matrices resulting from interactions with hydraulic fracturing fluid. Energy & Fuels 33, 6878-6889.Qin, Z., Arshadi, M., Piri, M., 2019. Micro-scale experimental investigations of multiphase flow in oil-wet carbonates. I. In situ wettability and low-salinity waterflooding. Fuel 257, 116014.Qin, Z., Arshadi, M., Piri, M., 2019. Micro-scale experimental investigations of multiphase flow in oil-wet carbonates. II. Tertiary gas injection and WAG. Fuel 257, 116012.Wang, G., Qin, X., Shen, J., Zhang, Z., Han, D., Jiang, C., 2019. Quantitative analysis of microscopic structure and gas seepage characteristics of low-rank coal based on CT three-dimensional reconstruction of CT images and fractal theory. Fuel 256, 115900.Yan, J., He, X., Zhang, S., Feng, C., Wang, J., Hu, Q., Cai, J., Wang, M., 2020. Sensitive parameters of NMR T2 spectrum and their application to pore structure characterization and evaluation in logging profile: A case study from Chang 7 in the Yanchang Formation, Heshui area, Ordos Basin, NW China. Marine and Petroleum Geology 111, 230-239.Liquid Chromatography/LC-MS/SFCArrizabalaga-Larra?aga, A., Rodríguez, P., Medina, M., Santos, F.J., Moyano, E., 2019. Simultaneous analysis of natural pigments and E-141i in olive oils by liquid chromatography–tandem mass spectrometry. Analytical and Bioanalytical Chemistry 411, 5577-5591.Becker, C., Jochmann, M.A., Teutenberg, T., Schmidt, T.C., 2020. A nebulizer interface for liquid chromatography - Flame ionization detection: Development and validation. Talanta 206, 120229.Cao, J.-L., Ma, L.-J., Wang, S.-P., Deng, Y., Wang, Y.-T., Li, P., Wan, J.-B., 2019. Comprehensive qualitative and quantitative analysis of ginsenosides in Panax notoginseng leaves by online two-dimensional liquid chromatography coupled to hybrid linear ion trap Orbitrap mass spectrometry with deeply optimized dilution and modulation system. Analytica Chimica Acta 1079, 237-251.Carrasco-Correa, E.J., Kubáň, P., Cocovi-Solberg, D.J., Miró, M., 2019. Fully automated electric-field-driven liquid phase microextraction system with renewable organic membrane as a front end to high performance liquid chromatography. Analytical Chemistry 91, 10808-10815.Chen, Y., Li, J., Schmitz, O.J., 2019. Development of an at-column dilution modulator for flexible and precise control of dilution factors to overcome mobile phase incompatibility in comprehensive two-dimensional liquid chromatography. Analytical Chemistry 91, 10251-10257.Dou, M., Tsai, C.-F., Piehowski, P.D., Wang, Y., Fillmore, T.L., Zhao, R., Moore, R.J., Zhang, P., Qian, W.-J., Smith, R.D., Liu, T., Kelly, R.T., Shi, T., Zhu, Y., 2019. Automated nanoflow two-dimensional reversed-phase liquid chromatography system enables in-depth proteome and phosphoproteome profiling of nanoscale samples. Analytical Chemistry 91, 9707-9715.Drotleff, B., L?mmerhofer, M., 2019. Guidelines for selection of internal standard-based normalization strategies in untargeted lipidomic profiling by LC-HR-MS/MS. Analytical Chemistry 91, 9836-9843.Horai, S., Yamauchi, N., Naraoka, H., 2019. Simultaneous total analysis of core and polar membrane lipids in archaea by high-performance liquid chromatography/high-resolution mass spectrometry coupled with heated electrospray ionization. Rapid Communications in Mass Spectrometry 33, 1571-1577.Hutchins, P.D., Russell, J.D., Coon, J.J., 2019. Accelerating lipidomic method development through in silico simulation. Analytical Chemistry 91, 9698-9706.Lazzari, E., Arena, K., Caram?o, E.B., Herrero, M., 2019. Quantitative analysis of aqueous phases of bio-oils resulting from pyrolysis of different biomasses by two-dimensional comprehensive liquid chromatography. Journal of Chromatography A 1602, 359-367.Rédei, C., Felinger, A., 2019. Modeling the competitive adsorption of sample solvent and solute in supercritical fluid chromatography. Journal of Chromatography A 1603, 348-354.S?rensen, L., McCormack, P., Altin, D., Robson, W.J., Booth, A.M., Faksness, L.-G., Rowland, S.J., St?rseth, T.R., 2019. Establishing a link between composition and toxicity of offshore produced waters using comprehensive analysis techniques – A way forward for discharge monitoring? Science of The Total Environment 694, 133682.Thakur, N., Wahab, M.F., Khanal, D.D., Armstrong, D.W., 2019. Synthetic aluminosilicate based geopolymers – Second generation geopolymer HPLC stationary phases. Analytica Chimica Acta 1081, 209-217.Thi?ner, J.B., Nett, L., Zhou, S., Preibisch, Y., Hollert, H., Achten, C., 2019. Identification of 7–9 ring polycyclic aromatic hydrocarbons in coals and petrol coke using High performance liquid chromatography – Diode array detection coupled to Atmospheric pressure laser ionization – Mass spectrometry (HPLC-DAD-APLI-MS). Environmental Pollution 252, 723-732.Wang, J., Liu, G., Xu, Y., Zhu, B., Wang, Z., 2019. Separation and characterization of new components and impurities in leucomycin by multiple heart-cutting two-dimensional liquid chromatography combined with ion trap/time-of-flight mass spectrometry. Chromatographia 82, 1333-1344.Wei, W., Hou, J., Yao, C., Bi, Q., Wang, X., Li, Z., Jin, Q., Lei, M., Feng, Z., Wu, W., Guo, D., 2019. A high-efficiency strategy integrating offline two-dimensional separation and data post-processing with dereplication: Characterization of bufadienolides in Venenum Bufonis as a case study. Journal of Chromatography A 1603, 179-189.Xiang, P., Yang, Y., Zhao, Z., Chen, A., Liu, S., 2019. Experimentally validating open tubular liquid chromatography for a peak capacity of 2000 in 3 h. Analytical Chemistry 91, 10518-10523.Xiang, P., Yang, Y., Zhao, Z., Chen, M., Liu, S., 2019. Ultrafast gradient separation with narrow open tubular liquid chromatography. Analytical Chemistry 91, 10738-10743.Xu, J., Zheng, L., Su, G., Sun, B., Zhao, M., 2019. An improved peak clustering algorithm for comprehensive two-dimensional liquid chromatography data analysis. Journal of Chromatography A 1602, 273-283.Zhang, T.-Y., Li, S., Zhu, Q.-F., Wang, Q., Hussain, D., Feng, Y.-Q., 2019. Derivatization for liquid chromatography-electrospray ionization-mass spectrometry analysis of small-molecular weight compounds. TrAC Trends in Analytical Chemistry 119, 115608.Mass Spectroscopy/ICR-FTMS/OrbitrapAlharbi, H.A., Morandi, G.D., Jones, P.D., Wiseman, S.B., Giesy, J.P., 2019. Comparison of the effects of extraction techniques on mass spectrometry profiles of dissolved organic compounds in oil sand process-affected water. Energy & Fuels 33, 7001-7008.Cao, J.-L., Ma, L.-J., Wang, S.-P., Deng, Y., Wang, Y.-T., Li, P., Wan, J.-B., 2019. Comprehensive qualitative and quantitative analysis of ginsenosides in Panax notoginseng leaves by online two-dimensional liquid chromatography coupled to hybrid linear ion trap Orbitrap mass spectrometry with deeply optimized dilution and modulation system. Analytica Chimica Acta 1079, 237-251.Hegazi, A.H., Fathalla, E.M., Andersson, J.T., 2019. Organic geochemically significant high-molecular-mass sulfur compounds of North African crude oils. Energy & Fuels 33, 6995-7000.Hutchins, P.D., Russell, J.D., Coon, J.J., 2019. Accelerating lipidomic method development through in silico simulation. Analytical Chemistry 91, 9698-9706.Luo, L., Chen, Z., Cheng, Y., Lv, J., Cao, D., Wen, B., 2019. Effects of dissolved organic carbon on desorption of aged phenanthrene from contaminated soils: A mechanistic study. Environmental Pollution 254, 113016.Maria, E., Cran?on, P., Lespes, G., Bridoux, M.C., 2019. Spatial variation in the molecular composition of dissolved organic matter from the podzol soils of a temperate pine forest. ACS Earth and Space Chemistry 3, 1685-1696.Niu, X.-Z., Harir, M., Schmitt-Kopplin, P., Croué, J.-P., 2019. Sunlight-induced phototransformation of transphilic and hydrophobic fractions of Suwannee River dissolved organic matter. Science of The Total Environment 694, 133737.Porto, C.F.C., Pinto, F.E., Souza, L.M., Madeira, N.C.L., Neto, ?.C., de Menezes, S.M.C., Chinelatto, L.S., Freitas, C.S., Vaz, B.G., Lacerda, V., Rom?o, W., 2019. Characterization of organosulfur compounds in asphalt cement samples by ESI(+)FT-ICR MS and 13C NMR spectroscopy. Fuel 256, 115923.Riva, M., Ehn, M., Li, D., Tomaz, S., Bourgain, F., Perrier, S., George, C., 2019. CI-Orbitrap: An analytical instrument to study atmospheric reactive organic species. Analytical Chemistry 91, 9419-9423.S?rensen, L., McCormack, P., Altin, D., Robson, W.J., Booth, A.M., Faksness, L.-G., Rowland, S.J., St?rseth, T.R., 2019. Establishing a link between composition and toxicity of offshore produced waters using comprehensive analysis techniques – A way forward for discharge monitoring? Science of The Total Environment 694, 133682.Tucker, L.H., Hamm, G.R., Sargeant, R.J.E., Goodwin, R.J.A., Mackay, C.L., Campbell, C.J., Clarke, D.J., 2019. Untargeted metabolite mapping in 3D cell culture models using high spectral resolution FT-ICR mass spectrometry imaging. Analytical Chemistry 91, 9522-9529.Xu, J.-X., Li, X.-M., Sun, G.-X., Cui, L., Ding, L.-J., He, C., Li, L.-G., Shi, Q., Smets, B.F., Zhu, Y.-G., 2019. Fate of labile organic carbon in paddy soil is regulated by microbial ferric iron reduction. Environmental Science & Technology 53, 8533-8542.Zhang, L., Peng, Y., Ge, Z., Xu, K., 2019. Fate of dissolved organic nitrogen during the Anammox process using ultra-high resolution mass spectrometry. Environment International 131, 105042.Kanawati, B., Schmitt-Kopplin, P. (Eds.), 2019. Fundamentals and Applications of Fourier Transform Mass Spectrometry, Elsevier, 786pp.Wanczek, K.P., Kanawati, B., 2019. Chapter 1 - Historical developments in Fourier transform ion cyclotron resonance mass spectrometry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 3-33.Makarov, A., Grinfeld, D., Ayzikov, K., 2019. Chapter 2 - Fundamentals of Orbitrap analyzer, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 37-61.Easterling, M.L., Agar, J.N., 2019. Chapter 3 - Fundamentals, strengths, and future directions for Fourier transform ion cyclotron resonance mass spectrometry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 63-88.Nikolaev, E.N., Kostyukevich, Y.I., Vladimirov, G., 2019. Chapter 4 - Fundamentals and simulations in FT-ICR-MS, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 89-111.Tsybin, Y.O., Nagornov, K.O., Kozhinov, A.N., 2019. Chapter 5 - Advanced fundamentals in Fourier transform mass spectrometry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 113-132.Kanawati, B., Wanczek, K.P., Schmitt-Kopplin, P., 2019. Chapter 6 - Data processing and automation in Fourier transform mass spectrometry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 133-185.Floris, F., O'Connor, P.B., 2019. Chapter 7 - Fundamentals of two dimensional Fourier transform mass spectrometry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 187-232.Fernandez-Lima, F., 2019. Chapter 8 - Trapped ion mobility spectrometry coupled to FT-ICR MS: Fundamentals and applications, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 233-251.Kreutzer, L., Aichler, M., Walch, A.K., 2019. Chapter 9 - In situ metabolomics in cancer tissue by high-resolution mass spectrometry imaging, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 253-279.Aubriet, F., Carré, V., 2019. Chapter 10 - Fourier transform ion cyclotron resonance mass spectrometry and laser: A versatile tool, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 281-322.Junot, C., Fenaille, F., 2019. Chapter 11 - Metabolomics using Fourier transform mass spectrometry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 325-356.Moritz, F., Hemmler, D., Kanawati, B., Schnitzler, J.-P., Schmitt-Kopplin, P., 2019. Chapter 12 - Mass differences in metabolome analyses of untargeted direct infusion ultra-high resolution MS data, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 357-405.Gonsior, M., 2019. Chapter 13 - FT-ICR MS and Orbitrap mass spectrometry approaches in environmental chemistry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 407-423.Kovalev, S.V., Lebedev, A.T., 2019. Chapter 14 - Identification of biologically active peptides by means of Fourier transform mass spectrometry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 425-468.Filho, J.F.A., Lacerda, V., Rom?o, W., 2019. Chapter 15 - Fourier transform mass spectrometry applied to Forensic Chemistry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 469-508.Pereira, I., de Aguiar, D.V.A., Vasconselos, G., Vaz, B.G., 2019. Chapter 16 - Fourier transform mass spectrometry applied to petroleomics, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 509-528.Vinh, J., 2019. Chapter 17 - Proteomics and proteoforms: Bottom-up or top-down, how to use high-resolution mass spectrometry to reach the Grail, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 529-567.Wanczek, K.P., Kanawati, B., 2019. Chapter 18 - Gas phase ion-molecule reactions of inorganic compounds in FT-ICR-MS, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 569-591.Dillinger, S., Niedner-Schatteburg, G., 2019. Chapter 19 - Cryo trapping by FT-MS for kinetics and spectroscopy, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 593-621.Duan, J., Amster, I.J., 2019. Chapter 20 - Application of FTMS to the analysis of glycosaminoglycans, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 623-649.Rychlik, M., Kanawati, B., Roullier-Gall, C., Hemmler, D., Liu, Y., Alexandre, H., Gougeon, R.D., Gmelch, L., Gotthardt, M., Schmitt-Kopplin, P., 2019. Chapter 21 - Foodomics assessed by Fourier transform mass spectrometry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 651-677.Hertzog, J., Carré, V., Aubriet, F., 2019. Chapter 22 - Contribution of Fourier transform mass spectrometry to bio-oil study, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 679-733.Mass Spectroscopy/OtherCantrell, T.P., Freeman, C.J., Paul, V.J., Agarwal, V., Garg, N., 2019. Mass spectrometry-based integration and expansion of the chemical diversity harbored within a marine sponge. Journal of The American Society for Mass Spectrometry 30, 1373-1384.Huang, X., Jiang, J., Zhang, Y., Zhan, L., Liu, C., Xiong, C., Nie, Z., 2019. A miniature particle mass spectrometer. Analytical Chemistry 91, 9393-9397.Huba, A.K., Mirabelli, M.F., Zenobi, R., 2019. Understanding and optimizing the ionization of polycyclic aromatic hydrocarbons in dielectric barrier discharge sources. Analytical Chemistry 91, 10694-10701.Jones, E.A., Simon, D., Karancsi, T., Balog, J., Pringle, S.D., Takats, Z., 2019. Matrix assisted rapid evaporative ionization mass spectrometry. Analytical Chemistry 91, 9784-9791.So, P.-K., Yang, B.-C., Li, W., Wu, L., Hu, B., 2019. Simple fabrication of solid-phase microextraction with surface-coated aluminum foil for enhanced detection of analytes in biological and clinical samples by mass spectrometry. Analytical Chemistry 91, 9430-9434.Su, Y., Ma, X., Page, J., Shi, R., Xia, Y., Ouyang, Z., 2019. Mapping lipid C=C location isomers in organ tissues by coupling photochemical derivatization and rapid extractive mass spectrometry. International Journal of Mass Spectrometry 445, 116206.Metabolomics/LipidomicsCantrell, T.P., Freeman, C.J., Paul, V.J., Agarwal, V., Garg, N., 2019. Mass spectrometry-based integration and expansion of the chemical diversity harbored within a marine sponge. Journal of The American Society for Mass Spectrometry 30, 1373-1384.Drotleff, B., L?mmerhofer, M., 2019. Guidelines for selection of internal standard-based normalization strategies in untargeted lipidomic profiling by LC-HR-MS/MS. Analytical Chemistry 91, 9836-9843.Haslauer, K.E., Hemmler, D., Schmitt-Kopplin, P., Heinzmann, S.S., 2019. Guidelines for the use of deuterium oxide (D2O) in 1H NMR metabolomics. Analytical Chemistry.Horai, S., Yamauchi, N., Naraoka, H., 2019. 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The latter, from the Late Miocene, is demonstrated in the present study.The fluorite system is characterized by the involvement of oil in the hydrothermal fluids. This oil was produced in the local environment of the deposit from the thermal maturation of the Albian Fahdene black shale source-rock at temperature range of~140?°C–~100?°C. Two brines were involved in the fluorite hydrothermal system. The first one (L1) is a Ca-rich brine (≥20?wt % bulk salinity), with Na/Ca ≤ 0.18, which is thought to have long resided in the basement, before its transfer into the Jurassic reservoir (Upper Nara Formation) and its eventual mobilization at the time of ore deposition. The second brine (L2), less saline (≤14?wt % bulk salinity) is more sodic, with Na/Ca up to 0.53, and represents unmodified brine originated from the nearby Triassic salt. The L1 brine was F-bearing, whereas the L2 brine was associated with oil. Fluorite deposition occurred at the estimated shallow depth of 1.7?km from cooling of the L1 brine due to the first isobaric cooling from ~160?°C to 135?°C under sub-lithostatic conditions (36?MPa). This stage is followed by mixing with the newly incoming L2 brines (transporting oil) along a sub-isochoric decompression path (down to the hydrostatic pressure at 17?MPa) and continuously cooling from 135?°C to 125?°C. The cooling and mixing caused fluorite deposition after which a transient heat advection episode (up to 145?°C) caused late calcite deposition prior to the end of hydrothermal circulation.Adepehin, E.J., Ali, C.A., Zakaria, A.A., Sali, M.S., 2019. An overview of 20 years’ hydrocarbon exploration studies and findings in the Late Cretaceous-to-Tertiary onshore Central Sarawak, NW Borneo: 1997–2017 in retrospect. Journal of Petroleum Exploration and Production Technology 9, 1593-1614. overview and integration of key petroleum exploration findings in the onshore Central Sarawak Basin, NW Borneo in the last 2 decades is presented. Findings revealed that critical moments for the generation and preservation of hydrocarbon may be found in the Early Oligocene, Early Miocene, and Late Miocene times. Geochemical data of ninety-five (95) source rocks suggest TOC values of 1.54 wt% (Miri Formation) to 70.00 wt% (Nyalau Formation) with promising S2 and S2/S3 ratios. TMax fell below the 435 °C maturation threshold. Reservoir facies of the Nyalau, Belait, and Lambir formations and their subsurface equivalents have moderate-to-poor poro-perm properties. Reservoir plays in the area are the Oligocene–Miocene clastics and limestones of Cycles I, II, III, and IV. Significant diagenetic modification is evident in analogue reservoir sandstones, and could constitute major poro-perm control in subsurface reservoir units. Observed predominance of structural related traps gleaned from seismic data is a reflection of the paleotectonic (Sarawak orogenic) event (ca. 40???36 Ma) associated with the region. Shale rocks overlying possible reservoirs and observed juxtaposition of reservoir units against impermeable beds provide seal integrity. Deeply seated faults are potential conduits, in addition to buoyancy. Concentration of future research efforts on petroleum/basin modeling and subsurface reservoir assessment was to further improve current understanding of the under-explored onshore Central Sarawak.Afshar, Z., Millard, A., Roberts, C., Gr?cke, D., 2019. The evolution of diet during the 5th to 2nd millennium BCE for the population buried at Tepe Hissar, north-eastern Central Iranian Plateau: The stable isotope evidence. Journal of Archaeological Science: Reports 27, 101983. study investigated subsistence economy and dietary changes during the Chalcolithic and Bronze Ages (the 5th to 2nd millennium BCE) in the Central Iranian Plateau through a study of skeletal remains buried at Tepe Hissar, Iran. Tepe Hissar experienced widespread socio-cultural and economic transitions during this period. These changes were accompanied by conflict, site abandonment, and reoccupation. This research hypothesised that these socio-cultural and economic changes impacted the subsistence economy and diet of the population. δ13C and δ15N was analysed in human bone collagen from 69 adult male and female skeletons from Chalcolithic and Bronze Age Tepe Hissar (Hissar I, II, and III Period). The data showed no significant change in diet during this time, with both sexes from different age-categories having a similar diet. This data did not support the working hypothesis stating that some dietary changes, probably, had occurred in this long period. The isotopic evidences suggested a mixed diet based on C3 terrestrial plants, animal protein, and a small proportion of fresh water resources. Thus the Tepe Hissar population may have had access to similar food resources during the three millennia of its existence, possibly due to climate continuity in this region. However, the remarkable cultural changes evidenced at this site appear not to have had a significant impact on the diet of people during this time.Akalin, E., Kim, Y.-M., Alper, K., Oja, V., Tekin, K., Durukan, I., Siddiqui, M.Z., Karag?z, S., 2019. Co-hydrothermal liquefaction of lignocellulosic biomass with Kukersite oil shale. Energy & Fuels 33, 7424-7435. co-hydrothermal liquefaction of black pine wood (BPW) with Kukersite oil shale (KOS) at different blend ratios of BPW/KOS (1:1, 1:2, and 2:1) was conducted at 300 °C for 30 min. No synergistic effects on oil yields from the co-hydrothermal processing have been observed. However, when the methanol was substituted with hot compressed water as the solvent, positive synergistic effects on the oil yields were observed for all blend ratios, but the heating values of the oils from hydrothermal processing were higher than those from supercritical methanol processing under identical conditions. Co-hydrothermal liquefaction of BPW with KOS produced oils with less oxygen than those from co-supercritical methanol processing of BPW with KOS under identical conditions. The highest heating value from co-processing was 30.22 MJ/kg, which was obtained from the co-hydrothermal liquefaction of BPW with KOS at a blend ratio of 1:2. Oils from the co-hydrothermal liquefaction of BPW with KOS contained phenols, acids, ketones, and aldehydes. Guaiacol was the primary compound detected in the oils from co-hydrothermal processing. The relative yield of this compound was highest at a blend ratio of 1:2 (BPW/KOS). The prominent compounds in oils from the co-supercritical methanol processing were esters and phenols.Al Disi, Z.A., Zouari, N., Dittrich, M., Jaoua, S., Al-Kuwari, H.A.S., Bontognali, T.R.R., 2019. Characterization of the extracellular polymeric substances (EPS) of Virgibacillus strains capable of mediating the formation of high Mg-calcite and protodolomite. Marine Chemistry 216, 103693. origin of dolomite –a common mineral in the geological record– is the subject of an ongoing debate. Among different hypotheses, it has been proposed that extracellular polymeric substances (EPS) excreted by microbes include organic molecules that catalyze the incorporation of Mg in the carbonate mineral. However, limited information exists on the composition of the EPS produced by Ca-Mg carbonate-forming microbes, which in turn hampers a precise understanding of their role in the mineralization mechanism. Here, we present the results of laboratory experiments in which we cultured different strains of microbes, characterized their EPS, and identified components associated with carbonate minerals with high mol% Mg. Two Virgibacillus strains known to mediate the formation of Mg-rich carbonates, as well as a strain of Bacillus licheniformis –a negative control that does not mediate mineral formation but produces EPS, were grown under different salinities and temperatures, which caused them to produce EPS with different compositions. The EPS were subsequently characterized by measuring total carbohydrate (TCHO) and total protein (TP) contents, as well as by Fourier-transform infrared spectroscopy (FTIR). At the tested conditions, we found that Mg-carbonates with a mol% Mg higher than 40% (i.e., potential dolomite precursor phases) formed exclusively in association with EPS rich in carbohydrates (TCHO > than 75% of the total mass). FTIR spectra of Ca-Mg carbonate-forming strains were distinct from those of the non-mineral-forming strain in areas associated with the protein structures responsible for the formation of hydrogels, which contribute to hydration or dehydration of ionic clusters; further differences have been observed in the regions of phosphoryl functional groups. These results provide insight on which fraction of organic molecules and specific functional groups are, among the many constituents of EPS, important for mineral nucleation and incorporation of Mg into carbonate minerals, a crucial step for the formation of dolomite in natural environments.Alam, M.A., Wu, J., Xu, J., Wang, Z., 2019. Enhanced isolation of lipids from microalgal biomass with high water content for biodiesel production. Bioresource Technology 291, 121834. present study, lipids were extracted from unbroken microalga Chlorella vulgaris with high water content (50% microalgal solution) through three-phase partitioning (TPP). The method was found to extract around 15.9% of total lipid transformable to methyl esters (LTMEs) from unbroken microalgal cells which is two times of Bligh and Dyer method. We investigated the effects of various parameters on TPP performance and were optimised through response surface methodology. The results indicated that incubation duration, temperature and extraction time were positively correlated with LTME extraction efficiency. The optimum temperature was 60?°C, incubation duration was 120?min, extraction time was 60?min, ratio of solvent to DKP was 1:1. The FAME yield was calculated as 12.05% and major fatty acids together accounted for 71.33% which indicated the great potential of the proposed lipid extraction procedure for microalga-based biodiesel production.Algazlan, M., Pinetown, K., Grigore, M., Chen, Z., Sarmadivaleh, M., Roshan, H., 2019. Petrophysical assessment of Australian organic-rich shales: Beetaloo, Cooper and Perth basins. Journal of Natural Gas Science and Engineering 70, 102952. extensive research conducted on North American and Chinese shale plays, fairly little has been reported on Australian gas-shales and no comparative study exists to assess their complexity associated with their geological setting and mineralogical compositions. We thus performed an extensive set of petrophysical characterizations including mineralogy, porosity, permeability, pore size distribution, fracture system, wettability, adsorption capacity, and mechanical properties of four organic-rich shale formations from across some of the major Australian sedimentary basins (Beetaloo, Perth, and Cooper).The results of the petrophysical characterisations reveal that the middle Velkerri formation from Beetaloo basin has the highest potential for future development amongst formations studied in these three basins. Generally, a) the samples show consistent water wet contact angles despite having fairly different TOC, b) the uniaxial compressive strength is not correlated to the amount of clay content of the samples and c) a positive correlation is observed between the Quartz content and TOC.Algeo, T.J., Brayard, A., Richoz, S., 2019. The Smithian-Spathian boundary: A critical juncture in the Early Triassic recovery of marine ecosystems. Earth-Science Reviews 195, 1-6. Smithian-Spathian boundary (SSB), i.e., the transition between the Smithian and Spathian substages of the Olenekian Stage (late Early Triassic), was a key interval associated with major climatic, oceanic and biotic changes at a global scale (Fig. 1). It coincided with the first sustained amelioration of marine conditions and recovery of marine ecosystems following the end-Permian crisis. Specifically, the SSB marked a shift away from the widely fluctuating and frequently extreme global environmental conditions that characterized the first ~2 million years of the Early Triassic (i.e., the Griesbachian, Dienerian, and Smithian substages) to less severe conditions during the latter part of the Early Triassic (i.e., the Spathian substage). At the SSB, a major cooling event was accompanied by re-invigorated global-ocean circulation and turnovers in a number of marine invertebrate clades. The present thematic issue explores these developments in a series of 11 studies covering aspects of the biostratigraphy, paleoecology, paleoceanography, and volcanic history of the late Early Triassic, with special emphasis on the SSB (Fig. 1, Fig. 2). These studies represent the current state of knowledge regarding the SSB event and lay the groundwork for future studies on this topic.Alharbi, H.A., Morandi, G.D., Jones, P.D., Wiseman, S.B., Giesy, J.P., 2019. Comparison of the effects of extraction techniques on mass spectrometry profiles of dissolved organic compounds in oil sand process-affected water. Energy & Fuels 33, 7001-7008. advances in mass spectrometry have facilitated chemical characterization and profiling of complex environmental mixtures such as oil sand process-affected water (OSPW) and identification of previously unresolved chemicals. However, because OSPW is a complex mixture of salts, metals, suspended particulate matter, and dissolved organics, extraction techniques are required to reduce the effects of signal suppression/enhancement. In this work, Orbitrap, ultrahigh resolution mass spectrometry was used to perform a comprehensive comparison of solid phase extraction (SPE) and liquid–liquid extraction (LLE) techniques on profiling of dissolved organic chemicals in OSPW. When operated in negative ion mode, extraction of naphthenic acid (NAs–O2) was dependent on acidification of OSPW samples for C18 and LLE techniques. However, when applying a hydrophilic lipophilic balance (HLB) sorbent (ABN) SPE technique, the extractability of NAs was independent of pH. When operated in positive ion mode, for all extraction methods, nitrogen- and sulfur-containing species were more abundant and diverse in basic extracts than in acidic extracts and ABN extracted the greatest number of chemical species including nitrogen-, sulfur-, and oxygen-containing species. Overall, this study supports the utility of HLB SPE techniques for profiling of species of dissolved organic chemicals in OSPW at environmentally relevant pH.Alkan, H., Szabries, M., Dopffel, N., Koegler, F., Baumann, R.-P., Borovina, A., Amro, M., 2019. Investigation of spontaneous imbibition induced by wettability alteration as a recovery mechanism in microbial enhanced oil recovery. Journal of Petroleum Science and Engineering 182, 106163. paper explores the potential of spontaneous imbibition (SI) induced by wettability alteration to improve incremental oil recovery during microbial enhanced oil recovery (MEOR). A laboratory work is presented that consists of SI and contact angle (CA) tests on reservoir and outcrop sandstone cores. The SI and CA measurements were conducted with aqueous phases with/without MEOR to assess the incremental recovery mechanism triggered by the wettability alteration during MEOR. It was observed that the oil recovery in the SI experiments with the MEOR nutrient solution reached a plateau at 0.62?±?0.05% of original oil in place (OOIP) while it was 0.32?±?0.02% of OOIP with the non-MEOR reference SI experiment conducted in outcrop sandstone cores. The CA of the oil droplet measured on polished reservoir rock sample decreased from 120° to 60° when exposed to the MEOR nutrient solutions. The observed changes occurred in parallel to the growth process of the bacteria in both SI and CA tests.The experimental data shows that the wettability alteration needs cell growth because SI experiments performed only with metabolites and without microbial cells exhibited negligible incremental recovery. Numerical models calibrated with SI experiments demonstrated the wettability alteration as one of the potential MEOR mechanisms. The bacterial network that forms a biofilm at the oil-water interface, and hence, creates a viscoelastic layer is thought to be the main cause of wettability alteration, which is supported by the oscillating pendant drop measurements.Alrowaie, M.A., Jubb, A.M., Schimmelmann, A., Mastalerz, M., Pratt, L.M., 2019. Hydrous heating experiments at 130?°C yield insights into the occurrence of hydrogen sulfide and light alkanes in natural gas reservoirs. Organic Geochemistry 137, 103901. understanding of the origin of produced volatiles from conventional reservoirs and unconventional source rocks is critical for petroleum exploration and production. A series of hydrous heating experiments using two immature Type II siliciclastic source rocks, Pennsylvanian Turner Mine shale (TMS) and Devonian New Albany Shale (NAS), at 130?°C over one to two years were conducted to assess gas generation at low temperature. Elemental sulfur (ES) was added to the NAS samples to evaluate the role of sulfur on thermochemical sulfate reduction (TSR). The produced volatile composition was investigated in situ using Raman spectroscopy at the end of the heating experiments. Results show that the two source rocks yield different types and concentrations of volatiles. Only CH4 and CO2 were detected following hydrous heating of the TMS source rock in contrast to CH4, C2H6, C3H8, and CO2 which were observed in experiments using NAS. Variations in the produced volatiles are likely the result of compositional differences within the respective source rock organic matter. Experiments involving ES show strong H2S signals that are likely due to the formation of H2S from the reaction of ES with water at 130?°C. H2S signals correlate with a greater relative concentration of CH4 and CO2 compared to experiments where ES was not added, on a time-normalized basis. The correlation between the presence of H2S and an increase in CH4 and CO2 concentration could indicate the occurrence of TSR. Here we propose that H2S in siliciclastic shale can be generated in the presence of ES at low temperatures via both disproportionation of ES into H2S and SO42?, and TSR. Our findings from this study provide experimental evidence that may aid efforts to interpret the origin of H2S in low-temperature sedimentary basins.?lvarez, E., Thoms, S., Bracher, A., Liu, Y., V?lker, C., 2019. Modeling photoprotection at global scale: The relative role of nonphotosynthetic pigments, physiological state, and species composition. Global Biogeochemical Cycles 33, 904-926. are capable of acclimating to dynamic light environments, as they have developed mechanisms to optimize light harvesting and photosynthetic electron transport. When absorption of light exceeds photosynthetic capacity, various physiological protective mechanisms prevent damage of the photosynthetic apparatus. Xanthophyll pigments provide one of the most important photoprotective mechanisms to dissipate the excess light energy and prevent photoinhibition. In this study, we coupled a mechanistic model for phytoplankton photoinhibition with the global biogeochemical model Regulated Ecosystem Model version 2. The assumption that photoinhibition is small in phytoplankton communities acclimated to ambient light allowed us to predict the photoprotective needs of phytoplankton. When comparing the predicted photoprotective needs to observations of pigment content determined by high-performance liquid chromatography, our results showed that photoprotective response seems to be mediated in most parts of the ocean by a variable ratio of xanthophyll pigments to chlorophyll. The variability in the ratio appeared to be mainly driven by changes in phytoplankton community composition. Exceptions appeared at high latitudes where other energy dissipating mechanisms seem to play a role in photoprotection and both taxonomic changes and physiological acclimation determine community pigment signature. Understanding the variability of community pigment signature is crucial for modeling the coupling of light absorption to carbon fixation in the ocean. Insights about how much of this variability is attributable to changes in community composition may allow us to improve the match between remotely sensed optical data and the underlying phytoplankton community.Alves, C.A., Romero Yanes, J.F., Feitosa, F.X., de Sant’Ana, H.B., 2019. Effect of temperature on asphaltenes precipitation: Direct and indirect analyses and phase equilibrium study. Energy & Fuels 33, 6921-6928. precipitation is still a challenge for the petroleum industry during crude oil production and processing. Pressure, composition, and temperature variation can induce asphaltenes destabilization and aggregation, leading to fouling and flow blocking in pipelines and wellbore pores. The present work aims to investigate the effect of temperature on asphaltene precipitation using n-heptane as the precipitant alkane. Three different Brazilian crude oils, here named BR1, BR2, and BR3, were studied at temperatures of 5, 25, and 50 °C, using two different asphaltene yield and precipitation onset analyses, defined as direct and indirect methods. It has been found that when temperature rises, there is a decrease in the asphaltenes precipitation yield, together with an increase in the precipitation onset, which could be related to the increase in the asphaltenes solubility. Temperature effects on the onset seem to be influenced by crude oil properties, being less significant for more stable asphaltenes. Asphaltenes precipitation phenomenon was properly modeled by the intermediate of the Regular Solution Model, showing a low molecular weight asphaltene distribution when temperature rises. When indirect method is used, it has been seen that new fractions of heavy compounds aggregate and precipitate at a second precipitation stage under an n-heptane excess.Amoozegar, M.A., Safarpour, A., Noghabi, K.A., Bakhtiary, T., Ventosa, A., 2019. Halophiles and their vast potential in biofuel production. Frontiers in Microbiology 10, 1895. doi: 10.3389/fmicb.2019.01895. warming and the limitations of using fossil fuels are the main concern of all societies thus the development of alternative fuel sources is crucial to improving the current global energy situation. Biofuels are known as the best alternatives of unrenewable fuels and justify increasing extensive research to develop new and less expensive methods for their production. The most frequent biofuels are bioethanol, biobutanol, biodiesel, and biogas. The production of these biofuels is the result of microbial activity on organic substrates like sugars, starch, oil crops, nonfood biomasses, and agricultural and animal wastes. Several industrial production processes are carried out in the presence of high concentrations of NaCl and therefore, researchers have focused on halophiles for biofuel production. In this review, we focus on the role of halophilic microorganisms and their current utilization in the production of all types of biofuels. Also, the outstanding potential of them and their hydrolytic enzymes in the hydrolysis of different kind of biomasses and the production of biofuels are discussed.Anderson, R.E., Sogin, M.L., Baross, J.A., 2014. Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents. FEMS Microbiology Ecology 91, 1-11. gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in very low abundance. However, the ecological role and distribution of rare and abundant lineages, particularly in deep, hot subsurface environments, remain unclear. Here, we use 16S rRNA tag sequencing to describe biogeographic patterning and microbial community structure of both rare and abundant archaea and bacteria in hydrothermal vent systems. We show that while rare archaeal lineages and almost all bacterial lineages displayed geographically restricted community structuring patterns, the abundant lineages of archaeal communities displayed a much more cosmopolitan distribution. Finally, analysis of one high-volume, high-temperature fluid sample representative of the deep hot biosphere described a unique microbial community that differed from microbial populations in diffuse flow fluid or sulfide samples, yet the rare thermophilic archaeal groups showed similarities to those that occur in sulfides. These results suggest that while most archaeal and bacterial lineages in vents are rare and display a highly regional distribution, a small percentage of lineages, particularly within the archaeal domain, are successful at widespread dispersal and colonization.Antoniewicz, M.R., 2019. Synthetic methylotrophy: Strategies to assimilate methanol for growth and chemicals production. Current Opinion in Biotechnology 59, 165-174. is an attractive and broadly available substrate for large-scale bioproduction of fuels and chemicals. It contains more energy and electrons per carbon than carbohydrates and can be cheaply produced from natural gas. Synthetic methylotrophy refers to the development of non-native methylotrophs such as Escherichia coli and Corynebacterium glutamicum to utilize methanol as a carbon source. Here, we discuss recent advances in engineering these industrial hosts to assimilate methanol for growth and chemicals production through the introduction of the ribulose monophosphate (RuMP) cycle. In addition, we present novel strategies based on flux coupling and adaptive laboratory evolution to engineer new strains that can grow exclusively on methanol.Arbabzadeh, M., Sioshansi, R., Johnson, J.X., Keoleian, G.A., 2019. The role of energy storage in deep decarbonization of electricity production. Nature Communications 10, 3413. decarbonization of electricity production is a societal challenge that can be achieved with high penetrations of variable renewable energy. We investigate the potential of energy storage technologies to reduce renewable curtailment and CO2 emissions in California and Texas under varying emissions taxes. We show that without energy storage, adding 60?GW of renewables to California achieves 72% CO2 reductions (relative to a zero-renewables case) with close to one third of renewables being curtailed. Some energy storage technologies, on the other hand, allow 90% CO2 reductions from the same renewable penetrations with as little as 9% renewable curtailment. In Texas, the same renewable-deployment level leads to 54% emissions reductions with close to 3% renewable curtailment. Energy storage can allow 57% emissions reductions with as little as 0.3% renewable curtailment. We also find that generator flexibility can reduce curtailment and the amount of energy storage that is needed for renewable integration.Archibald, J.M., 2019. Genomics reveals alga-associated cyanobacteria hiding in plain sight. Proceedings of the National Academy of Sciences 116, 15757-15759. occupy a special place in the pantheon of prokaryotic life. It is in the ancestors of these ubiquitous microbes that oxygenic photosynthesis first evolved more than 2 billion y ago (1), and it is from endosymbiotic cyanobacteria that the plastids (chloroplasts) of plants and algae are derived (2). Modern-day cyanobacteria are diverse in form and function; they include coccoid marine picoplankton such as Prochlorococcus (3), freshwater biofilm-forming genera [e.g., Gloeomargarita (4)], and filamentous taxa capable of fixing nitrogen [e.g., Nostoc (5)]. In PNAS, Nakayama et al. (6) add an exciting chapter to the story of cyanobacterial diversity. The authors describe the genome sequence of a cyanobacterium living ectosymbiotically on an eye-catching dinoflagellate named Ornithocercus magnificus. Their results provide insight into the nature of an enigmatic symbiotic relationship and reveal the existence of a cryptic, globally distributed cyanobacterial lineage that has until now gone unappreciated.Ornithocercus is indeed magnificent, even by dinoflagellate standards. The surface of this heterotrophic marine protist is decorated with crown-shaped, cellulosic outcroppings that extend from the cell body in different directions (Fig. 1) (7). The “upper” crown forms an extracellular chamber in which autofluorescent cyanobacteria reside, and microscopic evidence suggests that the bacteria can be vertically transmitted from mother to daughter chambers during host cell division (8). First observed more than 100 y ago (9), the biology of these so-called phaeosomes has long been mysterious. What type of cyanobacterium are they? How far do they roam? What is the nature of their interactions with the dinoflagellate host?Aronson, E.L., Dierick, D., Botthoff, J.K., Oberbauer, S., Zelikova, T.J., Harmon, T.C., Rundel, P., Johnson, R.F., Swanson, A.C., Pinto-Tomás, A.A., Artavia-León, A., Matarrita-Carranza, B., Allen, M.F., 2019. ENSO-influenced drought drives methane flux dynamics in a tropical wet forest soil. Journal of Geophysical Research: Biogeosciences 124, 2267-2276. atmospheric methane growth rates have wildly fluctuated over the past three decades, which may be driven by the proportion of tropical land surface saturated by water. The El Ni?o/Southern Oscillation Event (ENSO) cycle drives large‐scale climatic trends globally, with El Ni?o events typically bringing drier weather than La Ni?a. In a lowland tropical wet forest in Costa Rica, we measured methane flux bimonthly from March 2016 to June 2017 and using an automated chamber system. We observed a strong drying trend for several weeks during the El Ni?o in 2016, reducing soil moisture below normal levels. In contrast, soil conditions had high water content prior to the drought and during the moderate La Ni?a that followed. Soil moisture varied across the period studied and significantly impacted methane flux. Methane consumption was greater during the driest part of the El Ni?o period, while during La Ni?a and other time periods, soils had lower methane consumption. The mean methane flux observed was ?0.022 mg CH4‐C m?2 hr?1, and methane was consumed at all timepoints, with lower consumption in saturated soils. Our data show that month studied, and the correlation between soil type and month significantly drove methane flux trends. Our data indicate that ENSO cycles may impact biogenic methane fluxes, mediated by soil moisture conditions. Climate projections for Central America show dryer conditions and increased El Ni?o frequency, further exacerbating predicted drought. These trends may lead to negative climate feedbacks, with drier conditions increasing soil methane consumption from the atmosphere.Arrizabalaga-Larra?aga, A., Rodríguez, P., Medina, M., Santos, F.J., Moyano, E., 2019. Simultaneous analysis of natural pigments and E-141i in olive oils by liquid chromatography–tandem mass spectrometry. Analytical and Bioanalytical Chemistry 411, 5577-5591. work describes the development of an ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC–MS/MS) method for the determination of carotenoids (β-carotene, lutein, β-criptoxanthin, neoxanthin, violaxanthin) and chlorophylls, as well as their related compounds (chlorophyll A and B, pheophytin A and B and the banned dyes Cu–pyropheophytin A, Cu–pheophytin A and B) in olive oils. For this purpose, the feasibility of electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI) for the ionization of these compounds was evaluated and compared. Tandem mass spectrometry (MS/MS) fragmentation was discussed for each family of compounds, and the most characteristic and abundant product ions were selected to propose a selective and sensitive UHPLC–MS/MS method. The best results were obtained using APCI and APPI, while ESI provided the worst signal-to-noise ratio (S/N) for all compounds. For the analysis of olive oils, a simple solid-phase extraction (SPE) with silica cartridges was applied before the determination by UHPLC–MS/MS (APCI and APPI) in multiple reaction monitoring (MRM) mode. Method quality parameters were stablished, and the results demonstrate the good performance of the new methods, providing low limits of detection (0.004–0.9?mg?L?1), high extraction efficiencies (62–95%) and low matrix effects (<?25%). The developed UHPLC–API–MS/MS (APCI and APPI) methods were applied to the analysis of olive oil samples, and β-carotene, pheophytin A, pheophytin B and lutein were detected and quantified in all of them at concentrations ranging from 0.1 to 9.5?mg?L?1.Asif, M., Wenger, L.M., 2019. Heterocyclic aromatic hydrocarbon distributions in petroleum: A source facies assessment tool. Organic Geochemistry 137, 103896. study reports a novel source facies assessment application from distributions of heterocyclic aromatic hydrocarbons in petroleum, i.e., dibenzothiophene (DBT), dibenzofuran (DBF) and fluorene (F). To illustrate the approach initially, a large set of crude oils from global petroleum basins are geochemically characterized based on source facies, organic-matter type and environment of deposition variation. Petroleum bulk properties and molecular distributions of isoprenoids, terpanes, steranes and related parameters are applied to demonstrate the source facies and maturity of the entire oil suite and to delineate the oil suite into marine carbonate, marine shale, marine shale with terrigenous organic matter (OM), coaly and lacustrine source-facies families. From within this interpretive context, the relative percentages of hetercyclic aromatic hydrocarbons are reported and discussed from each of these source-facies families. A triplot drawn from the percentages of DBT, DBF and F is shown to effectively differentiate the oils source-facies classifications. Marine carbonate oils show highest %DBT plotted in the DBT vertex, freshwater lacustrine-sourced oils positioned near to 100% F vertex, coaly-sourced oils revealed highest %DBF. The marine shale and marine shale with terrigenous-OM oil families plotted away from three vertices and represent a distinctive position with in the triplot. These results establish an effective source-facies assessment tool triplot based on heterocyclic aromatic hydrocarbon distributions. These novel signatures which are derived from variations in the chemical composition of source rocks, hence kerogen, lead to the occurrence of kerogen catalysis in sedimentary reaction (like carbon catalysis) for the formation of heterocyclic aromatic hydrocarbons.Astuti, D.I., Purwasena, I.A., Putri, R.E., Amaniyah, M., Sugai, Y., 2019. Screening and characterization of biosurfactant produced by Pseudoxanthomonas sp. G3 and its applicability for enhanced oil recovery. Journal of Petroleum Exploration and Production Technology 9, 2279-2289. are one of the microbial bioproducts that are in most demand from microbial-enhanced oil recovery (MEOR). We isolated and screened potential biosurfactant-producing bacteria, followed by biosurfactant production and characterization, and a simulation of the MEOR application to biosurfactants in a sand-packed column. Isolate screening was conducted based on qualitative (hemolytic blood assay and oil-spreading test) and semi-qualitative (emulsification assay and interfacial tension measurement) parameters. Bacterial identification was performed using 16S rRNA phylogenetic analysis. Sequential isolation yielded 32 bacterial isolates, where Pseudomonas sp. G3 was able to produce the most biosurfactant. Pseudomonas sp. G3 had the highest emulsification activity (Ei?=?72.90%) in light crude oil and could reduce the interfacial tension between oil and water from 12.6 to 9.7?dyne/cm with an effective critical-micelle concentration of 0.73?g/L. The Fourier transform infrared spectrum revealed that the biosurfactant produced was a glycolipid compound. A stable emulsion of crude extract and biosurfactant formed at pH 2–12, up to 100?°C, and with a NaCl concentration of up to 10% (w/v) in the response-surface method, based on the Box–Behnken design model. The sand-packed column experiment with biosurfactant resulted in 20% additional oil recovery. Therefore, this bacterium and its biosurfactant show potential and the bacterium is suitable for use in MEOR applications.Atar, E., Christian, Aplin, A.C., Dellwig, O., Herringshaw, L.G., Lamoureux-Var, V., Leng, M.J., Schnetger, B., Wagner, T., 2019. Dynamic climate-driven controls on the deposition of the Kimmeridge Clay Formation in the Cleveland Basin, Yorkshire, UK. Climate of the Past 15, 1581-1601. Kimmeridge Clay Formation (KCF) is a laterally extensive, total-organic-carbon-rich succession deposited throughout northwest Europe during the Kimmeridgian–Tithonian (Late Jurassic). It has recently been postulated that an expanded Hadley cell, with an intensified but alternating hydrological cycle, heavily influenced sedimentation and total organic carbon (TOC) enrichment by promoting primary productivity and organic matter burial in the UK sectors of the Boreal Seaway. Consistent with such climate boundary conditions, petrographic observations, total organic carbon and carbonate contents, and major and trace element data presented here indicate that the KCF of the Cleveland Basin was deposited in the Laurasian Seaway under the influence of these conditions.Depositional conditions alternated between three states that produced a distinct cyclicity in the lithological and geochemical records: lower-variability mudstone intervals (LVMIs) which comprise clay-rich mudstone and higher-variability mudstone intervals (HVMIs) which comprise TOC-rich sedimentation and carbonate-rich sedimentation. The lower-variability mudstone intervals dominate the studied interval but are punctuated by three ～?2–4?m thick intervals of alternating TOC-rich and carbonate-rich sedimentation (HVMIs). During the lower-variability mudstone intervals, conditions were quiescent with oxic to suboxic bottom water conditions. During the higher-variability mudstone intervals, highly dynamic conditions resulted in repeated switching of the redox system in a way similar to the modern deep basins of the Baltic Sea. During carbonate-rich sedimentation, oxic conditions prevailed, most likely due to elevated depositional energies at the seafloor by current–wave action. During TOC-rich sedimentation, intermittent anoxic–euxinic conditions led to an enrichment of redox-sensitive and sulfide-forming trace metals at the seafloor and a preservation of organic matter, and an active Mn–Fe particulate shuttle delivered redox-sensitive and sulfide-forming trace metals to the seafloor. In addition, based on TOC–S–Fe relationships, organic matter sulfurization appears to have increased organic material preservation in about half of the analysed samples throughout the core, while the remaining samples were either dominated by excess Fe input into the system or experienced pyrite oxidation and sulfur loss during oxygenation events. New Hg∕TOC data do not provide evidence of increased volcanism during this time, consistent with previous work. Set in the context of recent climate modelling, our study provides a comprehensive example of the dynamic climate-driven depositional and redox conditions that can control TOC and metal accumulations in a shallow epicontinental sea, and it is therefore key to understanding the formation of similar deposits throughout Earth's history.Aubriet, F., Carré, V., 2019. Chapter 10 - Fourier transform ion cyclotron resonance mass spectrometry and laser: A versatile tool, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 281-322. the numerous ion sources coupled to Fourier transform ion cyclotron resonance mass spectrometers, the laser-based ion sources have a key role. Pulsed lasers have the unique ability to generate neutrals and/or ions from a condensed or gaseous sample in a non-invasive way and to be focused on a very thin area. Depending on both the laser beam and the sample features, various processes could happen during laser–matter interaction that directly impact the detected ions. In this chapter, the factors driving this interaction will be firstly described especially to understand that leading to: the laser desorption (LD), desorption/ionization with (MALDI) or without (LDI) matrix assistance and the laser ablation (LA). The resulting technical advances of laser ion sources, including those, which operate under atmospheric pressure are explained in detail in this chapter for achieving robust FT-ICR-MS measurements. The advent of high performance imaging mass spectrometry using laser ion sources also push up some new developments which will be summarized. A great number of applications demonstrate the versatility of the combination of laser and FT-ICR-MS and some of them will be illustrated in a last section.Azua-Bustos, A., González-Silva, C., Fernández-Martínez, M.?., Arenas-Fajardo, C., Fonseca, R., Martín-Torres, F.J., Fernández-Sampedro, M., Fairén, A.G., Zorzano, M.-P., 2019. Aeolian transport of viable microbial life across the Atacama Desert, Chile: Implications for Mars. Scientific Reports 9, 11024. we inspect whether microbial life may disperse using dust transported by wind in the Atacama Desert in northern Chile, a well-known Mars analog model. By setting a simple experiment across the hyperarid core of the Atacama we found that a number of?viable bacteria and fungi are in fact able to traverse the driest and most UV irradiated desert on Earth unscathed using wind-transported dust, particularly in the later?afternoon hours. This finding suggests that microbial life on Mars, extant or past, may have similarly benefited from aeolian transport to move across the planet and find suitable habitats to thrive and evolve.Baba, M.u., Parnell, J., Bowden, S., 2019. The geochemistry of oil in Cornish granites. Petroleum Geoscience 25, 298. residues in Variscan granites in Cornwall, SW England, preserve biomarker data which indicate an origin from marine source rocks. The biomarkers also indicate a thermal maturity that excludes an origin from the Devono-Carboniferous rocks intruded by the granites, but is similar to that of Jurassic-sourced oil to the east in the Wessex Basin. A suite of five different samples from the South Crofty tin mine are variably biodegraded, implying alteration after emplacement of oil in the granite. These characteristics are compatible with models for updip flow of fluids from offshore Mesozoic sediments into older granite topographical highs.Baghli, H., Mattioli, E., Spangenberg, J.E., Bensalah, M., Arnaud-Godet, F., Pittet, B., Suan, G., 2020. Early Jurassic climatic trends in the south-Tethyan margin. Gondwana Research 77, 67-81. Early Jurassic period was characterized by extreme environmental changes, as reflected by major global carbon isotope anomalies and abrupt changes in oxygen isotope and elemental records of marine organisms. Available data suggest an overall warm Early Jurassic climate interrupted by periods of severe cooling, with a climatic optimum during the early Toarcian. Available geochemical studies, however, have mainly focused on the northern margin of the Tethys Ocean, so that the palaeogeographic extent of these environmental perturbations, latitudinal palaeotemperature gradients and climate belt boundaries remain poorly constrained. Here we report the first stable isotope records of brachiopod shells (δ13C and δ18O values) from the Upper Sinemurian-Middle Toarcian interval in the southern margin of the Tethys Ocean (northwest Algeria). These data were used to better constrain the palaeoenvironmental evolution of the North Gondwana margin during the Early Jurassic, which likely played an important role on supra-regional climate. The diagenetic history of the analysed brachiopod shells was monitored using scanning electron microscopy, and elemental (manganese and strontium) compositions. The brachiopod δ13C and δ18O data show very similar trends as those reported for various Tethyan regions, and record negative carbon and oxygen isotope excursions near the Sinemurian–Pliensbachian and Pliensbachian–Toarcian transitions and during the Toarcian oceanic anoxic event (T-OAE). Despite these similarities, the carbon and oxygen isotope records are systematically offset towards more positive δ13C values (average +0.5‰) and more negative δ18O values (?1.0‰) compared to those obtained from sites of higher palaeolatitudes in the northern Tethyan margin. These offsets suggest a spatial heterogeneity in the stable isotope composition of dissolved inorganic carbon in the Early Jurassic Ocean and a marked latitudinal temperature gradient between the southern and northern margins of the Tethys.Bai, Y.-N., Wang, X.-N., Wu, J., Lu, Y.-Z., Fu, L., Zhang, F., Lau, T.-C., Zeng, R.J., 2019. Humic substances as electron acceptors for anaerobic oxidation of methane driven by ANME-2d. Water Research 164, 114935. substances (humics) are ubiquitous in terrestrial and aquatic environments where they can serve as electron acceptors for anaerobic oxidation of organic compounds. Methane is a powerful greenhouse gas, as well as the least reactive organic molecule. Anaerobic oxidation of methane (AOM) coupled to microbial reduction of various electron acceptors plays a crucial role in mitigating methane emissions. Here, we reported that humics could serve as terminal electron acceptors for AOM using enriched nitrate-reducing AOM microorganisms. AOM coupled to the reduction of humics was demonstrated based on the production of 13C-labelled carbon dioxide, and AOM activity was evaluated with different methane partial pressures and electron acceptor concentrations. After three-cycle reduction, both AOM activity and copy numbers of the archaea 16S rRNA and mcrA genes were the highest when anthraquinone-2,6-disulfonic acid and anthraquinone-2-sulfonic acid were electron acceptors. The high-throughput sequencing results suggested that ANME-2d were the dominant methane oxidation archaea after humics reduction, although the partner bacteria NC10 trended downward, other reported humics reduction bacteria (Geobactor and Anammox) appeared. The potential electron transfer models from ANME-2d to humics were proposed. These results enable a better understanding of available electron acceptors for AOM in natural environments and broaden our insight into the significant role of ANME-2d.Baker, A., Blyth, A.J., Jex, C.N., McDonald, J.A., Woltering, M., Khan, S.J., 2019. Glycerol dialkyl glycerol tetraethers (GDGT) distributions from soil to cave: Refining the speleothem paleothermometer. Organic Geochemistry 136, 103890. glycerol dialkyl glycerol tetraether (GDGT) paleothermometer has potential application as a speleothem paleoclimate proxy. However, the sources of GDGTs found in speleothems are poorly understood, with multiple potential sources of GDGTs from the soil to the speleothem surface. Here we analysed GDGTs in soils, soil leachates, in-cave surfaces and cave drip waters at two Australian montane caves. We observed significantly different GDGT distributions between soils, soil leachates, in-cave surfaces and drip waters and significant spatial differences in in-cave GDGT distributions. Comparison with published modern in-cave and karst groundwater GDGT datasets from Australia, Europe and China shows that speleothem GDGT distributions are different from those of all potential sources. We hypothesise that speleothem surfaces have a calcifying, alkaline, oxic, wet, carbon-available, environment that supports a microbial community that is different from other possible karst GDGT sources. We propose that the presence of GDGTs related to anoxic or methanogenic conditions, and observed in cave drip water and on in-cave surfaces, can be used to identify GDGTs from these sources. We confirm that TEX86 based paleothermometers are robust speleothem GDGT paleothermometers, whose calibration can be further refined through improved understanding and measurement of cave temperatures.Balzano, S., Villanueva, L., de Bar, M., Sahonero Canavesi, D.X., Yildiz, C., Engelmann, J.C., Marechal, E., Lupette, J., Sinninghe Damsté, J.S., Schouten, S., 2019. Biosynthesis of long chain alkyl diols and long chain alkenols in Nannochloropsis spp. (Eustigmatophyceae). Plant and Cell Physiology 60, 1666–1682. investigated potential biosynthetic pathways of long chain alkenols (LCAs), long chain alkyl diols (LCDs), and long chain hydroxy fatty acids (LCHFAs) in Nannochloropsis oceanica and Nannochloropsis gaditana, by combining culturing experiments with genomic and transcriptomic analyses. Incubation of Nannochloropsis spp. in the dark for one week led to significant increases in the cellular concentrations of LCAs and LCDs in both species. Consistently, 13C-labeled substrate experiments confirmed that both LCA and LCD were actively produced in the dark from C14–18 fatty acids by either condensation or elongation/hydroxylation, although no enzymatic evidence was found for the former pathway. Nannochloropsis spp. did, however, contain (1) multiple polyketide synthases (PKSs) including one type (PKS Clade II) that might catalyse incomplete fatty acid elongations leading to the formation of 3-OH-fatty acids, (2) 3-hydroxyacyl dehydratases (HADs), which can possibly form Δ2/Δ3 monounsaturated fatty acids, and (3) fatty acid elongases (FAEs) that could elongate 3-OH-fatty acids and Δ2/Δ3 monounsaturated fatty acids to longer products. The enzymes responsible for reduction of the long chain fatty acids to LCDs and LCAs are, however, unclear. A putative wax ester synthase/acyl coenzyme A (acyl-CoA):diacylglycerol acyltransferase (WS-DGAT) is likely to be involved in the esterification of LCAs and LCDs in the cell wall. Our data thus provide useful insights in predicting the biosynthetic pathways of LCAs and LCDs in phytoplankton suggesting a key role of FAE and PKS enzymes.Bao, R., Jia, G., Zhang, C., 2019. Spatiotemporal variation of organic geochemical properties since the mid-Miocene in the deep South China Sea (IODP Expedition 349). Journal of Asian Earth Sciences 183, 103961. performed an extensive survey of total organic carbon (OC) and stable OC composition of in the deep South China Sea sediments from the International Ocean Discovery Program (IODP) Expedition 349 Sites U1431, U1433 and Ocean Drilling Program (ODP) Leg 184 Site 1148. Our results reveal dramatic spatial and temporal variations in organic geochemical characteristics among the three Sites. Before ~8?Ma, OC deposited at Site U1431 may be predominantly terrigenous, whereas OC deposited at Sites U1433 and 1148 is mainly of marine origin. After ~8?Ma, OC accumulation at the three Sites progressively increases, mainly due to enhancement of marine primary productivity and input of terrestrial organic matter; the three sites receive mainly marine OC, whereas Sites U1433 and 1148 receive relatively more terrestrial OC compared with Site 1431. Additionally, methane concentrations vary from ~20 to ~100,000?ppmv at Site U1433 and from ~10 to ~600?ppmv at Site 1148 with higher geothermal gradients (78 and 84?°C/km, respectively). In contrast, methane concentrations are <5?ppmv at Site U1431 with lower geothermal gradient (14.8?°C/km). Such high methane concentrations and ratios of methane to ethane at Site U1433 suggest that the gaseous hydrocarbons in the southwestern sub-basin (deep water depth, >4000?km) are primarily sourced from microbial production. Our findings suggest that the sources, trajectories, and fates of OC buried in the deep South China Sea since the mid-Miocene are spatially and temporally variable, controlled by sedimentological processes in the sub-basins, and regional tectonic evolution and long-term paleoenvironmental changes.Baratta, G.A., Accolla, M., Chaput, D., Cottin, H., Palumbo, M.E., Strazzulla, G., 2019. Photolysis of cometary organic dust analogs on the EXPOSE-R2 mission at the International Space Station. Astrobiology 19, 1018-1036. describe the results obtained on a set of organic samples that have been part of the experiment “Photochemistry on the Space Station (PSS)” on the EXPOSE-R2 mission conducted on the EXPOSE-R facility situated outside the International Space Station (ISS). The organic samples were prepared in the Catania laboratory by 200?keV He+ irradiation of N2:CH4:CO icy mixtures deposited at 17?K, on vacuum UV (VUV) transparent MgF2 windows. This organic material contains different chemical groups, including triple CN bonds, that are thought to be of interest for astrobiology. It is widely accepted that materials similar to that produced in the laboratory by ion irradiation of frozen ices could be present in some astrophysical environments such as comets. Once expelled from comets, these materials are exposed to solar radiation during their interplanetary journey. In the young Solar System, some of these processed materials could have reached early Earth and contributed to its chemical and prebiotic evolution. The samples were exposed for 16 months to the unshielded solar UV photons. It was found that, if an interplanetary dust particle (IDP) containing organic material (50% vol) is large enough (>20–30?μm), relevant chemical groups, such as those containing the CN triple bond, can survive for many years (>104 years) in the interplanetary medium.Bava, Y.B., Geronés, M., Giovanetti, L.J., Andrini, L., Erben, M.F., 2019. Speciation of sulphur in asphaltenes and resins from Argentinian petroleum by using XANES spectroscopy. Fuel 256, 115952. crude oil samples from different origins have been processed to separate in the four fractions Saturates, Aromatics, Resins, and Asphaltenes (SARA). Asphaltene and resin fractions were extracted using n-pentane and n-heptane as precipitating solvents. Sulphur contents of the samples were determined by elemental analysis and X-ray Absorption Spectroscopy at the Sulphur K-edge was used to perform sulphur speciation for resin and asphaltene fractions. Reduce sulphur as sulphides, disulphides and thiophenes dominate the spectra of asphaltenes, resins I and crude oils samples. A higher abundance of sulfoxide forms were found in the resin II fraction. In addition, it was found that the asphaltenes are more enriched in aromatic sulphur (thiophene) when the n-heptane solvent is employed. From the sulphur speciation determination it was possible to incorporate different sulphur forms in the hypothetical average molecular structures for the Argentinian asphaltenes.Becker, C., Jochmann, M.A., Teutenberg, T., Schmidt, T.C., 2020. A nebulizer interface for liquid chromatography - Flame ionization detection: Development and validation. Talanta 206, 120229. this study, a novel liquid chromatography (LC)/flame ionization detector (FID) interface was improved. In contrast to previously published interface concepts, the main nebulizer body and the transfer capillary was made of stainless steel. Previously reported problems such as blocking of the transfer capillary were investigated. The simple design of the here presented nebulizer interface allows a convenient handling and the exchangeability of all nebulizer parts targets fast maintenance during routine analysis.A significant advantage is the capability to implement the novel interface into most common gas chromatography (GC)/FID systems. The effects of the instrumental parameters such as backpressure, gas flow, distance between nebulizer nozzle and FID collector or FID temperature on the signal were analyzed and optimized. The influence of the nebulizer material on flame stability and capillary blockage, a well-known problem of former coupling systems, was investigated, too. Finally, the novel interface was validated for the analysis of selected compounds known from literature. Obtained results for chromatographic separation of the alcohols propanol, butanol, pentanol and hexanol, used within previous studies in the field of LC/FID coupling are shown.Limits of detection (LODs), sensitivity and linearity found within this work are compared with LC/FID interfaces developed in the past.Begum, M., Yassin, M.R., Dehghanpour, H., 2019. Effect of kerogen maturity on organic shale wettability: A Duvernay case study. Marine and Petroleum Geology 110, 483-496. reviewed and evaluated the wettability of organic-rich shale plugs from 6 wells drilled in the Duvernay Formation, which is a self-sourced reservoir. We divided our samples into Upper (UD) and Lower (LD) Duvernay based on the variations in depth and kerogen maturity levels. UD and LD samples belong to oil and gas windows, respectively. We compared spontaneous imbibition of oil and brine into 17 twin plugs with wide range of kerogen maturity level and total organic carbon (TOC) content. We also characterized the shale samples by analyzing the results of tight-rock analysis (TRA), x-ray diffraction (XRD), and rock-eval pyrolysis tests to identify the petrophysical properties, mineralogy, and organic-carbon properties, respectively. To investigate the size, abundance, and morphology of pores, we analyzed scanning electron microscopy (SEM) of the shale samples. Finally, we investigated the relationships between the results of spontaneous-imbibition tests and geochemical properties to understand the effects of kerogen maturity level on shale wettability.The results of wettability tests show higher normalized imbibed volume of oil (Io) compared with that of brine (Iw), suggesting that the uncleaned dry plugs are strongly oil-wet. The positive correlations of TOC content with effective porosity and pressure-decay permeability indicate that a significant fraction of the pore space is within the organic matter (OM), supported by the SEM images. The abundance of organic pores may explain the strong wetting affinity of the shale samples to oil. We observed negative and positive correlations between TOC content and equilibrated Io (Ioeq) of UD and LD samples, respectively. This discrepancy can be explained by the smaller number of organic pores of UD samples with lower thermal maturity (oil window), confirmed by the results of SEM analysis and pore size distribution (N2 sorption) tests. Furthermore, the free hydrocarbons content (S1 in rock-eval data) in the form of oil in the UD samples is higher than that in the LD samples. The existence of free hydrocarbons content may reduce the pore space available for oil imbibition, leading to lower Ioeq for the UD samples with higher TOC content.Bergner, J.B., Martín-Doménech, R., ?berg, K.I., J?rgensen, J.K., Artur de la Villarmois, E., Brinch, C., 2019. Organic complexity in protostellar disk candidates. ACS Earth and Space Chemistry 3, 1564-1575. present ALMA observations of organic molecules toward five low-mass Class 0/I protostellar disk candidates in the Serpens cluster. Three sources (Ser-emb 1, Ser-emb 8, and Ser-emb 17) present emission of CH3OH as well as CH3OCH3, CH3OCHO, and CH2CO, while NH2CHO is detected in just Ser-emb 8 and Ser-emb 17. Detecting hot corino-type chemistry in three of five sources represents a high occurrence rate given the relative sparsity of these sources in the literature, and this suggests a possible link between protostellar disk formation and hot corino formation. For sources with CH3OH detections, we derive column densities of 1017–1018 cm–2 and rotational temperatures of ～200–250 K. The CH3OH-normalized column density ratios of large, oxygen-bearing COMs in the Serpens sources and other hot corinos span 2 orders of magnitude, demonstrating a high degree of chemical diversity at the hot corino stage. Resolved observations of a larger sample of objects are needed to understand the origins of chemical diversity in hot corinos, and the relationship between different protostellar structural elements on disk-forming scales.Bezerra, F.H., de Castro, D.L., Maia, R.P., Sousa, M.O.L., Moura-Lima, E.N., Rossetti, D.F., Bertotti, G., Souza, Z.S., Nogueira, F.C.C., 2020. Postrift stress field inversion in the Potiguar Basin, Brazil – Implications for petroleum systems and evolution of the equatorial margin of South America. Marine and Petroleum Geology 111, 88-104. and related normal stress regime in the equatorial continental margin of Brazil ceased during the Late Cretaceous, when the stress regimes in eastern South America and West Africa changed to induce strike-slip or reverse motion. In this study, we explore the postrift tectonic, geomorphic, magmatic, and sedimentary responses to stress changes using the Potiguar Basin, the easternmost basin in the equatorial margin of Brazil, as a case study. We use field and topographic data, 2D seismic reflection lines, vertical electric soundings, and geochronological and borehole data to constrain the stress evolution of the Potiguar Basin from the Late Cretaceous to the Quaternary, discussing the role of basin inversion on sedimentation and landforms. Our results indicate the presence of two strike-slip stress regimes after rifting. The first stress field (SF1) occurred from Late Cretaceous to the middle Miocene and consisted of a N-S-oriented maximum subhorizontal compression and an E-W-oriented extension. The second stress field (SF2) took place from the middle Miocene to the present day and included subhorizontal E-W to NW-SE compression combined with N-S and NE-SW subhorizontal extension. Emplacement of volcanic rocks occurred along transtensional faults, with a principal peak during SF1 at 20–30?Ma and a subordinate peak during SF2 at 5–10?Ma. In response to shortening during SF2, a 70-km-long and 50-km-wide dome formed, where marine Miocene strata were uplifted to ~250?m asl. This uplift induced the displacement of alluvial channels away from the dome. Anticlines formed by transpression along the main NE-SW-striking faults during both SF1 and ST2 acted as traps in the petroleum system. Similar shifts and stress field inversions documented in other areas of the Brazilian continental margin are consistent with the Neogene rise of the Andes and may have implications for reconstructing the tectonic history of the Equatorial Atlantic margin of South America.Bi, W., Wang, J.J., Dodla, S.K., Gaston, L.A., DeLaune, R.D., 2019. Lignin chemistry of wetland soil profiles in two contrasting basins of the Louisiana Gulf coast. Organic Geochemistry 137, 103902. studies indicate that loss of soil organic matter (SOM) from coastal wetlands can contribute to the hypoxia in the northern Gulf of Mexico along the Louisiana coast. In this study, coastal marsh soil profiles of two contrasting basins were investigated for lignin composition in order to assess organic matter source and degradation status under these different wetland formations. The Atchafalaya Basin is undergoing land building whereas the Barataria Basin is experiencing land loss. Lignin monomers were extracted using alkaline CuO oxidation followed by gas chromatography–mass spectrometry characterization. Marsh soil profiles from the Barataria Basin showed strong lignin storage with two-fold higher lignin contents (sum of vanillyl, syringyl, and cinnamyl phenols, Λ8) than those in the Atchafalaya Basin. Source SOM inputs in the Barataria Basin were non-woody angiosperms, whereas in the Atchafalaya Basin inputs were non-woody angiosperms and some gymnosperm inputs. Principal component analysis (PCA) showed that different soil environmental factors dominated the status of soil organic matter degradation. Soil pH was negatively related to the lignin degradation in the Atchafalaya Basin, whereas high total N contents inhibited lignin degradation in the Barataria Basin. Increasing electrical conductivity inhibited organic matter degradation in the low salinity wetlands of the Atchafalaya Basin, but positively influenced lignin decomposition in the higher salinity marsh soil profiles of Barataria Basin. Despite SOM in the Barataria Basin being more degraded than in the Atchafalaya, the nearly 10-fold greater amount of organic carbon (C) in the Barataria, coupled with net land loss, indicates that it is greater source of oxygen-consuming organic C, thus contributes more to the hypoxia in the Gulf.Billi, D., Staibano, C., Verseux, C., Fagliarone, C., Mosca, C., Baqué, M., Rabbow, E., Rettberg, P., 2019. Dried biofilms of desert strains of Chroococcidiopsis survived prolonged exposure to space and Mars-like conditions in low Earth orbit. Astrobiology 19, 1008-1017. biofilms and dried multilayered planktonic counterparts obtained from three desert strains of Chroococcidiopsis were exposed to low Earth conditions by using the EXPOSE-R2 facility outside the International Space Station. During the space mission, samples in Tray 1 (space vacuum and solar radiation, from λ?≈?110?nm) and Tray 2 (Mars-like UV flux, λ > 200?nm and Mars-like atmosphere) received total UV (200–400?nm) fluences of about 4.58?×?102 kJ/m2 and 4.92?×?102 kJ/m2, respectively, and 0.5 Gy of cosmic ionizing radiation. Postflight analyses were performed on 2.5-year-old samples due to the space mission duration, from launch to sample return to the lab. The occurrence of survivors was determined by evaluating cell division upon rehydration and damage to the genome and photosynthetic apparatus by polymerase chain reaction–stop assays and confocal laser scanning microscopy.Biofilms recovered better than their planktonic counterparts, accumulating less damage not only when exposed to UV radiation under space and Mars-like conditions but also when exposed in dark conditions to low Earth conditions and laboratory control conditions. This suggests that, despite the shielding provided by top-cell layers being sufficient for a certain degree of survival of the multilayered planktonic samples, the enhanced survival of biofilms was due to the presence of abundant extracellular polymeric substances and to additional features acquired upon drying.Birolli, W.G., Lima, R.N., Porto, A.L.M., 2019. Applications of marine-derived microorganisms and their enzymes in biocatalysis and biotransformation, the underexplored potentials. Frontiers in Microbiology 10, 1453. doi: 10.3389/fmicb.2019.01453. biodiversity has been explored in the search for novel enzymes, including forests, savannas, tundras, deserts and finally the sea. Marine microorganisms and their enzymes are capable of being active in high-salt concentration, large range of temperature and, high incidence of light and pressure, constituting an important source of unique biocatalysts. This review presents studies employing whole cells processes of marine bacteria and fungi aiming new catalysts for different reactions in organic synthesis, such as reduction, oxidation, hydroxylation, hydrolysis, elimination and conjugation. Genomics and protein engineering studies were also approached, and reactions employing isolated enzymes from different classes (oxidoreductases, hydrolases, lyases and ligases) were described and summarized. Future biotechnological studies and process development should focus on molecular biology for the obtention of enzymes with interesting and fascinating properties, as the biocatalyst obtained from the exploration of the microorganisms from the marine environment. This review aims the literature about the use of marine-derived bacteria, fungi and their enzymes for biocatalytic reactions of organic compounds. Promoting a discussion about the possibilities of these microorganisms in the synthesis of different compounds.Biver, N., Bockelée-Morvan, D., 2019. Complex organic molecules in comets from remote-sensing observations at millimeter wavelengths. ACS Earth and Space Chemistry 3, 1550-1555. observations of comets, especially using high spectral resolution millimeter spectroscopy, have enabled the detection of over 25 molecules in comets for the last 20 years. Among the molecules identified at radio wavelengths, complex organic molecules (COMs), such as acetaldehyde, ethylene glycol, formamide, methyl formate, or ethanol, have been observed in several comets and their abundances relative to water and methanol have been precisely determined. Significant upper limits on the abundance of several other COMs have been determined and put constraints on the dominant isomer for three of them. The abundances measured in comets are generally of comparable order of magnitude to those measured in star-forming regions, suggesting that comets contain preserved material from the presolar cloud from which the solar system was born.Blattmann, T.M., 2019. Ideas and perspectives: Emerging contours of a dynamic exogenous kerogen cycle. Biogeosciences Discussions 2019, 1-7. evidence points to the dynamic role that kerogen is playing on the Earth's surface in controlling atmospheric chemistry over geologic time. Although quantitative constraints on weathering of kerogen remain loose, its changing weathering behavior modulated by the activity of glaciers, suggest that this largest pool of reduced carbon on Earth may have played a key part in atmospheric CO2 variability across recent glacial-interglacial times and beyond.Bokelmann, L., Hajdinjak, M., Peyrégne, S., Brace, S., Essel, E., de Filippo, C., Glocke, I., Grote, S., Mafessoni, F., Nagel, S., Kelso, J., Prüfer, K., Vernot, B., Barnes, I., P??bo, S., Meyer, M., Stringer, C., 2019. A genetic analysis of the Gibraltar Neanderthals. Proceedings of the National Academy of Sciences 116, 15610-15615. Significance: The remains of 2 Neanderthals were found in Gibraltar: the first at Forbes’ Quarry in 1848 and the second at Devil’s Tower in 1926. Since their discovery, present-day human DNA contamination has accumulated in the specimens. By developing a DNA library preparation method that reduces modern contamination before sequencing, we were able to isolate enough endogenous DNA from the specimens to determine their sex and to infer that the Forbes’ Quarry Neanderthal is more similar to 60,000- to 120,000-y-old Neanderthal specimens in Europe and western Asia than to younger Neanderthals. The laboratory protocols presented here improve access to ancient DNA from specimens that are highly contaminated with present-day human DNA.Abstract: The Forbes’ Quarry and Devil’s Tower partial crania from Gibraltar are among the first Neanderthal remains ever found. Here, we show that small amounts of ancient DNA are preserved in the petrous bones of the 2 individuals despite unfavorable climatic conditions. However, the endogenous Neanderthal DNA is present among an overwhelming excess of recent human DNA. Using improved DNA library construction methods that enrich for DNA fragments carrying deaminated cytosine residues, we were able to sequence 70 and 0.4 megabase pairs (Mbp) nuclear DNA of the Forbes’ Quarry and Devil’s Tower specimens, respectively, as well as large parts of the mitochondrial genome of the Forbes’ Quarry individual. We confirm that the Forbes’ Quarry individual was a female and the Devil’s Tower individual a male. We also show that the Forbes’ Quarry individual is genetically more similar to the ～120,000-y-old Neanderthals from Scladina Cave in Belgium (Scladina I-4A) and Hohlenstein-Stadel Cave in Germany, as well as to a ～60,000- to 70,000-y-old Neanderthal from Russia (Mezmaiskaya 1), than to a ～49,000-y-old Neanderthal from El Sidrón (El Sidrón 1253) in northern Spain and other younger Neanderthals from Europe and western Asia. This suggests that the Forbes’ Quarry fossil predates the latter Neanderthals. The preservation of archaic human DNA in the warm coastal climate of Gibraltar, close to the shores of Africa, raises hopes for the future recovery of archaic human DNA from regions in which climatic conditions are less than optimal for DNA preservation.Brailsford, F.L., Glanville, H.C., Golyshin, P.N., Johnes, P.J., Yates, C.A., Jones, D.L., 2019. Microbial uptake kinetics of dissolved organic carbon (DOC) compound groups from river water and sediments. Scientific Reports 9, 11229. organic matter (DOM) represents a key component of carbon (C) cycling in freshwater ecosystems. While the behaviour of bulk dissolved organic carbon (DOC) in aquatic ecosystems is well studied, comparatively little is known about the turnover of specific DOC compounds. The aim of this study was to investigate the persistence of 14C-labelled low molecular weight (LMW) DOC at a wide range of concentrations (0.1??M to 10?mM), in sediments and waters from oligotrophic and mesotrophic rivers within the same catchment. Overall, rates of DOC loss varied between compound groups (amino acids?>?sugars?=?organic acids?>?phenolics). Sediment-based microbial communities contributed to higher DOC loss from river waters, which was attributed, in part, to its greater microbial biomass. At higher DOC compound concentrations, DOC loss was greater in mesotrophic rivers in comparison to oligotrophic headwaters. A lag-phase in substrate use within sediments provided evidence of microbial growth and adaptation, ascribed here to the lack of inorganic nutrient limitation on microbial C processing in mesotrophic communities. We conclude that the higher microbial biomass and available inorganic nutrients in sediments enables the rapid processing of LMW DOC, particularly during high C enrichment events and in N and P-rich mesotrophic environments.Brandenburg, A., 2019. The limited roles of autocatalysis and enantiomeric cross-inhibition in achieving homochirality in dilute systems. Origins of Life and Evolution of Biospheres 49, 49-60. understand the effects of fluctuations on achieving homochirality, we employ a Monte-Carlo method where autocatalysis and enantiomeric cross-inhibition, as well as racemization and deracemization reactions are included. The results of earlier work either without autocatalysis or without cross-inhibition are reproduced. Bifurcation diagrams and the dependencies of the number of reaction steps on parameters are studied. In systems with 30,000 molecules, for example, up to a billion reaction steps may be needed to achieve homochirality without autocatalysis.Büchel, C., 2019. How diatoms harvest light. Science 365, 447-448. on Earth relies on organisms that build up biomass and release oxygen through photosynthesis. Eukaryotic photosynthesis has mainly been studied in vascular plants; other eukaryotes such as diatoms, a family of single-celled photosynthetic algae, have only recently received attention. Diatoms produce about 25% of Earth's oxygen (1). On page 463 of this issue, Pi et al. (2) describe the molecular structure of one of the main protein complexes responsible for photosynthesis in diatoms. Together with an earlier study (3), the findings provide the basis for a precise understanding of how light energy is collected and converted by diatoms.Diatoms are distantly related to plants, having acquired their photosynthetic capability when a eukaryote engulfed a relative of red algae. This eukaryotic alga was reduced to an organelle (the chloroplast) where photosynthesis takes place. However, photosystems I and II (PSI and PSII), protein-pigment complexes in the chloroplast, are highly conserved in all organisms that carry out oxygen-producing photosynthesis. The core of PSII consists of about 25 subunits, which are essentially unchanged in plants and diatoms. The core is surrounded by membrane proteins generally called light-harvesting complex proteins (LHCs) but referred to as fucoxanthin-chlorophyll proteins (FCPs) in diatoms. The proteins belong to the same family and bind most pigments that collect sunlight. The pigments are noncovalently bound and their energy levels tuned depending on the protein environment. Some LHCs/FCPs are strongly associated with PSII or PSI; others form an additional, less tightly bound pool.The pigments bound to FCPs give diatoms a brown color. In plants, the main pigments in LHCs are chlorophyll (Chl) a, Chl b, and the carotenoid lutein, giving plants their green color. Diatoms also contain Chl a but have Chl c and fucoxanthin instead of Chl b and lutein. In plant LHC, more Chl than carotenoids is bound, whereas diatoms use more carotenoids than Chl for light harvesting. Despite the difference in bound pigments, all LHC and FCP proteins are similar in sequence. Many members of this family are expressed in diatoms, but little is known about their function.Wang et al. (3) reported the molecular structure of an FCP belonging to the group less tightly bound to PSII or PSI (see the first figure). The arrangement of the three membrane-spanning helices and some of the Chl-binding sites is highly conserved in all LHCs and FCPs, as is the binding of the two central carotenoids (fucoxanthin in FCPs and lutein in LHCII, the major LHC associated with PSII in plants). However, in contrast to the trimeric LHCII of plants, the FCP analyzed by Wang et al. is a dimer, in which the subunits are arranged in a unique way: Monomers interact through the helices that are perpendicular to the membrane plane, whereas in all LHCs studied so far, oligomerization proceeds by interaction of this helix with the two other helices of the adjacent monomer.Another difference is the arrangement of pigments. In LHCII, a cluster of three energetically coupled Chl a molecules transfers energy to neighboring complexes; in the FCP studied by Wang et al., the central Chl a in this cluster is replaced by Chl c, whose higher energy level prevents energetic coupling of the three Chls. Thus, energy transfer to other complexes must proceed differently. A spectroscopic study of energy transfer pathways between pigments in FCPs also identified major differences to LHCII (4). Wang et al.'s structure will enable modeling of these pathways. This should elucidate the energy transfer network in light-harvesting complexes with a high concentration of carotenoids and explain the high efficiency of energy transduction and photoprotection in FCPs.Pi et al. also highlight the variability of light-harvesting proteins. Their structure of a PSII-FCP supercomplex confirms the conservation of the PSII core. Only proteins shielding the Mn-Ca cluster that catalyzes water splitting deviate partly from those of plants. The FCP complexes are, however, arranged in a different manner than in plant LHCs (see the second figure): Instead of the LHCII trimers in plants, two FCP tetramers are bound. Monomeric FCPs are in different locations than the monomeric LHC proteins in plants.Pi et al. suggest that one monomer (FCP-D) is in a central position in the energy excitation pathway. FCP-D is unusual in that it binds no Chl c and less carotenoid than other FCPs. It belongs to a protein subgroup usually found around PSI. Another peculiarity is the connection of an FCP tetramer to the core through a subunit (PsbG) that had not been reported before. PsbG binds one Chl a molecule and helps to build the energy transduction network into the reaction center of PSII.The dimeric FCP described by Wang et al. was isolated from Phaeodactylum tricornutum (whose genome has been sequenced), a model species for diatoms with bilateral cell symmetry. The PSII-FCP complex was isolated from Chaetoceros gracilis (not yet sequenced), which has radial cell symmetry. Pi et al. detected only two different FCP sequences that could be used for modeling the molecular structure. However, the authors identified at least four structurally different FCPs in the PSII-FCP supercomplex: three monomers and subunits of the tetramers. They modeled the tetrameric FCPs using one polypeptide, but according to the structural data, these FCPs are not completely symmetric, pointing to an even larger number of different polypeptides. Thus, these data cannot identify all FCPs that are present around the PSII cores in diatoms.There are surprising differences between the FCP dimer studied by Wang et al. and the FCPs in the PSII-FCP supercomplex reported by Pi et al. The membrane-parallel fucoxanthin in the dimer is missing in all FCPs close to the PSII core. Wang et al. identified two Chl c pigments per FCP monomer, whereas for most of the FCPs around PSII, Pi et al. attributed three densities to Chl c. Diadinoxanthin, present in the dimer and thought to play a role in photoprotection after de-epoxidation, was found only in FCP-D in the supercomplex. Are these differences due to the fact that two distantly related diatom species were analyzed, or do they point to differences between the pool of less tightly bound FCPs and those arranged closer to the core of PSII? The two structures are milestones on the way to understanding the high flexibility of LHC/FCP proteins, where the same purpose is served by similar proteins in a very different manner.References1. C. B. Field et al., Science 281, 237 (1998).2. X. Pi et al., Science 365, eaax4406 (2019).3. W. Wang et al., Science 363, eaav0365 (2019).4. T. P. J. Krüger et al., Proc. Natl. Acad. Sci. U.S.A. 114, E11063 (2017).5. Z. Liu et al., Nature 428, 287 (2004).6. X. Wei et al., Nature 534, 69 (2016).7. S. Caffarri et al., EMBO J. 28, 3052 (2009).Bulguroglu, M.E., Milkov, A.V., 2020. Thickness matters: Influence of dolerite sills on the thermal maturity of surrounding rocks in a coal bed methane play in Botswana. Marine and Petroleum Geology 111, 219-229. studies suggest that igneous intrusions usually have thermal aureole thicknesses between 30% and 250% of the intrusion thickness. Here, we discuss data and 1D thermal maturity models from nine coreholes (wells) drilled in Botswana to explore for coal bed gas. The coreholes penetrated multiple dolerite sills with thicknesses ranging from 1.2?m to 73.4?m. The sills intruded the sedimentary rocks in the Jurassic period and significantly affected the rank, properties and thermal maturity of Permian coals. The thermal influence of the sills extends for >5–53?m away from their contacts with surrounding rocks. The relatively thick (>13?m) sills have thermal aureole thicknesses of >31–137% of the sill thickness, in line with global observations. However, the relatively thin (<5?m) sills have aureole thicknesses of 276 to >1000% of the sill thickness, significantly larger than previously reported from most other locations affected by igneous intrusions. Thin sill intrusions in coals and organic-rich shales may lead to the generation of larger volumes of CH4, other hydrocarbon gases, and CO2 than previously thought, affecting the safety in coal mines and gas resources.Burke, S.A., Wik, M., Lang, A., Contosta, A.R., Palace, M., Crill, P.M., Varner, R.K., 2019. Long-term measurements of methane ebullition from thaw ponds. Journal of Geophysical Research: Biogeosciences 124, 2208-2221.: Arctic regions are experiencing rapid warming, leading to permafrost thaw and formation of numerous water bodies. Although small ponds in particular are considered hot spots for methane (CH4) release, long‐term studies of CH4 efflux from these surfaces are rare. We have collected an extensive data set of CH4 ebullition (bubbling) measurements from eight small thaw ponds (<0.001 km2) with different physical and hydrological characteristics over four summer seasons, the longest set of observations from thaw ponds to date. The measured fluxes were highly variable with an average of 20.0 mg CH4 · m?2 · day?1 (median: 4.1 mg CH4 · m?2 · day?1, n = 2,063) which is higher than that of most nearby lakes. The ponds were categorized into four types based on clear and significant differences in bubble flux. We found that the amount of CH4 released as bubbles from ponds was very weakly correlated with environmental variables, like air temperature and atmospheric pressure, and was potentially more related to differences in physical characteristics of the ponds. Using our measured average daily bubble flux plus the available literature, we estimate circumpolar thaw ponds <0.001 km2 in size to emit between 0.2 and 1.0 Tg of CH4 through ebullition. Our findings exemplify the importance of high‐frequency measurements over long study periods in order to adequately capture the variability of these water bodies. Through the expansion of current spatial and temporal monitoring efforts, we can increase our ability to estimate CH4 emissions from permafrost pond ecosystems now and in the future.Plain Language Summary: Long‐term studies of methane emissions from thaw ponds are rare but essential for our understanding of how these ecosystems are responding to Arctic warming. Our study incorporates over 2,000 measurements of methane gas, collected over four summer seasons from eight small ponds located within one single peatland in northern Sweden. These ponds formed when frozen soil thawed due to increasing air temperatures. Ponds like these are known to release methane, a strong greenhouse gas, through bubbling, diffusion along a concentration gradient, and transport through plant internal structure, though bubbling is the least understood. We also used photographs collected with a drone to estimate the area of each pond. We found the ponds to vary widely in methane emission over time as well as between ponds. We also found that meteorological variables like air temperature and atmospheric pressure explained little of the variability in bubble flux we measured. Our measurements represent the longest record of bubble measurements from climate sensitive ponds to date and help us to better understand the amount of methane released and what controls it. It is important to include these bodies of water in our understanding of how Arctic areas are changing with increasing air temperatures.Cai, J., Zhu, X., Zhang, J., Song, M., Wang, Y., 2020. Heterogeneities of organic matter and its occurrence forms in mudrocks: Evidence from comparisons of palynofacies. Marine and Petroleum Geology 111, 21-32. buried at different depths in a single well exhibiting different sedimentary environments and lithologies were collected from the Dongying Sag of the Jiyang Depression of eastern China to investigate the heterogeneities of organic matter (OM) and its occurrence forms. In this study, both bulk rocks and their organo-clay composites (i.e., <2?μm clay-sized fractions) were subjected to palynofacies analysis. The results demonstrate that palynological OM abundance and total organic carbon (TOC) content for bulk rocks are positively correlated with those in organo-clay composites respectively, suggesting that the palynological OM in organo-clay composites is intimately related to that in bulk rocks. However, other numerous variations between them exist: a) OM in the organo-clay composites is aquatic and prone to type I, while it is both terrestrial and aquatic and has multiple types of OM in bulk rocks; b) the palynological organic components in the organo-clay composites, which are mostly amorphous OM (AOM) with an average abundance exceeding 90%, are substantially different from those in bulk rocks, which possess both AOM and terrestrial OM (palynomorphs and structured OM); and c) at different depths, sedimentary environments and lithologies, the percentages of individual palynological organic components are relatively stable in organo-clay composites, whereas they vary over a wide range in bulk rocks. As many previous studies have indicated that OM occurrence is dominantly in the form of organo-clay composites, our results reveal that OM in mudrocks is heterogeneous with respect to its components and occurrence forms, namely, free OM and organo-clay composites, within which OM is greatly varied in association with minerals and its palynofacies. Free OM is physically coexisted with minerals and has different palynological organic components, while OM in organo-clay composites is combined with minerals and is dominantly composed of AOM. Our work demonstrates that OM occurrence in mudrocks has two distinct forms and their palynological organic components are greatly varied, which should be concerned in studies of source rock for further understanding the source material of petroleum.Cai, S., Zhu, L., Wang, S., Wisthaler, A., Li, Q., Jiang, J., Hao, J., 2019. Time-resolved intermediate-volatility and semivolatile organic compound emissions from household coal combustion in northern China. Environmental Science & Technology 53, 9269-9278. combustion in low-efficiency household stoves results in the emission of large amounts of nonmethane organic compounds (NMOCs), including intermediate-volatility compounds (IVOCs) and semivolatile organic compounds (SVOCs). This conceptual picture is reasonably well established, however, quantitative assessment of I/SVOC emissions from household stoves is rare. We used a proton-transfer-reaction time-of-flight mass spectrometer (PTR-ToF-MS) to quantify the emissions of organic gases from a typical Chinese household coal stove operated with anthracite and bituminous coals. Most NMOCs (approximately 64–88%) were dominated by hydrocarbons and emitted during the ignition and flaming phases. The ratio of oxidized hydrocarbons increased during the flaming and smoldering stages due to the elevated combustion efficiency. The average emission factors of NMOCs were 121 ± 25.7 and 3690 ± 930 mg/kg for anthracite and bituminous coals, respectively. I/SVOCs contributed to approximately 30% of the total emitted NMOC mass during bituminous coal combustion, much higher than the contribution of biomass burning (approximately 1.5%). Furthermore, I/SVOCs may contribute over 70% of the secondary organic aerosol (SOA) mass formed from gaseous organic species emitted as a result of bituminous coal combustion. This study highlights the importance of inventorying coal-originated I/SVOCs when conducting SOA formation simulation studies.Cairns, A.J., Hull, K.L., Sayed, M., 2019. From design to practice: Development of new acid platforms to address upstream oil and gas production challenges, in: Rahimi, P., Ovalles, C., Zhang, Y., Adams, J.J. (Eds.), Chemistry Solutions to Challenges in the Petroleum Industry. American Chemical Society, Washington DC, pp. 3-21. acidizing technologies for stimulating hydrocarbon-bearing formations continue to be developed. However, the quest to identify “fit-for-purpose” acid systems that possess chemical and physical properties superior to existing methodologies remains very challenging. The criteria for choosing a suitable acid system are governed by several factors including the mineralogy of the reservoir and the nature of the treatment. Desirable characteristics for emerging acid systems rely on preserving the key advantages of existing technologies, specifically with respect to availability and cost, thermal stability, dissolving power, and reaction product solubility. Meanwhile, addressing the limitations associated with safety and complexity at the wellsite, fluid pumpability, casing corrosion, and suitable acid–substrate reaction kinetics continue to pose a significant challenge. This chapter provides a brief historical perspective on acidizing and highlights the state-of-the-art technologies and motivation for choosing an acid system, advantages and limitations associated with this selection, and the various treatment designs employed to stimulate subterranean formations. We report on the rational design, characterization, and optimization of two new acid platforms that allow for potential on-demand placement in the zone of interest. One proposed strategy uses a redox chemistry approach whereby bromate selectively oxidizes a series of ammonium-based salts to generate a variety of acids in situ. Second, a hybrid inorganic/organic acid platform was developed for delivery of concentrated acid deep into the formation where kinetic control is achieved by fine-tuning the free water in the system.C?mara, J.M.D.A., Sousa, M.A.S.B., Barros Neto, E.L., Oliveira, M.C.A., 2019. Application of rhamnolipid biosurfactant produced by Pseudomonas aeruginosa in microbial-enhanced oil recovery (MEOR). Journal of Petroleum Exploration and Production Technology 9, 2333-2341. this study, the biosurfactant produced by Pseudomonas aeruginosa was evaluated in view of its ability to be used in Microbial-Enhanced Oil Recovery (MEOR). This microorganism was isolated from a soil artificially contaminated with crude oil and used to produce rhamnolipid using glycerol as the carbon source. The biosurfactant efficiently reduced water surface tension from 72 to 35.26?mN/m at its critical micelle concentration of 127?mg/L and emulsification rate (E24) of 69% for the crude oil. Furthermore, it was demonstrated that the rhamnolipid can recover oil, even 2?months after its production, which shows that its biodegradability is not a disadvantage to the application in MEOR. The best result, for a biosurfactant concentration of 100% above the Critical Micelle Concentration (CMC) and petroleum with API gravity of 21.90, showed that the total recovery factor was 50.45?±?0.79%, of which 11.91?±?0.39% corresponds to MEOR.Canavelli, P., Islam, S., Powner, M.W., 2019. Peptide ligation by chemoselective aminonitrile coupling in water. Nature 571, 546-549. bond formation is one of the most important reactions in both chemistry and biology, but there is currently no chemical method of achieving α-peptide ligation in water that tolerates all of the 20 proteinogenic amino acids at the peptide ligation site. The universal genetic code establishes that the biological role of peptides predates life’s last universal common ancestor and that peptides played an essential part in the origins of life. The essential role of sulfur in the citric acid cycle, non-ribosomal peptide synthesis and polyketide biosynthesis point towards thioester-dependent peptide ligations preceding RNA-dependent protein synthesis during the evolution of life. However, a robust mechanism for aminoacyl thioester formation has not been demonstrated. Here we report a chemoselective, high-yielding α-aminonitrile ligation that exploits only prebiotically plausible molecules—hydrogen sulfide, thioacetate and ferricyanide or cyanoacetylene—to yield α-peptides in water. The ligation is extremely selective for α-aminonitrile coupling and tolerates all of the 20 proteinogenic amino acid residues. Two essential features enable peptide ligation in water: the reactivity and pKaH of α-aminonitriles makes them compatible with ligation at neutral pH and N-acylation stabilizes the peptide product and activates the peptide precursor to (biomimetic) N-to-C peptide ligation. Our model unites prebiotic aminonitrile synthesis and biological α-peptides, suggesting that short N-acyl peptide nitriles were plausible substrates during early evolution.Cantrell, T.P., Freeman, C.J., Paul, V.J., Agarwal, V., Garg, N., 2019. Mass spectrometry-based integration and expansion of the chemical diversity harbored within a marine sponge. Journal of The American Society for Mass Spectrometry 30, 1373-1384. sponges and their associated symbionts produce a structurally diverse and complex set of natural products including alkaloids, terpenoids, peptides, lipids, and steroids. A single sponge with its symbionts can produce all of the above-mentioned classes of molecules and their analogs. Most approaches to evaluating sponge chemical diversity have focused on major metabolites that can be isolated and characterized; therefore, a comprehensive evaluation of intra- (within a molecular family; analogs) and inter-chemical diversity within a single sponge remains incomplete. We use a combination of metabolomics tools, including a supervised approach via manual library search and literature search, and an unsupervised approach via molecular networking and MS2LDA analysis to describe the intra and inter-chemical diversity present in Smenospongia aurea. Furthermore, we use imaging mass spectrometry to link this chemical diversity to either the sponge or the associated cyanobacteria. Using these approaches, we identify seven more molecular features that represent analogs of four previously known peptide/polyketide smenamides and assign the biosynthesis of these molecules to the symbiotic cyanobacteria by imaging mass spectrometry. We extend this analysis to a wide diversity of molecular classes including indole alkaloids and meroterpenes.Cao, J.-L., Ma, L.-J., Wang, S.-P., Deng, Y., Wang, Y.-T., Li, P., Wan, J.-B., 2019. Comprehensive qualitative and quantitative analysis of ginsenosides in Panax notoginseng leaves by online two-dimensional liquid chromatography coupled to hybrid linear ion trap Orbitrap mass spectrometry with deeply optimized dilution and modulation system. Analytica Chimica Acta 1079, 237-251. notoginseng leaves (PNL) was considered as a potential medicinal part with abundant protopanaxdiol type ginsenosides. In this study, an integrated system was developed for simultaneously qualitative and quantitative analysis of ginsenosides in PNL using online comprehensive two-dimensional hydrophilic interaction chromatography and reversed-phase liquid chromatography coupled to a hybrid linear ion trap-Orbitrap mass spectrometry (online HILIC?×?RP-ESI/HRMS/MSn). The system was configured based on the combination of a XBridge amide column (150?mm?×?2.1?mm, 2.5?μm) and Accucore phenyl-hexyl (50?mm?×?4.6?mm, 2.6?μm) for the first and second dimensions, respectively. An additional water phase was introduced to dilute the eluent from the first dimension to decrease its elution strength in the second dimension. The online dilution, modulation interface and the second-dimension gradient program were deeply optimized to reduce possible sample loss and improve system resolution. Under the optimal conditions, a total of 226 ginsenosides were unambiguously identified or tentatively characterized by aid of high-resolution accurate mass and MSn fragment data in both negative and positive ion modes, and 93 of them were discovered as potentially new ginsenosides in PNL. Besides, the online HILIC?×?RP-LTQ-MS method was validated and applied to the determination of 24 ginsenosides directly on 2D-EIC contour plots in nine batches of PNL samples. The powerful separation capability acquired using the developed online HILIC?×?RP system could afford not only reliable structural information for identification, but also accurate quantitation. This combined system can also be applied to characterize and quantify bioactive ingredients in the samples with complex matrices.Capitanio, F.A., Nebel, O., Cawood, P.A., Weinberg, R.F., Clos, F., 2019. Lithosphere differentiation in the early Earth controls Archean tectonics. Earth and Planetary Science Letters 525, 115755. processes that operated on the early Earth and the tectonic regimes in which it was shaped are poorly constrained, reflecting the highly fragmentary rock record and uncertainty in geodynamic conditions. Most models of early Earth geodynamics invoke a poorly mobile lid regime, involving little or episodic movement of the lithosphere, above a convecting mantle. However, such a regime does not reconcile with the record of Archean tectonics, which displays contrasting environments associated with either non-plate tectonics or plate tectonics. Here, we propose a regime for the early Earth in which progressive melt extraction at sites of divergence led to the formation of large portions of stiffer lithospheric lid, called proto-plates. These proto-plates enabled stress propagation to be focussed at their margins, which were then the locus for extension as oppose to shortening, under-thrusting and thickening to form adjoining proto-cratons. We test this hypothesis embedding lithospheric stiffening during melt extraction in thermo-mechanical models of mantle convection, under conditions that prevailed in the Archean. We demonstrate the emergence of migrating, rigid proto-plates in which regions of prolonged focused compression coexist with remnants of the stagnant lid, thereby reproducing the widespread dichotomy proposed for the Archean tectonic record. These diverse tectonic modes coexist in a single regime that is viable since the Hadean and lasted until the transition to modern plate tectonics.Cappuyns, V., Claes, H., Geris, P., Maquil, R., Swennen, R., 2019. Mineralogical and geochemical characterization of Mo-rich black shales in the Grand Duchy of Luxembourg. Journal of Geochemical Exploration 206, 106351.“Schistes carton”, Jurassic black shale rocks occurring in the south-western part of the Grand Duchy of Luxembourg, were investigated, based on a combined mineralogical and geochemical approach. The major aim of this study was to understand the lateral and vertical variation in mineralogy, and the distribution of major and trace elements within the different black shale lithologies, as well as in the overlying soils. The mobility of trace metal(loids) in the black shale and in the soil developed upon the black shale was also addressed. The “Schistes carton” bedrock consists mainly of illite and kaolinite, quartz, calcite and pyrite. Framboidal pyrite is found in the clay matrix, while stratiform pyrite lenses are found in calcitic beds or in lag deposits. At a depth of 4.25?m, pyrite is altered to goethite and gypsum. The acidity generated by pyrite oxidation is neutralized by calcite dissolution, resulting in neutral to slightly alkaline pH conditions. The “Shistes Carton” bedrock is characterized by variable concentrations of Ca, S, Cd, Mo and Zn. Compared to the surrounding matrix, the (stratiform) pyrites found in the “Schistes carton” express an enrichment with As, Cd, Pb and Zn, while the lag deposit contained high concentrations of As, Cd, Mn, Zn, and P. Mo concentrations in the bedrock and the soils up to 74?mg/kg were found, which is comparable with Mo concentrations in soils developed on black shales at other locations in the World. Most trace elements are not leached from the shales under the prevailing pH conditions (7–7.5), except Mo, which leaches in concentrations up to 85?μg/l. This study highlights the importance of small and large-scale variations in bedrock composition and its influence on soil geochemistry, which should be taken into account during the development of national and regional guidelines and regulations on soil quality.Carrasco-Correa, E.J., Kubáň, P., Cocovi-Solberg, D.J., Miró, M., 2019. Fully automated electric-field-driven liquid phase microextraction system with renewable organic membrane as a front end to high performance liquid chromatography. Analytical Chemistry 91, 10808-10815. article reports for the first time a programmable-flow-based mesofluidic platform that accommodates electric-field-driven liquid phase microextraction (μ-EME) in a fully automated mode. The miniaturized system is composed of a computer-controlled microsyringe pump and a multiposition rotary valve for handling aqueous and organic solutions at a low microliter volume and acts as a front-end to online liquid chromatographic separation. The organic membrane is automatically renewed and disposed of in every analytical cycle, thus minimizing analyte carry-over effects while avoiding analyst intervention. The proof-of-concept applicability of the automated mesofluidic device is demonstrated by the liquid chromatographic determination of nonsteriodal anti-inflammatory drugs in μ-EME processed complex samples (such as urine and influent wastewater) using online heart-cut approaches. Using 5 μL of 1-octanol, 7.5 μL of untreated sample and 7.5 μL of acceptor solution (25 mM NaOH), and 250 V for only 10 min in a stopped-flow mode, the extraction recoveries for the μ-EME of ibuprofen, ketoprofen, naproxen, and diclofenac exceed 40% in real samples. The flow-through system features moderately selective extraction regardless of the sample matrix constituents with repeatability values better than 13%.Carrión Marco, Y., Vives-Ferrándiz Sánchez, J., 2019. Rethinking the perishable: Identifying organic remains in metal objects at the Iron Age site of La Bastida de les Alcusses (Moixent, Spain). Journal of Archaeological Science: Reports 27, 101970. use of certain perishable materials for handicraft, such as wood, has been underestimated in archaeological investigation due to their poor preservation. Its study through indirect evidence (other non-perishable materials, ethnographic sources) is partial, and does not account for the real importance of wood in domestic, craft and ritual contexts in past societies. In this review we reclaim the use of wood as a co-constitutive material of objects by focusing on Iron Age tools, weapons and carpentry elements from a case-study in the Western Mediterranean. We also suggest the adoption of protocols for sampling and analysing the remains of wood adhered to metal objects, which may contribute to increase our knowledge about the use of this raw material in the past.Castro-Morales, K., Schürmann, G., K?stler, C., R?denbeck, C., Heimann, M., Zaehle, S., 2019. Three decades of simulated global terrestrial carbon fluxes from a data assimilation system confronted with different periods of observations. Biogeosciences 16, 3009-3032. the last decade, carbon cycle data assimilation systems (CCDAS) have focused on improving the simulation of seasonal and mean global carbon fluxes over a few years by simultaneous assimilation of multiple data streams. However, the ability of a CCDAS to predict longer-term trends and variability of the global carbon cycle and the constraint provided by the observations have not yet been assessed. Here, we evaluate two near-decade-long assimilation experiments of the Max Planck Institute – Carbon Cycle Data Assimilation System (MPI-CCDAS v1) using spaceborne estimates of the fraction of absorbed photosynthetic active radiation (FAPAR) and atmospheric CO2 concentrations from the global network of flask measurement sites from either 1982 to 1990 or 1990 to 2000. We contrast these simulations with independent observations from the period 1982–2010, as well as a third MPI-CCDAS assimilation run using data from the full 1982–2010 period, and an atmospheric inversion covering the same data and time. With 30 years of data, MPI-CCDAS is capable of representing land uptake to a sufficient degree to make it compatible with the atmospheric CO2 record. The long-term trend and seasonal amplitude of atmospheric CO2 concentrations at station level over the period 1982 to 2010 is considerably improved after assimilating only the first decade (1982–1990) of observations. After 15–19 years of prognostic simulation, the simulated CO2 mixing ratio in 2007–2010 diverges by only 2±1.3?ppm from the observations, the atmospheric inversion, and the MPI-CCDAS assimilation run using observations from the full period. The long-term trend, phenological seasonality, and interannual variability (IAV) of FAPAR in the Northern Hemisphere over the last 1 to 2 decades after the assimilation were also improved. Despite imperfections in the representation of the IAV in atmospheric CO2, model–data fusion for a decade of data can already contribute to the prognostic capacity of land carbon cycle models at relevant timescales.Cerón-Romero, M.A., Maurer-Alcalá, X.X., Grattepanche, J.-D., Yan, Y., Fonseca, M.M., Katz, L.A., 2019. PhyloToL: A taxon/gene-rich phylogenomic pipeline to explore genome evolution of diverse eukaryotes. Molecular Biology and Evolution 36, 1831-1842. multiple sequence alignments (MSAs) and inferring phylogenies are essential for many aspects of comparative biology. Yet, many bioinformatics tools for such analyses have focused on specific clades, with greatest attention paid to plants, animals, and fungi. The rapid increase in high-throughput sequencing (HTS) data from diverse lineages now provides opportunities to estimate evolutionary relationships and gene family evolution across the eukaryotic tree of life. At the same time, these types of data are known to be error-prone (e.g., substitutions, contamination). To address these opportunities and challenges, we have refined a phylogenomic pipeline, now named PhyloToL, to allow easy incorporation of data from HTS studies, to automate production of both MSAs and gene trees, and to identify and remove contaminants. PhyloToL is designed for phylogenomic analyses of diverse lineages across the tree of life (i.e., at scales of >100 My). We demonstrate the power of PhyloToL by assessing stop codon usage in Ciliophora, identifying contamination in a taxon- and gene-rich database and exploring the evolutionary history of chromosomes in the kinetoplastid parasite Trypanosoma brucei, the causative agent of African sleeping sickness. Benchmarking PhyloToL’s homology assessment against that of OrthoMCL and a published paper on superfamilies of bacterial and eukaryotic organellar outer membrane pore-forming proteins demonstrates the power of our approach for determining gene family membership and inferring gene trees. PhyloToL is highly flexible and allows users to easily explore HTS data, test hypotheses about phylogeny and gene family evolution and combine outputs with third-party tools (e.g., PhyloChromoMap, iGTP).Chang, J., Bai, Z., Sun, Y., Peng, Y., Qin, S., Shen, B., 2019. High resolution bio- and chemostratigraphic framework at the Frasnian-Famennian boundary: Implications for regional stratigraphic correlation between different sedimentary facies in South China. Palaeogeography, Palaeoclimatology, Palaeoecology 531, 108299. one of the “Big Five” mass extinctions in Phanerozoic, the Frasnian-Famennian (F-F) boundary event records the extinction of 40 % of marine invertebrate genera. The F-F boundary is defined by the first appearance of conodont Palmatolepis subperlobata as well as the abundant occurrences of Pa. ultima at the base of the Lower Pa. triangularis Zone. The F-F boundary is also broadly coincident with a positive excursion in carbon isotopes, suggesting the possible linkage between the perturbation of marine carbon cycle and the biotic crisis. However, the correlation between conodont biostratigraphy and carbon isotope chemostratigraphy has not been established yet, preventing the high-resolution regional stratigraphic correlation among different sedimentary facies. In this study, we studied the conodont biostratigraphy and analyzed carbonate carbon (δ13Ccarb) and organic carbon (δ13Corg) isotopes of the Baisha section in the Guangxi Province, South China. The first appearance of index conodont fossil Pa. subperlobata for the Lower Pa. triangularis Zone, i.e. the F-F boundary, is coincident with the onset of a 3‰ positive excursion in δ13Ccarb, while Pa. triangularis and Pa. subperlobata occur nearly simultaneously, but predate the disappearances of Pa. linguiformis and other typical Frasnian elements. In addition, a positive excursion in δ13Corg is associated with the decline of δ13Ccarb near the base of the Middle Pa. triangularis Zone, which is marked by the first appearance of Pa. delicatula. Another important Famenian element Pa. minuta, the index fossil for the Upper Pa. triangularis Zone, first appears when δ13Corg starts to decline. The offset between δ13Corg and δ13Ccarb excursions could be attributed to the oceanic anoxia (the Kellwasser Event) near the F-F boundary, followed by the mixing of surface and deep water in earliest Famenian. The high resolution bio- and chemostratigraphic framework can be used as the standard for regional stratigraphic correlation and identification of the F-F boundary in different depositional environments in South China. We propose that the F-F boundary can be identified from a conodont-poor carbonate section by the onset of the positive excursion in δ13Ccarb, whereas the F-F boundary in a non-fossiliferous siliciclastic section might be placed slightly below the positive excursion in δ13Corg.Chang, J., Peng, S., Ciais, P., Saunois, M., Dangal, S.R.S., Herrero, M., Havlík, P., Tian, H., Bousquet, P., 2019. Revisiting enteric methane emissions from domestic ruminants and their δ13CCH4 source signature. Nature Communications 10, 3420. knowledge of 13C isotopic signature (δ13C) of methane from each source is crucial for separating biogenic, fossil fuel and pyrogenic emissions in bottom-up and top-down methane budget. Livestock production is the largest anthropogenic source in the global methane budget, mostly from enteric fermentation of domestic ruminants. However, the global average, geographical distribution and temporal variations of the δ13C of enteric emissions are not well understood yet. Here, we provide a new estimation of C3-C4 diet composition of domestic ruminants (cattle, buffaloes, goats and sheep), a revised estimation of yearly enteric CH4 emissions, and a new estimation for the evolution of its δ13C during the period 1961–2012. Compared to previous estimates, our results suggest a larger contribution of ruminants’ enteric emissions to the increasing trend in global methane emissions between 2000 and 2012, and also a larger contribution to the observed decrease in the δ13C of atmospheric methane.Chattaraj, S., Mohanty, D., Kumar, T., Halder, G., Mishra, K., 2019. Comparative study on sorption characteristics of coal seams from Barakar and Raniganj formations of Damodar Valley Basin, India. International Journal of Coal Geology 212, 103202. methane retention mechanism in coal seams is markedly different from those of conventional gas reservoirs. Methane remains mainly as physically adsorbed molecules on micropore surface. Chemical and petrographic compositions of coal are the measures of maturity and type of organic matter that control the methane sorption characteristics of the coal. 99% of Indian coal occurrences are contributed by lower Gondwana sequences housed in two major geologic formations, younger Raniganj and older Barakar. The Raniganj Formation is best exposed in Raniganj Sub-basin and Barakar Formation is best exposed in Jharia Sub-basin of Damodar Valley. Present work attempts a systematic investigation on comparative account of methane sorption characteristics of coals from Raniganj Formation of Raniganj Sub-basin and Barakar Formations of Jharia Sub-basin in relation to their chemical composition and petrographic makeup. Chemical analyses shows that moisture, ash, volatile matter and fixed carbon varies between 2.5 and 4.6%, 10.0–27.2%, 38.8–40.2% (dmmf) and 59.8–61.2% (dmmf), respectively for Raniganj coals and, 0.5–1.1%, 16.7–32.9%, 20.7–22.0% (dmmf) and 78.0–79.3% (dmmf), respectively for Barakar coals. Carbon content is distinct for the suites of coal, 79.2–85.4% and 85.6–92.0% for Raniganj and Barakar coals, respectively. The vitrinite reflectance for the Raniganj coals ranges 0.53–0.72% and the Barakar coals ranges 1.09–1.23%. Based on the chemical composition and vitrinite reflectance value Raniganj coals belongs to high volatile bituminous type, whereas Barakar coals belongs to high to medium volatile bituminous type. Such variation in composition and maturity is mainly attributed to the variation in precursor organic matter as well as the basinal and thermal history of the sub-basins under consideration.H/C atomic ratio of the Raniganj and Barakar coals varies between 0.65 and 0.80 and 0.51–0.72 and O/C atomic ratio varies between 0.05 and 0.13 and 0.01–0.07, respectively. Coals of both the Raniganj and Barakar formations are mostly of kerogen Type-III with Raniganj coals falling in wet gas maturity stage approaching early-thermogenic methane generation whereas Barakar coals falling in condensate gas stage approaching peak-thermogenic methane generation. The Langmuir volume ranges from 9.3–21.8?cc/g (daf) for Raniganj coals and 21.1–29.1?cc/g (daf) for Barakar coals. Sorption capacity for the set of coals shows a strong rank dependency and increase with corresponding increase in rank down the stratigraphic column. Methane sorption capacity shows positive relationship with carbon content and vitrinite reflectance, and negative relationship with moisture content, ash and volatile matter. Moisture effect is more prominent in low rank Raniganj coals. The adsorption capacity shows a strong positive relation with vitrinite content and a moderate negative relation with inertinite content for both the Raniganj and Barakar coals, which may be attributed to dominancy of micropores in vitrinites with rank enhancement. The multiple regression analysis shows that the moisture is the main predictor of the VL, and the interaction of moisture with ash and reflectance mainly control the sorption capacity. A predictive model equation is developed for determination of sorption for Damodar basin coals from carbon, ash and moisture data.Chela-Flores, J., 2019. Testing S isotopes as biomarkers for Mars. International Journal of Astrobiology 18, 436-439. suggest testing S isotopes as biomarkers for Mars. An analogous robust biosignature has recently been proposed for the forthcoming exploration of the icy surface of Europa, and in the long term for the exploration of the surfaces of other icy moons of the outer solar system. We discuss relevant instrumentation for testing the presence of life itself in some sites, whether extinct or extant in order to complement a set of other independent biosignatures. We pay special attention to the possible early emergence of sulphate-metabolizing microorganisms, as it happened on the early Earth. Fortunately, possible sites happen to be at likely landing sites for future missions ExoMars and Mars 2020, including Oxia Planum and Mawrth Vallis. We suggest how to make additional feasible use of the instruments that have already been approved for future missions. With these instruments, the proposed measurements can allow testing S isotopes on Mars, especially with the Mars Organic Molecule Analyzer.Chen, B., Pawar, R.J., 2019. Capacity assessment and co-optimization of CO2 storage and enhanced oil recovery in residual oil zones. Journal of Petroleum Science and Engineering 182, 106342. oil zones (ROZs) are increasingly being commercially exploited using CO2-enhanced oil recovery (CO2-EOR) method. In this study, CO2 storage potential, long-term CO2 fate and oil recovery potential in ROZs are characterized based on a reservoir model for Goldsmith-Landreth San Andres Unit in the Permian Basin. The effects of CO2 injection rates, well patterns (five-spot and line-drive), well spacings, injection modes (continuous CO2 injection and water-alternating-gas injection) on the CO2 retention in the reservoir and the oil production are investigated. After the preliminary assessment of CO2 storage and EOR potentials in ROZs, we next develop a novel approach based on a newly developed optimization algorithm-Stochastic Simplex Approximate Gradient (StoSAG) and predictive empirical models constructed using machine learning technique to co-optimize CO2 storage and oil recovery in ROZs. The performance of co-optimization of CO2 storage and oil recovery is compared with the performance of optimization of only CO2 storage.Chen, J., Chen, J., Ni, Y., Fan, M., Liao, F., Wei, J., Han, Y., 2019. The origin and source of crude oils in the Jiuxi depression, Jiuquan Basin. Acta Petrolei Sinica 40, 761-776 crude oil that has been discovered in the Jiuxi depression, Jiuquan Basin is mainly distributed in the Qingxi sag and the southern uplift. There are three types of crude oils with different maturities in the Jiuxi depression; they are originated from the source rocks of different layers of the Lower Cretaceous in Qingnan subsag of the Qingxi sag. The first type is the low-maturity crude oil. It is mainly from the low-maturity source rocks of the Upper Member of Lower Cretaceous Xiagou Formation, and the upper source rocks of the Middle Member of Xiagou Formation also have a certain contribution to it. The second type is the medium-maturity crude oil, mainly from the source rocks of the Middle Member of Xiagou Formation, partially contributed by the upper source rocks of the Lower Member of Xiagou Formation. The third type is the high-maturity crude oil, originated from the source rocks of the Lower Member of Xiagou Formation and the Chijinpu Formation. The medium-shallow reservoir of the Liugouzhuang oilfield in the central part of Qingnan subsag is dominated by the second type of crude oil, accompanied with a small amount of the first type, which are derived from the source rocks of the Middle Member and Upper Member of Xiagou Formation in the central part of Qingnan subsag. The deep reservoir in the central part of Qingnan subsag is dominated by the third type of crude oil, derived from the source rocks of the Lower Member of Xiagou Formation and the Chijinpu Formation in the deep layer of the central part of Qingnan subsag. The Kulongshan tectonic belt in the south and the Liubei tectonic belt in the north are dominated by the third type crude oil, derived from the source rocks of the Lower Member of Xiagou Formation and the Chijinpu Formation in the southern and northern part of Qingnan subsag, respectively. The Yaerxia-Laojunmiao-Shiyougou tectonic belt is dominated by the second type of crude oil, derived from the source rocks of the Middle Member of Xiagou Formation in the central part of Qingnan subsag. The Middle Member and Lower Member of Xiagou Formation and the Chijinpu Formation in Qingnan subsag are the main source rocks of the Jiuxi depression.Chen, S., Xu, Y., Sun, S., Chen, F., 2019. Haloterrigena salifodinae sp. nov., an extremely halophilic archaeon isolated from a subterranean rock salt. Antonie van Leeuwenhoek 112, 1317-1329. novel extremely halophilic strain, designated ZY19T, was isolated from a rock salt sample from Yunnan salt mine, PR China. Strain ZY19T is neutrophilic, non-motile and requires at least 10% (w/v) NaCl for growth. Optimal growth is observed at 20–25% (w/v) NaCl, pH 7.5–8.0 and 42 °C. Mg2+ is not required for growth. The cells do not lyse in distilled water. On the basis of 16S rRNA gene sequence analysis, strain ZY19T belongs to the genus Haloterrigena (Htg.) and is closely related to Haloterrigena salina XH-65T (98.5% sequence similarity) and Haloterrigena turkmenica DSM 5511T (97.9%). Phylogenetic and phylogenomic analysis showed that strain ZY19T clusters with the species Htg. salina and Htg. turkmenica forming an independent clade separated from other members of the genus. The value of genomic average nucleotide identity (ANI) between strains ZY19T and its close relative, Htg. salina XH-65T was 94.2%. DNA–DNA relatedness between strains ZY19T and Htg. salina XH-65T revealed by in silico DNA–DNA hybridization (DDH) was 56.3%. Both the ANI value and the degree of in silico DDH are below the accepted threshold for members of the same species. The major polar lipids were found to consist of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, sulfated diglycosyl-diether-1 and mannose-2, 6-disulfate (1?→?2)-glucose glycerol diether. The genomic DNA G+C content was determined to be 64.5 mol%. Based on the results of the phenotypic, chemotaxonomic, genetic similarity and inferred phylogeny, strain ZY19T is distinct from other validly named species and thus represents a novel species within the genus Haloterrigena, for which the name Haloterrigena salifodinae sp. nov. is proposed. The type strain is ZY19T (=CGMCC 1.16114T=NBRC 112981T). Chen, X., Liu, Q., Meng, Q., Zhu, D., Liu, W., Fu, Q., 2019. Assessing effects of sulfate minerals on petroleum generation in sedimentary basins using hydrous pyrolysis: I. Light alkanes. Marine and Petroleum Geology 110, 737-746. series of hydrous pyrolysis experiments were conducted to assess the role of sulfate minerals on the chemical and isotopic compositions of light hydrocarbons generated during thermal degradation of kerogen. The shale source rock with low maturity (Tmax?=?425?°C) from Eagle Ford formation in southeast Texas was used in the experiments at 330?°C for the duration of 72?h, while the abundance of gypsum in each experiment varies from 0, 0.5, to 1?wt%. Under experimental conditions, the positive effect of gypsum on the yields of gaseous alkanes (C1 - C4) and CO2 has been explicitly observed, with an exponential relationship between the yield of each gas and the amount of gypsum. While the relative abundance of C2 - C4 alkanes has shown an increasing trend with gypsum, the gas dryness (C1/∑C1-4), however, decreased from 73.1% with no gypsum to 49.6% with gypsum of 1?wt%. It was attributed to lower overall yields and corresponding higher increased generation rates of C2 - C4 alkanes than methane through thermal cracking of kerogen and other organic compounds. The carbon isotope value of each alkane reached the highest in the experiment with 1?wt% gypsum. Compared to the experiment without gypsum, there was an increase of 11.5‰ for the δ13C value of methane with 1?wt% gypsum. The extent of this 13C enrichment between experiments with different amount of gypsum became less for C2 to C4. The δ13C value of CO2 was the highest among generated gases, ranging from ?4.7 to ?2.1‰. Combined with chemical compositions of gases, it suggested that enhanced thermal cracking reactions were predominant in generation of light alkanes with the presence of gypsum, whereas dissolution of carbonates was the main source of CO2. The reactions involving thermochemical sulfate reduction (TSR) were minor (if present) under experimental conditions, most likely due to the small quantity of gypsum (up to 1?wt%) and neutralization of acidity by carbonates. Nonetheless, the changes in chemical and isotopic compositions of light alkanes, which were ultimately caused by the presence of gypsum, need to be incorporated into geochemical proxies for assessing source rocks (maturation in particular) and their generation potential.Chen, Y., Li, J., Schmitz, O.J., 2019. Development of an at-column dilution modulator for flexible and precise control of dilution factors to overcome mobile phase incompatibility in comprehensive two-dimensional liquid chromatography. Analytical Chemistry 91, 10251-10257. the combination of different mechanisms, two-dimensional liquid chromatography has brought revolutionary changes compared to the traditional one-dimensional separation, which dramatically improve the peak capacity in separation and meet the ever-increasing demand for the analysis of complex samples in different research fields, such as chemistry, medicine, etc. However, the incompatibilities between two columns due to the transport of the large sample volume and the solvent effect always limit the wide use of two-dimensional liquid chromatography. In order to resolve this problem an at-column dilution (ACD) modulator was established to overcome the solvent incompatibility in the orthogonal combination within the comprehensive two-dimensional liquid chromatography. This interface is modified from normal two-dimensional interfaces by an additional transfer pump, which realize the at-column dilution without a flow split during the transportation. Moreover, with the control of the transfer flow and the second-dimensional gradient flow, it is able to precisely regulate the at-column dilution factor and conveniently optimize the separation conditions in both dimensions. In this work, a systematic research has been done between the setups with/without the at-column interface in the combination of reversed-phase liquid chromatography and hydrophilic interaction chromatography (RPLC × HILIC) and HILIC × RPLC, which proved that the at-column interface is able to resolve the solvent conflict problem very well. Furthermore, red ginseng was chosen as a real sample to investigate the applicability of the at-column dilution modulator for comprehensive two-dimensional chromatography with high orthogonality.Chen, Y., Richoz, S., Krystyn, L., Zhang, Z., 2019. Quantitative stratigraphic correlation of Tethyan conodonts across the Smithian-Spathian (Early Triassic) extinction event. Earth-Science Reviews 195, 37-51. small-scale extinctions occurred in the Early Triassic with one of them recognized close to the Smithian-Spathian boundary. In the last two decades, the end-Permian mass extinction as well as the subsequent recovery have been intensively studied throughout the Tethys region, but correlations within the Lower Triassic are difficult due to conodonts endemism. Here we use paleontological and geochemical methods to document a high-resolution biostratigraphy of the Smithian-Spathian boundary interval from two sections of Oman. In combination with previously published data from both South-Central Europe and South China, a quantitative stratigraphic correlation has been achieved with 7 conodont UA Zones recognized using the unitary association method. Based on conodonts and carbonate carbon isotope data, the Smithian-Spathian boundary is identified in the interval from UAZ4 to UAZ5 close to the last occurrence of Nv. pingdingshanensis in Oman and South China, and within the range of P. inclinata, Ns. planus, Pl. regularis, and Pl. corniger in South-Central Europe. UAZ7 fauna displays a clear diachronism as it starts from South China, arrives a bit later in Oman and even later in western Tethys. Foliella gardenae and Icriospathodus zaksi are reported from Oman for the first time and thus expand the geographical distribution of these rarely reported species.Chen, Z., Chen, S., Xiao, Z., Han, M., Qiu, W., 2019. Source of Chang 10 crude oil in Zhidan area, Ordos Basin, China. Petroleum Science and Technology 37, 2207-2212. studies on the oil source of Chang 10 reservoir in the Zhidan area were undertaken until now, but still have no definite conclusion. Based on the comparisons and analyses of geochemical parameters between Chang 7 to Chang 9 source rocks and Chang 10 crude oil, it is found that the forming environments of the crude oil in the Chang 10 member are similar to Chang 7 and Chang 9 source rocks, as they occur both in weak reduction environments. C30 hopane(C30H), Ts, C30 rearranged hopane(C30*), Ts/C30H and C30*/C30H range of two types of crude oil in the Chang 10 member are similar to those of Chang 7 and Chang 9 source rocks, respectively. The results show that the crude oil in the Chang 10 member is a mixed product of Chang 7 and Chang 9 source rocks.Cheng, J., Zhu, Y., Zhang, Z., Yang, W., 2019. Modification and improvement of microalgae strains for strengthening CO2 fixation from coal-fired flue gas in power plants. Bioresource Technology 291, 121850. CO2 capture using microalgae is a promising new method for reducing CO2 emission of coal-fired flue gas. The strain of microalgae used in this process plays a vital role in determining the rate of CO2 fixation and characteristics of biomass production. High requirements are put forward for algae strains due to high CO2 concentration and diverse pollutants in flue gas. CO2 can directly diffuse into the cytoplasm of cells by extra- and intracellular CO2 osmotic pressure under high CO2 concentrations. The flue gas pollutants, such as SOx, NOx and fly ashes, have negative effects on the growth of microalgae. This work reviewed the state-of-the-art advances on microalgae strains used for CO2 fixation, focusing on the modification and improvement of strains that are used for coal-fired flue gas. Methods such as genetic engineering, random mutagenesis, and adaptive evolution have the potential to facilitate photosynthesis, improve growth rate and reduce CO2 emission.Cheng, P., Okada, S., Zhou, C., Chen, P., Huo, S., Li, K., Addy, M., Yan, X., Ruan, R.R., 2019. High-value chemicals from Botryococcus braunii and their current applications – A review. Bioresource Technology 291, 121911. braunii is known for its high yield of extracellular hydrocarbons and polysaccharides. Hydrocarbons, especially botryococcenes and squalene can be used as not only fuels but also alternative feedstock for other fossil-based products. Exopolysaccharides excreted from B. braunii can be used as scaffolds for polyesters production, and have a notable potential for synthesis of nanoparticles. B. braunii is also a rich source of carotenoids, especially the unique secondary carotenoids such as botryoxanthins that have never been found in other microalgae. The morphology, physiology, and outer cell walls of B. braunii are complex. Understanding the colony structure shall provide insights into the mechanism of cell growth and chemicals secretion. It is possible to improve the production economics of the alga with advanced culture systems. Moreover, investigation of metabolic pathways for B. braunii may help us understand their regulation and provide valuable information for strain selection and optimal production of high-value chemicals.Cheung, S., Mak, W., Xia, X., Lu, Y., Cheung, Y., Liu, H., 2019. Overlooked genetic diversity of ammonia oxidizing archaea lineages in the global oceans. Journal of Geophysical Research: Biogeosciences 124, 1799-1811.: In this study, we used miTAG approach to analyze the distributional pattern and fine‐scale genetic diversity of the ammonia oxidizing archaea (AOA) lineages in the global oceans with the metagenomics data sets of the Tara Oceans global expedition (2009–2013). Using the ammonium monooxygenase alpha subunit gene as a biomarker, the AOA communities in the global oceans were recovered with highly diverse operational taxonomic units that affiliated to previously defined clades, including water column A (WCA), water column B (WCB), and SCM1‐like clades. In general, the AOA communities were obviously segregated with depth (except the upwelling regions), and the communities in the euphotic zones were more heterogeneous than in the mesopelagic zones (MPZs). The WCA distributed more evenly and widely in the euphotic zone and MPZs, while WCB and SCM1‐like clade mainly distributed in MPZ and high‐latitude waters, respectively. At fine‐scale genetic diversity, SCM1‐like and 2 WCA subclades showed distinctive niche separations of distributional pattern. We further divided the AOA subclades into ecological significant taxonomic units (ESTUs), which were delineated from the distribution pattern of their corresponding subclades. For example, ESTUs of WCA have different correlations with depth, nitrate to silicate ratio, and salinity; SCM1‐like A was negatively correlated with irradiation, whereas other SCM1‐like ESTUs preferred low‐temperature and high‐nutrient conditions. Our result showed that the previously defined AOA clades and ecotypes consist of highly diverse sublineages, whose diversity might be overlooked in the past. The distribution patterns of different ESTUs imply their ecophysiological characteristics and potential roles in biogeochemical cycling.Plain Language Summary: In the ocean, ammonia oxidizing archaea (AOA) are widely distributed microbes that play important roles in the marine nitrogen cycling and the emission of the highly potent greenhouse gas (N2O). However, the majority of the marine AOA are currently uncultivated; the physiology of marine AOA and the factors that mediate their distribution still remain unclear. In this study, we have analyzed the fine‐scale phylogenetic diversity and community structures of the AOA in the global ocean. Based on the results, the genetic diversity of marine AOA might be overlooked in the past since highly diverse groups that showed differential distribution patterns in the previously defined AOA ecotypes are found. Besides, by analyzing the correlations of their distributions with the varied environmental conditions in the global oceans, the diverse AOA groups were delineated with particular physiochemical factors. At a finer resolution than the previously defined ecotypes, our findings provide new insights into the determinants and the ecophysiology of the widely distributed but uncultivated AOA groups.Cornet, Y., Fran?ois, C., Compère, P., Callec, Y., Roberty, S., Plumier, J.C., Javaux, E.J., 2019. New insights on the paleobiology, biostratigraphy and paleogeography of the pre-Sturtian microfossil index taxon Cerebrosphaera. Precambrian Research 332, 105410. biological and geological events occurred during the early to middle Neoproterozoic. Among diversifying eukaryotic assemblages, populations of Cerebrosphaera, a distinctive and robust organic-walled vesicular microfossil (acritarch), show restricted stratigraphic distribution in several late Tonian to early Cryogenian worldwide successions. Here, we report the first occurrence of this taxon in Africa, in the Bouenza Subgroup (Republic of the Congo), enlarging its paleogeographic distribution and biostratigraphic significance. We also attempt to determine its biological affinity, using a combined analytical approach on specimens from the Kanpa and Hussar formations, Australia, and from the Svanbergfjellet Formation, Spitsbergen. Morphological and quantitative analyses were performed using light microscopy and scanning electron microscopy. The analyses show fine-scale morphological details and a morphological continuum between the former species Cerebrosphaera ananguae and Cerebrosphaera buickii, confirming their synonymy as proposed by a recently revised taxonomy. These observations also highlighted the presence of a thin external envelope, previously reported but formerly described and illustrated here for the first time. The characteristics of this envelope, the large diameter range of the vesicles, and the absence of excystment structure, suggest that Cerebrosphaera was a metabolically active growing cell. Ultrastructural analyses performed with TEM revealed a complex multilayered wall ultrastructure. The molecular composition and thermal maturity of the organic walls were estimated using Infrared and Raman microspectroscopies. The wall of Cerebrosphaera has a highly aromatic composition with short/highly branched aliphatic chains. The complex morphology and wall ultrastructure, combined with the large size (not a criterion by itself) of Cerebrosphaera, confirm its eukaryotic nature. Comparison with strikingly similar modern analogues permits to suggest a possible affinity to stem metazoan eggs, based on morphology and ultrastructure, but the chemical composition is unlike known biopolymers. This hypothesis is also consistent with estimates from molecular clocks. If confirmed, our results would provide an older direct evidence for stem metazoans than the Cryogenian biomarker and Ediacaran body fossil records. Our study reveals that Cerebrosphaera populations are important for Neoproterozoic biostratigraphy, but also participated to the diversification of eukaryotes in worldwide connected oceans.Cottin, H., Rettberg, P., 2019. EXPOSE-R2 on the International Space Station (2014–2016): Results from the PSS and BOSS astrobiology experiments. Astrobiology 19, 975-978. facilities were ESA multiuser facilities mounted outside the International Space Station for astrobiology experiments. Between 2008 and 2016, three series of experiments were conducted involving chemical and biological samples to test their resistance and evolution in the space environment in low Earth orbit. In this Astrobiology special collection, results from two experiments of the EXPOSE-R2 campaign (2014–2016) are presented: Biofilm Organisms Surfing Space (BOSS) relating to biology and Photochemistry on the Space Station (PSS) dealing with astrochemistry. Coussot, G., Le Postollec, A., Faye, C., Baqué, M., Vandenabeele-Trambouze, O., Incerti, S., Vigier, F., Chaput, D., Cottin, H., Przybyla, B., Berger, T., Dobrijevic, M., 2019. Photochemistry on the space station—antibody resistance to space conditions after exposure outside the International Space Station. Astrobiology 19, 1053-1062. analytical instruments are under development to detect signatures of life on planetary bodies. Antibodies are molecular recognition reagents able to detect their target at sub-nanomolar concentrations, with high affinity and specificity. Studying antibody binding performances under space conditions is mandatory to convince space agencies of the adequacy of this promising tool for planetary exploration.To complement previous ground-based experiments on antibody resistance to simulated irradiation, we evaluate in this paper the effects of antibody exposure to real space conditions during the EXPOSE-R2 mission outside the International Space Station. The absorbed dose of ionizing radiation recorded during the 588 days of this mission (220?mGy) corresponded to the absorbed dose expected during a mission to Mars. Moreover, samples faced, at the same time as irradiation, thermal cycles, launch constraints, and long-term storage. A model biochip was used in this study with antibodies in freeze-dried form and under two formats: free or covalently grafted to a solid surface.We found that antibody-binding performances were not significantly affected by cosmic radiation, and more than 40% of the exposed antibody, independent of its format, was still functional during all this experiment. We conclude that antibody-based instruments are well suited for in situ analysis on planetary bodies.Coussot, G., Le Postollec, A., Incerti, S., Baqué, M., Faye, C., Vandenabeele-Trambouze, O., Cottin, H., Ravelet, C., Peyrin, E., Fiore, E., Vigier, F., Caron, J., Chaput, D., Przybyla, B., Berger, T., Dobrijevic, M., 2019. Photochemistry on the space station—aptamer resistance to space conditions: Particles exposure from irradiation facilities and real exposure outside the International Space Station. Astrobiology 19, 1063-1074. microarray-based instruments that use bioaffinity receptors such as antibodies or aptamers are under development to detect signatures of past or present life on planetary bodies. Studying the resistance of such instruments against space constraints and cosmic rays in particular is a prerequisite. We used several ground-based facilities to study the resistance of aptamers to various types of particles (protons, electrons, neutrons, and carbon ions) at different energies and fluences. We also tested the resistance of aptamers during the EXPOSE-R2 mission outside the International Space Station (ISS). The accumulated dose measured after the 588 days of this mission (220 mGy) corresponds to the accumulated dose that can be expected during a mission to Mars. We found that the recognition ability of fluorescently labeled aptamers was not significantly affected during short-term exposure experiments taking into account only one type of radiation at a time. However, we demonstrated that the same fluorescent dye was significantly affected by temperature variations (?21°C to +58°C) and storage throughout the entirety of the ISS experiment (60% of signal loss). This induced a large variability of aptamer signal in our analysis. However, we found that >50% of aptamers were still functional after the whole EXPOSE-R2 mission. We conclude that aptamer-based instruments are well suited for in situ analysis on planetary bodies, but the detection step requires additional investigations.Crowther, T.W., van den Hoogen, J., Wan, J., Mayes, M.A., Keiser, A.D., Mo, L., Averill, C., Maynard, D.S., 2019. The global soil community and its influence on biogeochemistry. Science 365, eaav0550.: Soil organisms represent the most biologically diverse community on land and govern the turnover of the largest organic matter pool in the terrestrial biosphere. The highly complex nature of these communities at local scales has traditionally obscured efforts to identify unifying patterns in global soil biodiversity and biogeochemistry. As a result, environmental covariates have generally been used as a proxy to represent the variation in soil community activity in global biogeochemical models. Yet over the past decade, broad-scale studies have begun to see past this local heterogeneity to identify unifying patterns in the biomass, diversity, and composition of certain soil groups across the globe. These unifying patterns provide new insights into the fundamental distribution and dynamics of organic matter on land.Editor's summary: Microbes' role in soil decomposition. Soils harbor a rich diversity of invertebrate and microbial life, which drives biogeochemical processes from local to global scales. Relating the biodiversity patterns of soil ecological communities to soil biogeochemistry remains an important challenge for ecologists and earth system modelers. Crowther et al. review the state of science relating soil organisms to biogeochemical processes, focusing particularly on the importance of microbial community variation on decomposition and turnover of soil organic matter. Although there is variation in soil communities across the globe, ecologists are beginning to identify general patterns that may contribute to predicting biogeochemical dynamics under future climate change.Structured AbstractBackground: Soil is the largest repository of organic matter on land, storing ~1500 Gt carbon, which is at least as much as the vegetation (~560 Gt) and atmosphere (~750 Gt) combined. The turnover of this organic material (the rate at which it enters and leaves the soil) is governed by the most diverse community on Earth. By determining the rate and biochemical pathway of organic matter processing, fungi, bacteria, archaea, animals, and protists regulate soil fertility, plant growth, and the climate. Given their roles in regulating the exchanges of elements between terrestrial and atmospheric pools, the effective management of this soil community is among our most powerful weapons in the fight against the global threats of biodiversity loss and climate change. However, despite the critical importance of these organisms, the hyperdiverse nature of local soil communities has traditionally obscured efforts to identify general global patterns. As such, environmental factors have traditionally been used as proxies to represent the variation in soil functioning across landscapes. But it is the organisms—not only the environment—that directly drive the turnover of organic material. Given that different organisms have varying impacts on elemental cycling, exploring the functional biogeography of soil communities is likely to be critical for improving confidence in global biogeochemical model predictions.Advances: Over the past decade, a growing body of evidence highlights that regional differences in the soil community drive considerable variation in biogeochemistry. Just as the transition from forests to grasslands drive vast differences in ecosystem functioning, differences in the structure of soil communities can drive enormous variation in elemental cycling. By expanding our horizons to see beyond the complexity of local soil communities, ecologists have begun to identify general patterns in the biomass, composition, and diversity of soil communities. Despite the immense diversity of these organisms, the global soil community appears to be dominated by a manageable number of groups, which are likely to play a prominent role in the regulation of soil biogeochemistry. The metabolic activity and species richness of most soil organisms generally increase toward warm, moist tropical regions, where rapid elemental cycling depletes soil carbon relative to the higher latitudes. In addition, the huge accumulation of organic matter stocks in cold Arctic and sub-Arctic regions leads to huge abundances of soil microbes and animals at high latitudes. These global trends reveal key insights into the biological mechanisms that drive the distribution of organic matter on land as well as the vulnerability of different carbon stocks to future global change. Each new layer of global ecological information reveals distinct biogeographic patterns that provide insights into the fundamental distribution and dynamics of organic matter on land.Outlook: The field of soil ecology continues to uncover critical mechanisms that govern the turnover of organic matter at local scales. But placing these mechanisms into context necessitates that we continue to expand our understanding of the global biogeography of soil organisms. These communities can be viewed at multiple levels of ecological resolution, starting from the biomass of overall communities, which can then be divided into different functional groups, taxa, and functional traits. As we move down this list, we gain mechanistic detail at the expense of predictive understanding. While we continue to refine our detailed understanding of microbial taxa and trait compositions, we also need to step back to characterize the biomass distributions of the major functional groups of soil organisms, which reflect considerable differences in biogeochemical processing rates. As we generate this global ecological data, sensitivity analyses will then be necessary to identify the mechanisms that are most critical for improving biogeochemical model performance. These insights have the potential to improve predictions of soil fertility, plant production, and the climate. Ultimately, this emerging perspective of the most diverse and abundant community on land will provide fundamental insights into the organization of life on Earth.Cui, G., Yang, Z., Liu, J., Li, Z., 2019. A comprehensive review of metal corrosion in a supercritical CO2 environment. International Journal of Greenhouse Gas Control 90, 102814. capture and storage (CCS) is the most effective way to reduce CO2 emissions. In CCS, CO2 transportation plays an important role for the transmission of CO2 from the capturing facility to the location of permanent storage. In order to increase the CO2 density and avoid two-phase flow, CO2 needs to be transformed into the supercritical state. The supercritical CO2 environment poses a threat to pipeline safety because it is a high pressure environment with gaseous impurities. In this paper, the influencing factors of pipeline corrosion under supercritical CO2 environment and the current prevention and control methods for SC CO2 corrosion are reviewed. To begin, the supercritical CO2 corrosion environment and corrosion evaluation methods are introduced. Then, the effects of some factors, such as the water content, gaseous impurities, acids, alkalis, salts, temperature, pressure, flow rate, exposure angle, and pipeline steel, on corrosion are comprehensively reviewed. New research areas, such as the use of coatings and inhibitors, are also reviewed. Finally, future development directions for studying corrosion in a supercritical CO2 environment are proposed.Cui, Y.J., Li, Y., Si, X.Y., Yang, L.X., Liu, Z.F., Sun, F.X., Li, X.Y., Zheng, H.W., Du, J.G., 2019. Tectonic controls on near-surface variations in CH4 and CO2 concentrations along the northwestern margin of the Ordos Block, China. Geofluids 2019, 7909483. controls on near-surface CH4 and CO2 concentrations were investigated by measuring CH4 and CO2 concentrations at the surface and a height of 1.5?m, in the different tectonic units that comprise the northwestern margin of Ordos Block, China, which has a complex tectonic structure and a history of strong earthquakes. CH4 and CO2 concentrations varied from 1905 to 2472?ppb and 397.5 to 458.5?ppm, respectively. Surface CH4 and CO2 concentrations were generally higher than those measured at 1.5?m, but showed similar trends, indicating that the measured CH4 and CO2 predominantly originated from underground gases. The CH4 and CO2 concentrations increased with an increasing strike-slip rate across the faults, and concentrations in the blocks with high internal deformation were much higher than those measured in the stable blocks. Regions of extensional deformation had higher gas concentrations than regions that had experienced compressional deformation. The spatial distribution of CH4 and CO2 at the study site had similar trends to faults associated with the Yinchuan Graben. The results of this study indicated that gas source, gas migration pathway, and tectonic stress were the main factors that influenced gas emission. The key factor is tectonic stress, which controlled the formation of tectonic structures, changed the pathway of degassing, and acted as the driving force for gas migration. The results of this study clarify the mechanism of CH4 and CO2 degassing in faulted regions and suggest that CH4 and CO2 concentrations may be useful precursors in the monitoring of seismic activity. The results may also help inform future assessments of the contribution of geological sources to greenhouse gas emissions.D'Andres, J., Kendrick, M.A., Bennett, V.C., Nutman, A.P., 2019. Halogens in serpentinites from the Isua supracrustal belt, Greenland: An Eoarchean seawater signature and biomass proxy? Geochimica et Cosmochimica Acta 262, 31-59. in modern seafloor and ophiolitic environments incorporates and often retains high concentrations of atmospheric noble gases and seawater-derived halogens. Ancient serpentinites therefore provide the potential to trace the composition of early surface environments. Antigorite-serpentinites locally carbonated to talc-magnesite schist outcropping in a low strain zone within the Eoarchean Isua supracrustal belt (Greenland) are investigated here, to test the retention of paleo-atmospheric noble gases and Eoarchean seawater halogens, and to further determine the genetic setting and metamorphic history of some of Earth’s oldest serpentinites.Based on field relationships, whole rock major and trace element geochemistry, and mineral chemistry, the investigated serpentinites are shown to represent hydrated and variously carbonated magmatic olivine?±?orthopyroxene?+?Cr-spinel cumulates emplaced at the base of a lava flow of boninitic affinity pillowed in its upper portion. In addition, rare zircons extracted from one of the serpentinised cumulates have distinct magmatic trace element signatures and a U-Pb age of 3721?±?27?Ma indicating the pillowed lava flow erupted on the Eoarchean seafloor.The serpentinites have high concentrations of noble gases, but the presence of parentless radiogenic ‘excess’ 40Ar, introduced by crustal-derived metamorphic fluids, obscures the 40Ar/36Ar ratio of Eoarchean seawater. Local carbonation of the serpentinites also caused halogen loss and fractionation. However, the least carbonated antigorite serpentinites preserve Br/Cl and I/Cl ratios within the range of modern seafloor serpentinites, which is interpreted as indicating Archaean serpentinising fluids were similar in composition to modern seawater-derived fluids. Importantly, the lowest measured I/Cl ratio of 29 (±2)?×?10?6, taken as a maximum value for the Eoarchean ocean, is an order of magnitude lower than estimates for the primitive mantle I/Cl value. Iodine has a low concentration relative to Cl in modern seawater because it is sequestered by organic matter. If the inferred low I/Cl of Eoarchean seawater is correct, then similar I-sequestration was likely occurring in the Eoarchean, a process requiring the presence of significant biomass in Earth’s early oceans. Further constraining the Precambrian evolution of seawater I/Cl via serpentinites or other proxies may provide a novel method to explore the emergence and evolution of terrestrial biomass.D’Hondt, S., Pockalny, R., Fulfer, V.M., Spivack, A.J., 2019. Subseafloor life and its biogeochemical impacts. Nature Communications 10, 3519. microbial activities are central to Earth’s biogeochemical cycles. They control Earth’s surface oxidation and major aspects of ocean chemistry. They affect climate on long timescales and play major roles in forming and destroying economic resources. In this review, we evaluate present understanding of subseafloor microbes and their activities, identify research gaps, and recommend approaches to filling those gaps. Our synthesis suggests that chemical diffusion rates and reaction affinities play a primary role in controlling rates of subseafloor activities. Fundamental aspects of subseafloor communities, including features that enable their persistence at low catabolic rates for millions of years, remain unknown.Dahl, T.W., Siggaard-Andersen, M.-L., Schovsbo, N.H., Persson, D.O., Husted, S., Houg?rd, I.W., Dickson, A.J., Kj?r, K., Nielsen, A.T., 2019. Brief oxygenation events in locally anoxic oceans during the Cambrian solves the animal breathing paradox. Scientific Reports 9, 11669. is a prerequisite for all large and motile animals. It is a puzzling paradox that fossils of benthic animals are often found in black shales with geochemical evidence for deposition in marine environments with anoxic and sulfidic bottom waters. It is debated whether the geochemical proxies are unreliable, affected by diagenesis, or whether the fossils are transported from afar or perhaps were not benthic. Here, we improved the stratigraphic resolution of marine anoxia records 100–1000 fold using core-scanning X-Ray Fluorescence and established a centennial resolution record of oxygen availability at the seafloor in an epicontinental sea that existed ~501–494 million years ago. The study reveals that anoxic bottom-water conditions, often with toxic hydrogen sulfide present, were interrupted by brief oxygenation events of 600–3000 years duration, corresponding to 1–5?mm stratigraphic thickness. Fossil shells occur in some of these oxygenated intervals suggesting that animals invaded when conditions permitted an aerobic life style at the seafloor. Although the fauna evidently comprised opportunistic species adapted to low oxygen environments, these findings reconcile a long-standing debate between paleontologists and geochemists, and shows the potential of ultra-high resolution analyses for reconstructing redox conditions in past oceans.De Corte, D., Martínez, J.M., Cretoiu, M.S., Takaki, Y., Nunoura, T., Sintes, E., Herndl, G.J., Yokokawa, T., 2019. Viral communities in the global deep ocean conveyor belt assessed by targeted viromics. Frontiers in Microbiology 10, 1801. doi: 10.3389/fmicb.2019.01801. are an abundant, diverse and dynamic component of marine and terrestrial ecosystems. In the ocean, viruses play a key role in the biogeochemical cycles and controlling microbial abundance, diversity and evolution. Recent metagenomics studies assessed the structure of the viral community in the upper ocean. However, little is known about the compositional changes in viral communities along the deep ocean conveyor belt. To assess potential changes in the viral community in the global deep-water circulation system, water samples were collected in the core of the North Atlantic Deep Water (~2,500 m) and Pacific Antarctic Bottom Water (~4,000 m). Microbial and viral abundance were evaluated by flow cytometry. Subsequently, flow cytometry was used to sort virus-like particles and next generation sequencing was applied to build DNA libraries from the sorted virus populations. The viral communities were highly diverse across different oceanic regions with high dissimilarity between samples. Only 18% of the viral protein clusters were shared between the North Atlantic Deep Water and the Pacific Antarctic Bottom Water. Few viral groups, mainly associated with uncultured environmental and uncultured Mediterranean viruses were ubiquitously distributed along the global deep-water circulation system. Thus, our results point to a few groups of widely distributed abundant viruses in addition to the presence of rare and diverse types of viruses at a local scale.Demongeot, J., Seligmann, H., 2019. More pieces of ancient than recent theoretical minimal proto-tRNA-like RNA rings in genes coding for tRNA synthetases. Journal of Molecular Evolution 87, 152-174. minimal RNA rings were designed to mimick life’s primordial RNAs by forming stem-loop hairpins and coding once for each of the 20 amino acids, a start and a stop codon. At most 25 22-nucleotide long RNA rings follow these criteria. These align well with a consensus tRNA sequence, predicting for each RNA ring an anticodon and an associated cognate amino acid. Hypotheses on cognate amino acid order of inclusion in the genetic code produce evolutionary ranks for theoretical RNA rings. This evolutionary hypothesis predicts that pieces of RNA rings with more ancient cognate amino acid should be more frequent in modern genes than those from RNA rings with late cognate amino acids. Analyses of genes for tRNA synthetases, among the most ancient proteins, from archaeal, bacterial, eukaryote and viral superkingdoms overall confirm these predictions, least for tRNA synthetases with early cognate amino acids and for the neogene-enriched genome of the giant virus Tupanvirus. Hence early tRNA synthetase genes and late RNA rings evolved separately. Results indicate that RNA rings and tRNA synthetases with the same cognate amino acid are less separated for relatively recent cognate amino acids, suggesting that over evolutionary time the components of the molecular apparatus became more integrated, perhaps in cell-like membrane-bound systems. Results confirm that theoretical considerations in the design of minimal RNA rings recreated RNAs close to the actual primordial RNA population that produce genes by accretion, and confirm the hypothesis of homology of minimal RNA rings with tRNAs and their proto-tRNA status.Derrien, M., Brogi, S.R., Gon?alves-Araujo, R., 2019. Characterization of aquatic organic matter: Assessment, perspectives and research priorities. Water Research 163, 114908. matter (OM) refers to the largest reactive reservoir of carbon-based compounds on Earth. Aside of its role as a source of carbon, OM is also actively involved in a wide range of ecological functions. It also plays an important role in the solubility, toxicity, bioavailability, mobility and distribution of pollutants. Therefore, OM is a key component in the local and global carbon cycle. About 12,000 articles containing organic matter in the title were published during the past decade, with a continuous increasing number each year (ISI Web of Science). Although this topic was widely explored and its interest has significantly increased, some limitations remain. These limitations can be technical (e.g., pre-treatment processes, low-resolution instrument, data handling) and can be related to the current approach. In this review, we first present the current strategies and tools to characterize the organic matter in the aquatic environment, then we tackle several aspects of current characterization limitations. Finally, we suggest new perspectives and priorities of research to improve the current limitations. From our point of view, simultaneous studies of particulate and dissolved OM fractions should be prioritized and multi-disciplinary approach, creation of databases, controlled experiments and collaborative works should be the next targets for future OM research priorities.Derrien, M., Shin, K.-H., Hur, J., 2019. Biodegradation-induced signatures in sediment pore water dissolved organic matter: Implications from artificial sediments composed of two contrasting sources. Science of The Total Environment 694, 133714. is one of the main processes causing the changes in amount, composition and properties of organic matter in sediment and water-sediment interface. The degradation processes of sediment organic matter lead to a release of dissolved organic matter (DOM) into the pore water via hydrolysis and depolymerization of particulate organic matter (POM). Whereas the pore waters represent a reactive zone in sediment closely linked to biogeochemistry of the substrate, they are still poorly characterized under diagenetic processes. In this study, we examined the DOM alterations in sediment pore water originating from the mixtures of two contrasting POM sources at known ratios through controlled incubation experiments with two different oxygen conditions (i.e., oxic versus anoxic). The changes in pore water DOM were tracked using fluorescence and absorbance spectroscopy and size exclusion chromatography. The results based on the sediments artificially mixed of two end-member sources (e.g., soil and algae) showed that the most affected parameter during the biodegradation process was the amount of the pore water DOM. It was also demonstrated that the changes in the spectroscopic and molecular properties were more dependent on the POM sources and the mixing ratios rather than on the oxygen conditions. This study provides insights into the responding features of DOM in a reactive sediment zone as pore water to the main biogeochemical process.Dillinger, S., Niedner-Schatteburg, G., 2019. Chapter 19 - Cryo trapping by FT-MS for kinetics and spectroscopy, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 593-621. we describe the reasoning for cryo FT-MS technologies in terms of pressure broadening and activation by black body radiation, and the development and achievements of such technologies in chemistry and nuclear physics, shortly referring to other cryo ion technologies. We present an illustrative example on isotope effects in black body induced radiative dissociation (BIRD), and some recent experiments on the elucidation of transition metal (TM) cluster surface morphologies and of TM complexes by cryo FT-MS. Such studies record infrared spectra by multiple photon dissociation (IR-MPD), and adsorption kinetics by reaction delay scans. Some most recent studies invoke a combination of cryo FT-MS with another cryo ion trap thus enabling tandem cryo trapping experiments. One of these studies revealed the interaction of molecular co-adsorbates on TM clusters. We conclude by and outlook onto future directions of cryo FT-MS.Dim, C.I.P., Mode, A.W., Okwara, I.C., 2019. Signatures of key petroleum system elements: outcrop examples from the Anambra Basin, Southeastern Nigeria. Journal of Petroleum Exploration and Production Technology 9, 1615-1631. several works have proved the existence of oil and gas in the Campanian to Maastrichtian strata of the Anambra Basin, it is still considered a frontier basin due to the challenges associated with interpretation of stratigraphy and structure arising from non-availability of subsurface data. This has led to poor understanding of the petroleum system and hindered exploration activity within the basin. This research paper aims to discuss the signatures of essential petroleum system elements, based on the study of high-quality outcrop examples. Detailed field studies reveal the presence of source, reservoir and seal rocks, and traps exposed within the four lithostratigraphic units outcropping in the basin, across the southeastern part of Nigeria. The shales of Enugu Formation, offer good source rocks. The shales, coals, coaly shales and sandstones with repeated occurrence of shale–silt–sand heteroliths of the Mamu Formation provide possible source and reservoir rocks. Thick extensive sandstones with clay laminae of the Ajali Formation offer potential reservoir that are partly compartmentalized. The shales with interstratified sandstone of the Nsukka Formation provide potential cap and overburden rocks. The presence of anastomosing fracture bands, extensional joints and faults, small-scale growth faults, and rollover anticlinal structures are good evidence of structural and stratigraphic configuration that could allow for possible migration, accumulation and entrapment of hydrocarbon. These recognized signatures of the key elements of a petroleum system and oil seeps encountered in the basin are an indication of the presence of an active petroleum system.Ding, H., Wang, Y., Shapoval, A., Zhao, Y., Rahman, S., 2019. Macro- and microscopic studies of “smart water” flooding in carbonate rocks: An image-based wettability examination. Energy & Fuels 33, 6961-6970. date, numerous studies have shown that “smart water” flooding can enhance the oil recovery of carbonate reservoirs by altering the rock wettability. In particular, the Ca2+, Mg2+, and SO42– ions in smart water play important roles in altering the wettability of carbonate rocks, although their symbiotic effects are still under debate. In this study, we employ both macro- and microscopic methods, including ζ-potential measurements, contact angle measurements, and micro X-ray computed tomography (μ-CT) scanning to examine the effects of several “smart waters”, e.g., increasing SO42– concentrations or decreasing Ca2+ and Mg2+ concentrations in seawater, in changing the wettability of Austin chalk. ζ-potential results confirm that the surface potentials of chalk samples become more negative in smart waters than in seawater. Contact angle results suggest that smart waters are more effective in making the chalk surface more water-wet than seawater. However, seawater with four times the SO42– concentration (SW4SO) and seawater with one-fourth of the Ca2+ concentration (SW0.25Ca) show more potential in enhancing the alteration of chalk wettability compared to other smart waters. The μ-CT images offer a microscopic view of the fluid distribution in the porous media of chalk samples after flooding with seawater and followed by SW4SO or SW0.25Ca, which shows that SW4SO contributes to the increase in water-wetness in nanopores (or subscale porous structure), whereas SW0.25 contributes to the increase in water-wetness in micropores. In addition, the “effective contact angles” of chalk samples decreases approximately 10° after SW4SO and SW0.25Ca flooding, resulting in an increase in the “microscopic oil recovery” by 18.6 and 20.2%, respectively. Thus, this result suggests that SW0.25Ca is more effective in enhancing the water-wetness of chalk samples than SW4SO.Ding, M., Wang, Y., Wang, W., Zhao, H., Liu, D., Gao, M., 2019. Potential to enhance CO2 flooding in low permeability reservoirs by alcohol and surfactant as co-solvents. Journal of Petroleum Science and Engineering 182, 106305. gas-soluble chemical modifiers were dissolved in pure CO2 to improve the ability to extract, and displace, crude oil from low-permeability reservoirs. It was found that the ability of the modifiers to enhance crude oil extraction using CO2 increased in the order: water, ethanol, TX100, TX100/ethanol, TX45, and TX45/ethanol. As to oil displacements, the best performing system was CO2/TX45/ethanol which generated a significantly greater oil-recovery factor (by 13.8%) than pure CO2, making it a good candidate to replace pure CO2, however, when displacing bypassed oil, the enhancement in oil recovery gained by using CO2/TX45/ethanol was reduced to 6.0% (during the primary soaking stage) and it also failed to remove the majority of the bypassed oil (with a low oil-recovery factor of 23.3%). The secondary huff-n-puff using CO2/TX45/ethanol was more effective than the previous soaking process (increasing the oil-recovery factor to 88.1%), while also generally outperforming the recovery achieved using pure CO2 (depending on pressure depletion).Dogan, S., Gulluce, M., Alaylar, B., Karadayi, M., 2019. Isolation and molecular identification of bacteria with magnesite enrichment potential from Turanocak and Ortaocak quarries in Kütahya-Turkey. Geomicrobiology Journal 36, 826-830. this study, bacteria were isolated from two different magnesite quarries in Turanocak and Ortaocak mine in Kütahya-Eski?ehir region, one of the largest processed magnesite reserves in Turkey. The obtained isolates have a potential to solve important magnesite pollutant CaCO3 but incapable to solve magnesium that has the most crucial role in the industry. Thus, potential bacteria were identified to be used for magnesite enrichment studies. The obtained isolates were identified and characterized according to the morphological, physiological, biochemical, and molecular techniques (16S rDNA PCR). According to the gene sequencing analysis Bacillus genus bacteria have the ability to solve CaCO3. The data of the 16S rDNA gene sequence showed that there were 13 active strains grouped in Bacillus. These active strains; Bacillus sp (3), Bacillus atrophaeus (2), Bacillus thuringiensis (1), Bacillus circulans (1), Bacillus simplex (3), Bacillus endophyticus (1) Bacillus drentensis (1) and Bacillus idriensis (1).Donadelli, J.A., Cánneva, A., Erra, G., Calvo, A., 2019. XPS direct analysis on shale rocks: Correlation with kerogen type and maturity. Fuel 257, 116004. method to study kerogen type and maturity of organic matter in source rocks using XPS was developed. Samples from three Argentinian shale rocks containing different kerogen types were analyzed by XPS directly, without kerogen isolation. Analysis focused on characterizing the chemical structure of kerogen, in particular of carbon species. Two new parameters were proposed: (%Cox/OCxps) that measures the oxidized organic carbon content, and ArP related to aromaticity ratio. A relationship was found between (%Cox/OCxps) and kerogen origin, allowing changes in kerogen type (from Type II to Type III) to be recognized. The aromaticity was estimated from Csp2 XPS peak and was compared to traditional maturity parameters such as vitrinite reflectance or pyrolysis Rock-Eval Tmax. A correlation between the methods was observed, suggesting the direct XPS analysis of shale rock as an estimation of kerogen maturity. Both maturity and kerogen type can be determined in the same measurement, performed directly on the sample, without organic matter isolation.Dong, C., Ma, T., Liu, R., Lai, Q., Shao, Z., 2019. Hydrocarboniclastica marina gen. nov., sp. nov., a marine hydrocarbonoclastic bacterium isolated from an in situ enriched hydrocarbon-degrading consortium in sea sediment. International Journal of Systematic and Evolutionary Microbiology 69, 2250-2257. Gram-stain-negative, motile, non-spore-forming, aerobic and rod-shaped bacterial strain, Soil36-7T, was isolated from an in situ enriched hydrocarbon-degrading consortium in South China Sea sediment. Strain Soil36-7T grew at 4–40?°C (optimum 28–32?°C), at pH 5–10 (pH 7–8) and in the presence of 1–12?%?(w/v) NaCl (3–6?%). Phylogenetic analyses based on 16S rRNA gene sequences and a genome-based approach using UBCGs (up-to-date bacterial core genes) showed Soil36-7T formed a distinct branching lineage within the family Alteromonadaceae . 16S rRNA gene sequence similarity was 92.9, 92.1 and >88.3?% between strain Soil36-7T and the type species of the genera Marinobacter, Tamilnaduibacter and the other genera of the family Alteromonadacea , respectively. The major fatty acids in Soil36-7T were C16?:?0, C16?:?1ω6/7c, C16?:?0 10-methyl, C18?:?1ω7c, C12?:?0 and C18?:?0. The predominant respiratory quinone was Q-9, with a minor amount of Q-10 (3.5?%). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and various unidentified glycolipids, phospholipids, aminophospholipids and other polar lipids. The DNA G+C content was 57.9?mol%. On the basis of phylogenetic, genomic, phenotypic and chemotaxanomic characteristics, strain Soil36-7T could be classified as representing a novel species of a new genus within the family Alteromonadacea , for which the name Hydrocarboniclastica marina gen. nov., sp. nov. is proposed. The type strain of the type species is Soil36-7T (=MCCC 1A12105T=KCTC 62334T). The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene, chromosomal genome and plasmid sequences of strain Soil36-7T are MH572220, CP031093 and CP031094, respectively.D?rner, M., Berner, U., Erdmann, M., Barth, T., 2019. Carbon isotopic analysis of reactive organic matter using a new pyrolysis-cryotrapping-isotope ratio mass spectrometry method: The isotope variation of organic matter within the S1 and S2 peaks of Rock-Eval. Organic Geochemistry 136, 103886. source material, the mode of photosynthesis, the organic matter (OM) type, the paleoenvironmental conditions and thermal degradation all determine the isotopic composition of OM. This study presents a novel analytical technique and demonstrates its potential to enhance the understanding of the preservation and maturation-related isotopic compositional changes in OM from different paleoenvironments. A new Rock-Eval type pyrolysis coupled to isotope ratio mass spectrometry (py-IRMS) method has been developed to monitor the isotopic changes during Rock-Eval type pyrolysis while simultaneously recording pyrograms to obtain S1 and S2 peaks compatible with standard Rock-Eval pyrolysis. An automated cryotrapping method allows the sequential sampling of product from defined pyrolysis portions. Each subsample is subsequently transferred to the isotopic ratio mass spectrometer for carbon isotopic measurements. In addition, the cryotrap serves to focus sample peaks, enabling robust and reproducible results even at standard Rock-Eval heating rates. In combination with a standard elemental analyser coupled to an isotopic ratio mass spectrometer (EA–IRMS) it was possible to deconvolute the carbon isotope composition of the reactive components, bitumen and inert components of OM. This allowed us to observe depositional control as well as changes imposed by maturation. Our initial results show the potential of the proposed isotopic screening method to deduce a variety of organic geochemical properties of different OM types based on differences in their carbon isotope compositions. Our results suggest that the ability to produce significant isotopic fractionation during the proposed pyrolysis method is highly dependent on the preservation state of the OM and the thermal maturity.Dorofeev, A.G., Nikolaev, Y.A., Mardanov, A.V., Pimenov, N.V., 2019. Cyclic metabolism as a mode of microbial existence. Microbiology 88, 402-415. review deals with specific bacterial physiological groups developing under periodically varying ambient conditions and possessing a cyclic type of metabolism (CTM). CTM is characterized by unbalanced two-phase growth occurring during the period less than the generation time. During the first phase, the carbon and/or energy source are accumulated, while during the second phase biomass biosynthesis occurs using the accumulated substrate. Known CTM organisms of the groups of phosphate-accumulating and glycogen-accumulating bacteria are described, and their major biochemical models are discussed. Development of microorganisms with obligate CTM is probably impossible or significantly suppressed under stable ambient conditions, which may be the reason why the major CTM organisms can not be cultured using traditional batch and continuous cultivation, while highly enriched cultures may be obtained by cyclic cultivation. Ecological aspects of CTM are discussed, and the possible environments for CTM microorganisms in natural ecosystems are determined.Dou, M., Tsai, C.-F., Piehowski, P.D., Wang, Y., Fillmore, T.L., Zhao, R., Moore, R.J., Zhang, P., Qian, W.-J., Smith, R.D., Liu, T., Kelly, R.T., Shi, T., Zhu, Y., 2019. Automated nanoflow two-dimensional reversed-phase liquid chromatography system enables in-depth proteome and phosphoproteome profiling of nanoscale samples. Analytical Chemistry 91, 9707-9715. reversed-phase capillary liquid chromatography (2D RPLC) separations have enabled comprehensive proteome profiling of biological systems. However, milligram sample quantities of proteins are typically required due to significant losses during offline fractionation. Such a large sample requirement generally precludes the application samples in the nanogram to low-microgram range. To achieve in-depth proteomic analysis of such small-sized samples, we have developed the nanoFAC (nanoflow Fractionation and Automated Concatenation) 2D RPLC platform, in which the first dimension high-pH fractionation was performed on a 75-μm i.d. capillary column at a 300 nL/min flow rate with automated fraction concatenation, instead of on a typically used 2.1 mm column at a 200 μL/min flow rate with manual concatenation. Each fraction was then fully transferred to the second-dimension low-pH nanoLC separation using an autosampler equipped with a custom-machined syringe. We have found that using a polypropylene 96-well plate as collection device as well as the addition of n-Dodecyl β-d-maltoside (0.01%) in the collection buffer can significantly improve sample recovery. We have demonstrated the nanoFAC 2D RPLC platform can achieve confident identifications of ～49,000–94,000 unique peptides, corresponding to ～6,700–8,300 protein groups using only 100–1000 ng of HeLa tryptic digest (equivalent to ～500–5,000 cells). Furthermore, by integrating with phosphopeptide enrichment, the nanoFAC 2D RPLC platform can identify ～20,000 phosphopeptides from 100 μg of MCF-7 cell lysate.Drotleff, B., L?mmerhofer, M., 2019. Guidelines for selection of internal standard-based normalization strategies in untargeted lipidomic profiling by LC-HR-MS/MS. Analytical Chemistry 91, 9836-9843. to variation in instrument response caused by various sources of errors throughout an analytical assay, data normalization plays an indispensable role in untargeted LC-MS profiling, yet limited accepted guidelines on this topic exist. In this work, a systematic comparison of several normalization techniques, mainly focusing on internal standard-based approaches, has been performed to derive some general recommendations. For generation of untargeted lipidomic data, a comprehensive ultra-high performance liquid chromatography (UHPLC)-electrospray ionization (ESI)-quadrupole time of flight (QTOF)-MS/MS method was utilized. To monitor instrument stability and evaluate normalization performance, quality control (QC) samples, prepared from aliquots of all experimental samples, were embedded in the sequence. Stable isotope labeled standards, representing differing lipid classes, were spiked to each sample as internal standards for postacquisition normalization. Various metrics were used to compare distinct normalization strategies, with reduction of variation in QC samples being the critical requirement for acceptance of successful normalization. The comparison of intragroup coefficients of variation (CVs), median absolute deviations (MADs), and variance enables simple selection of the best performance of normalization with improved and coherent results. Furthermore, the importance for normalization in critical data sets, showing only minor effects between groups with high variation and outliers, is pointed out. Apart from normalization, also, influences of used raw data types are demonstrated. In addition, effects of various factors throughout the processing workflow were investigated and optimized. Eventually, implementation of quality control samples, even if not required for normalization, provided a useful basis for assessing data quality. Due to lack of consensus for selecting optimum normalization, suggestions for validating data integrity are given.Du, X., Ding, W., Jiao, B., Zhou, Z., Xue, M., Liu, T., 2019. Characteristics of hydrocarbon migration and accumulation in the Linhe-Jilantai area, Hetao Basin, China. Petroleum Science and Technology 37, 2182-2189. on the seismic data analysis, source rock geochemistry and reservoir physical properties, the source reservoir allocation and reservoir forming conditions in the Linhe-Jilantai area in Hetao Basin were studied. The results show that the source rocks of the Lower Cretaceous and the Oligocene in the study area reach the standard of fair-good source rocks, and the lithology of reservoirs is mainly feldspar sandstone and lithic feldspathic sandstone with good physical properties. Combined with vertical and lateral migration pathways, three hydrocarbon accumulation models of near source, far source and inside source are proposed. The research results can provide reference and guidance for the further hydrocarbon exploration in Hetao Basin.Duan, J., Amster, I.J., 2019. Chapter 20 - Application of FTMS to the analysis of glycosaminoglycans, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 623-649. (GAGs) are linear chain glycans consisting of repeating uronic sugar and amino sugar copolymers and play major roles in fundamental biological processes. Despite being ubiquitous in cells, the structure of GAGs remains relatively elusive and is challenging to characterize with mass spectrometry. This chapter discusses how Fourier transform mass spectrometry (FTMS) plays a vital role in developing methods for high throughput structural elucidation of GAGs. High mass accuracy measurements of the mass spectrum allow for composition assignment of the intact glycan; tandem mass spectrometry with various ion activation techniques have been used to determine the location of structural microheterogeneities with high specificity. Software analysis packages for GAGs have also been developed recently, allowing for the option of high-throughput analysis without the need for any user supervision. New and promising developments in FTMS have significantly improved structural characterization possibilities in the field of glycomics.Duong, C., Bower, C., Hume, K., Rock, L., Tessarolo, S., 2019. Quest carbon capture and storage offset project: Findings and learnings from 1st reporting period. International Journal of Greenhouse Gas Control 89, 65-75. is a fully integrated Carbon Capture and Storage (CCS) project that started CO2 injection in August of 2015. The Quest CCS Project is located near Fort Saskatchewan, Alberta, Canada. It includes a capture facility which uses a Shell amine technology, a pipeline of about 65?km length, and three injection well pads. Each injection well pad has an injection well, a deep monitoring well, and shallow groundwater wells. The storage complex is geologically defined by the injection reservoir, a deep saline aquifer called the Basal Cambrian Sand (BCS) (about 45?m thick) and several seals, including the Middle Cambrian Shale (about 50?m thick) and Lotsberg Salts (about 120?m thick). As of August 2018, over three million tonnes of CO2 have been safely injected and permanently stored in the BCS. The Alberta Carbon Competitiveness Incentive Regulation (CCIR) requires the use of standard methods of quantification for reporting greenhouse gas (GHG) emissions for facilities with over 100,000?tonnes of carbon dioxide equivalent (CO2e) per year. An emission offset project is required to comply with CCIR, associated standards and protocols, to demonstrate a reduction in the specified gas emissions and, in the case of Quest, geological sequestration. Quest is the first CCS project to implement an offset project in the context of commercial scale on-shore CO2 geological sequestration within a saline aquifer. Quest uses the Quantification Protocol for CO2 Capture and Permanent Storage in Deep Saline Aquifers, from Alberta Environment and Parks. An offset project must develop an offset project plan (OPP) which demonstrates how the project meets the requirement of the protocol, describes how GHG emissions reductions are achieved, identifies risks associated with the quantification of emission reduction benefits, and describes methodologies used to quantify sources and sinks. Subsequent to completing the OPP, an offset project will put together offset project reports (OPR) to report on the net reductions of GHG emissions for a specific period. The intent of this paper is a) to provide an overview of the OPP and OPR for the Quest CCS project, and b) to discuss learnings from the initial compilation and submission of offset project reports. The key learning at this time is associated to the equipment improvements to the injection gas online analyzer.Dutta, M., Pathiparampil, A., Quon, D., Tan, J., Poirier, L., Berhane, L., Lopez-Linares, F., 2019. Total chloride analysis in petroleum crude samples: Challenges and opportunities, in: Rahimi, P., Ovalles, C., Zhang, Y., Adams, J.J. (Eds.), Chemistry Solutions to Challenges in the Petroleum Industry. American Chemical Society, Washington DC, pp. 281-310. presence of chlorides in crude oil needs to be continuously monitored because it is necessary to control the presence of these salts before introducing crude oil to the refining units. These chlorides, if not removed, can react to form a highly corrosive hydrochloric acid in areas such as crude tower overheads, leading to severe operational issues. Additionally, the presence of high-boiling-point salts is very detrimental; small quantities could provoke severe damage in different units such as heaters and exchangers.Therefore, a portfolio of analytical techniques or industry standard methods is routinely used to quantify chloride in crude. Regardless of the analytical method selected, essential aspects, such as potential bias among technologies, compatibility of sample type with the detection technique, as well the potential impact on the detection technique of having variable heteroatom content, such as sulfur and nitrogen present in the feed, could compromise data reliability. In this chapter, our goal is to address these aspects by evaluating different detection techniques such as combustion ion chromatography, monochromatic wavelength dispersive X-ray fluorescence spectrometry, and inductively coupled plasma mass spectrometry (single quadrupole) on a standard reference material such as National Institute for Standards and Technology 1634c (Trace Elements in Fuel Oil) and on a suite of selected crude oil samples having different characteristics. Additionally, we will discuss how the nature of the sample is the key to obtaining the most accurate and reliable data. Finally, understanding the challenges associated with the homogeneity of the sample on the total chloride quantitation in petroleum crudes using monochromatic wavelength dispersive X-ray fluorescence spectrometry, a technique that is widely used in the oil and gas industry, will be addressed.Easterling, M.L., Agar, J.N., 2019. Chapter 3 - Fundamentals, strengths, and future directions for Fourier transform ion cyclotron resonance mass spectrometry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 63-88. for a range of uses from chemical purification to analytical instrumentation have exploited the constant relationship between a confining magnetic field and its captured charged particle. The path to mass spectrometry from particle physics was clearly evolutionary containing key and bit players along the development pathway. Modern Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers retain notable characteristics of many stepwise advancements dating back to the simple copper cyclotron of Lawrence. Common themes among these milestones were flexibility and performance that seemingly transcended the sum of parts of a simple device that relied on a simple physical relationship. Recent advances to this simplistic concept have enabled dramatic increases in analytical figures-of-merit beyond what could be imagined even a decade ago. The emerging instrumentation has a core competence for separation of complex mixtures to include isotopologue masses of individual isotopic peaks in those very mixtures. With this routine capability comes new ideas for analysis of biomolecules and effectively supplements the advantage of selectivity for complex mixtures with specificity of their composition or heteroatom content.Edilbi, A.N.F., Sherwani, G.H., 2019. Petrography and source rock potential of Chia Gara Formation (Late Jurassic–Early Cretaceous) in Northern Iraq and Kurdistan Region. Journal of Petroleum Exploration and Production Technology 9, 1801-1818. petrographic characteristics and petroleum potential of Chia Gara Formation (Late Jurassic–Early Cretaceous; Tithonian–Berriasian) in Northern Iraq are studied. In order to find out the disparity of Chia Gara Formation in different tectonic zones, two outcrops (Banik and Barsarin sections) and well-Aj-12 were used for this study. In general, the Chia Gara Formation is lithologically composed of black shale, thin-bedded brown argillaceous limestone, thin to medium yellowish limestone. Petrographic study shows that the matrix is mainly composed of micrite, and various diagenetic processes had influenced limestones of Chia Gara Formation, such as neomorphism, dissolution, calcification, cementation and compaction. Fracture, vuggy and moldic are common types of porosity that were observed in this study. However, porosity was later destroyed by some diagenetic processes. The destruction of porosity resulted in considerably low permeability. In addition to petrography, the source rock potential of Chia Gara Formation was also studied. The average values for Total Organic Carbon in percentage (TOC%) of the formation were 1.70, 3.40 and 0.89 for Barsarin, Banik and Aj-12 sections, showing good, very good, and fair organic carbon content, respectively. The pyrolysis executed for studied samples revealed that kerogen type of Chia Gara Formation in Banik section and well Aj-12 belongs to type-II and type-III kerogens, whereas Barsarin section belongs to type-III and type-IV kerogens. The plot of TOC% versus generation potential (S1?+?S2) indicated poor to very good potential of hydrocarbon generation for studied samples. The values of the Tmax (the temperature that results in the maximum release of hydrocarbons (S2) during pyrolysis program) suggested that the organic matter in Banik and Barsarin sections is in mature stage, whereas it is thermally immature (or late immature) in well Aj-12. Vitrinite reflectance (R%) also indicated Oil Window to Early Gas Window in Barsarin, Oil Window in Banik, and Early Oil Window in Aj-12. This study revealed that the studied sections from different tectonic zones show slightly different stages of thermal maturity. The high thermal maturity in Barsarin area can be resulted in different type of kerogen compared to the other sections.El-Shenawy, M.I., Kim, S.-T., 2019. Disordering of 13C–18O bonds in CO2 gas over a heated quartz surface at 50–1100?°C: Insights into the abundance of mass 47 (?47) in CO2 gas at thermodynamic equilibrium. Chemical Geology 524, 213-227. clumped isotope composition or the ?47 value of CO2 relates the abundance of 13C18O16O among all the CO2 isotopologues to the formation temperature of a carbonate mineral or the equilibration temperature of CO2 gas. The ?47 data typically requires several standardization steps and one of which heavily relies on true or equilibrium Δ47 values from different temperatures. However, they have not yet been experimentally quantified and only theoretically predicted Δ47 values are available to the community (e.g., Wang et al. 2004). In this study, a series of CO2 gases were cleaned using a custom-designed automated CO2 cleaning system, baked in a pre-cleaned dry quartz tube and then measured for their ?47 values (the CBM protocol) to examine ?47 change kinetics of CO2 gas over a heated quartz surface between 50 and 1100?°C. In another test, a series of CO2 gases were baked first, cleaned subsequently, and finally measured for their ?47 values (the BCM protocol) to evaluate the effect of the CO2 cleaning on the ?47 value in a routine ?47 measurement. Our experimental results showed that ?47 value of the CO2 gas over a heated quartz surface attained thermodynamic equilibrium in 191, 7, 0.23 and 0.1?h at 50, 100, 491 and 1000?°C, respectively. We also reported the first experimentally determined equilibrium ?47–T relation in CO2 gas between 50 and 1100?°C as follows (?47 in ‰, T in °C; R2?=?0.99, P?<?0.0001):Absolute?47=0.9791±0.0029×e?0.0045TThe comparison between the two CO2 preparation protocols also revealed that the CO2 cleaning step after the baking in the BCM protocol could alter the original ?47 signature of CO2 gas by 0.04 and 0.07‰ at 100 and 1000?°C, respectively, increasing the empirical transfer function (ETF) slope to >1. Therefore, the isotope scrambling effect reported in the literature (e.g., Dennis et al. 2011) might be resulted from CO2 cleaning process because isolating the CO2 cleaning effect (before the baking) yielded an ETF slope of 1, implying that instrumental or analytical artifacts that could affect the measured ?47 were not significant. We suggest using a set of heated CO2 gases prepared by the BCM protocol from several different temperatures as an alternative for the conventional use of heated and water-equilibrated CO2 gases to construct an absolute reference frame and standardize Δ47.Fang, H., Sang, S., Liu, S., Du, Y., 2019. Methodology of three-dimensional visualization and quantitative characterization of nanopores in coal by using FIB-SEM and its application with anthracite in Qinshui basin. Journal of Petroleum Science and Engineering 182, 106285. of the three-dimensional (3D) visualization and reconstruction methods of nanopores, and its morphology and connectivity are the key to explore the storage and migration mechanism of coalbed methane (CBM). The Bofang (BF) sample collected from the Qinshui basin was scanned by the focused ion beam scanning electron microscopy (FIB-SEM), which can simultaneously image the nanopores through 2D slice image and 3D reconstruction image. Firstly, the 2D morphology and development characteristics of nanopores were analyzed. Secondly, the 3D visualization and reconstruction of nanopores were carried out. Then, the pore connectivity, permeability, and geometric characteristics were discussed. Finally, the effect of pore structure on the storage and migration of CBM was emphatically analyzed. The results show that the organic pores, inorganic pores, shrinkage-induced pores and micro-fractures were developed in coal, and their morphology and connectivity were significant differences. The pores and throats can be extracted from the digital cores with sub-volume of 4.9?×?4.9?×?4.5?μm3, the pore number and throat length (avg.) of BF sample are 21951 and 18.2789?nm, respectively, the porosity and permeability of BF sample is 2.004% and 4.405?×?10?3 mD, respectively, which all indicates the BF reservoir has good storage and connectivity capacity. For pores <50?nm, the number, volume and area indicate that the BF sample has good storage capacity. For pores >200?nm, the pores are all interconnected, which indicates the BF sample can provide effective channels for CBM migration. The distribution of pores and throats and their geometric and topological structures indicate that the BF sample has good migration ability. This study on the methodology of 3D visualization and quantitative characterization of nanopores using FIB-SEM can broaden the research method of pores, and lay good foundations for studying the storage and migration of CBM.Fang, Y., Wei, J., Lu, H., Liang, J., Lu, J.a., Fu, J., Cao, J., 2019. Chemical and structural characteristics of gas hydrates from the Haima cold seeps in the Qiongdongnan Basin of the South China Sea. Journal of Asian Earth Sciences 182, 103924. structure, cage occupancy, and gas composition are important gas hydrate characteristics, which can be used to calculate the gas hydrate’s stability and to estimate the energy potential. In May and October of 2015, a Guangzhou Marine Geological Survey team investigated two sites in the Haima cold seeps in the Qiongdongnan Basin, northern South China Sea. They recovered massive gas hydrate samples by conventional gravity coring. After the Shenhu Sea area and Dongsha Sea area, the Qiongdongnan Basin became a new area on the northern slope of the South China Sea where gas hydrates have been found. In order to reveal the structural and geochemical characteristics of the natural gas hydrates, samples were analyzed by micro-Raman spectroscopy and X-ray diffraction under ambient pressure and low-temperature conditions. The results indicate that the gas hydrate samples from the Haima cold seeps are typical structure I hydrates with a hydration number of 6.12–6.19. In addition, trace amounts of H2S trapped in the hydrate were identified based on its characteristic vibrational signature. The gas composition and δ13C-CH4 of the hydrate-bound gas samples were analyzed for gas-source correlation. All of the gas samples are dominated by methane with small amounts of ethane and propane and had relatively light δ13C-CH4, indicating that all of the hydrate-bound gases are mixtures of biogenic and thermogenic gas. The thermogenic gas is inferred to be mainly derived from the coal layers of the Late Miocene-Pliocene Yacheng Formation in the northern Lingshui sag.Fankhauser, A.M., Antonio, D.D., Krell, A., Alston, S.J., Banta, S., McNeill, V.F., 2019. Constraining the impact of bacteria on the aqueous atmospheric chemistry of small organic compounds. ACS Earth and Space Chemistry 3, 1485-1491. this study, we use a modeling approach to evaluate the potential impact of microbial metabolism on the organic composition of cloud droplets and atmospheric aerosols. Microbial consumption rates for small organic molecules typically found in cloud and aerosol water were incorporated into a 0-D multiphase photochemical atmospheric chemistry model. We then use the model to simulate the evolution of the organic content of individual cloud and aerosol particles, along with the atmospheric gas phase. We find that metabolically active microorganisms may significantly impact organic acid concentrations in the individual aerosols and cloud droplets in which they reside. However, as a result of the low density of metabolically active cells in the atmosphere, the impact of these processes on the chemical composition of the overall population of cloud droplets or aerosols, or on gas-phase chemistry, is likely negligible.Fantasia, A., Adatte, T., Spangenberg, J.E., Font, E., Duarte, L.V., F?llmi, K.B., 2019. Global versus local processes during the Pliensbachian–Toarcian transition at the Peniche GSSP, Portugal: A multi-proxy record. Earth-Science Reviews 198, 102932. Toarcian Oceanic Anoxic Event (T-OAE, ~ 183?Ma) was an episode of extreme warmth, environmental changes and carbon cycle perturbation. We present a high-resolution study of the Peniche section (Lusitanian Basin, Portugal), recently defined as the Toarcian Global Stratotype Section and Point, to provide a review of the Pliensbachian–Toarcian (Pl–To) environmental and climatic changes. A large ~7‰-negative carbon-isotope excursion (CIE) is recorded within the T-OAE interval in bulk organic matter. Distinct small-scale δ13C negative shifts, modulating the T-OAE carbon isotope signal, are correlated across different European basins, which have implications on the estimation of the T-OAE duration. The increase in kaolinite content and chemical index of alteration from the Pl–To boundary up to the T-OAE interval is interpreted as reflecting a shift towards warmer and wetter climate conditions. The common occurrence of coarse-grained turbidites within the T-OAE interval is possibly linked with changes of the hydrological cycle and storm intensity. Low total organic carbon contents together with the absence of redox-sensitive trace element enrichments indicate oxygen-deficient conditions unfavourable for organic matter preservation. Mercury data show a clear increase at the base of the T-OAE CIE followed by a return to background values, providing further evidence that Karoo-Ferrar volcanism might have triggered the series of environmental disturbances during the early Toarcian. However, the highest mercury values are recorded in samples containing abundant pyritized wood fragments, highlighting the influence of local chemical processes on mercury enrichments, which should be considered before any interpretation of the Hg records.Fegel, T., Boot, C.M., Broeckling, C.D., Baron, J.S., Hall, E.K., 2019. Assessing the chemistry and bioavailability of dissolved organic matter from glaciers and rock glaciers. Journal of Geophysical Research: Biogeosciences 124, 1988-2004. glaciers thaw in response to warming, they release dissolved organic matter (DOM) to alpine lakes and streams. The United States contains an abundance of both alpine glaciers and rock glaciers. Differences in DOM composition and bioavailability between glacier types, like rock and ice glaciers, remain undefined. To assess differences in glacier and rock glacier DOM we evaluated bioavailability and molecular composition of DOM from four alpine catchments each with a glacier and a rock glacier at their headwaters. We assessed bioavailability of DOM by incubating each DOM source with a common microbial community and evaluated chemical characteristics of DOM before and after incubation using untargeted gas chromatography?mass spectrometry-based metabolomics. Prior to incubations, ice glacier and rock glacier DOM had similar C:N ratios and chemical diversity, but differences in DOM composition. Incubations with a common microbial community showed that DOM from ice glacier meltwaters contained a higher proportion of bioavailable DOM and resulted in greater bacterial growth efficiency. After incubation, DOM composition from each source was statistically indistinguishable. This study provides an example of how MS-based metabolomics can be used to assess effects of DOM composition on differences in bioavailability of DOM. Furthermore, it illustrates the importance of microbial metabolism in structuring composition of DOM. Even though rock glaciers had significantly less bioavailable DOM than ice glaciers, both glacial types still have potential to be important sources of bioavailable DOM to alpine headwaters over the coming decades.Feng, J., Yang, S., Wang, H., Liang, J., Fang, Y., Luo, M., 2019. Methane source and turnover in the shallow sediments to the west of Haima cold seeps on the northwestern slope of the South China Sea. Geofluids 2019, 1010824. Haima cold seeps are active cold seep areas that were recently discovered on the northwestern slope of the South China Sea (SCS). Three piston cores (CL30, CL44, and CL47) were collected within an area characterized by bottom simulating reflectors to the west of Haima cold seeps. Porewater profiles of the three cores exhibit typical kink-type feature, which is attributed to elevated methane flux (CL30) and bubble irrigation (CL44 and CL47). By simulating the porewater profiles of SO42-, CH4, PO43-, Ca2+, Mg2+, and dissolved inorganic carbon (DIC) in CL44 and CL47 using a steady-state reaction-transport model, we estimated that the dissolved SO42- was predominantly consumed by anaerobic oxidation of methane (AOM) at rates of 74.3?mmol?m?2?yr?1 in CL44 and 85.0?mmol?m?2?yr?1 in CL47. The relatively high AOM rates were sustained by free gas dissolution rather than local methanogenesis. Based on the diffusive Ba2+ fluxes and the excess barium contents in the sediments slightly above the current SMTZ, we estimated that methane fluxes at core CL44 and CL47 have persisted for ca. 3?kyr and 0.8-1.6?kyr, respectively. The non-steady-state modeling for CL30 predicted that a recent increase in upward dissolved methane flux was initiated ca. 85?yr ago. However, the required time for the formation of the barium front above the SMTZ at this core is much longer (ca. 2.2-4.2?kyr), which suggests that the depth of SMTZ possibly has fluctuated due to episodic changes in methane flux. Furthermore, using the model-derived fractions of different DIC sources and the δ13CDIC mass balance calculation, we estimated that the δ13C values of the external methane in cores CL30, CL44, and CL47 are -74.1‰, -75.4‰, and -66.7‰, respectively, indicating the microbial origin of methane. Our results suggest that methane seepage in the broader area surrounding the Haima cold seeps probably has persisted at least hundreds to thousands of years with changing methane fluxes.Fernandez-Lima, F., 2019. Chapter 8 - Trapped ion mobility spectrometry coupled to FT-ICR MS: Fundamentals and applications, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 233-251. the introduction of Trapped Ion Mobility Spectrometry in 2011, a major transformation is happening on the way gas-phase; post-ionization mobility separations can be performed and coupled to existing mass spectrometry workflows. The possibility to decouple the mobility analysis from the experimental time scale, allows for better coupling of mobility and mass analysis; in particular, when current mass analyzers require seconds to achieve ultrahigh mass resolution and high mass accuracy. In this chapter, we will cover the history of trapped IMS and FT-ICR MS, the principles of a TIMS analyzer, modes of operation, mobility calibration of a TIMS-FT-ICR MS datasets, and the comparison of TIMS-TOF MS and FT-ICR MS during the analysis of complex mixtures.Ferreiro, B., Andrade, J.M., Paz-Quintáns, C., López-Mahía, P., Muniategui-Lorenzo, S., Rey-Garrote, M., Vázquez-Padín, C., Vales, C., 2019. Improved sensitivity of natural gas infrared measurements using a filling gas. Energy & Fuels 33, 6929-6933. trends to get greener cities and protect the environment imply substituting traditional diesel/gasoline engines for gas (gas-hybrid) powered engines. To accomplish this, straightforward quality control of liquefied and/or compressed natural gas is needed. This communication shows that the broadening effect of an auxiliary inert gas (Ar) enhances their infrared (IR) gaseous spectra and improves usual analytical performance parameters by 50%, which paves the way to use IR routinely to assess the composition of natural gas samples.Fiebig, J., Stefánsson, A., Ricci, A., Tassi, F., Viveiros, F., Silva, C., Lopez, T.M., Schreiber, C., Hofmann, S., Mountain, B.W., 2019. Abiogenesis not required to explain the origin of volcanic-hydrothermal hydrocarbons. Geochemical Perspectives Letters 11, 23–27. formation of n-alkane hydrocarbons has been postulated to occur within Earth's crust. Apparent evidence was primarily based on uncommon carbon and hydrogen isotope distribution patterns that set methane and its higher chain homologues apart from biotic isotopic compositions associated with microbial production and closed system thermal degradation of organic matter. Here, we present the first global investigation of the carbon and hydrogen isotopic compositions of n-alkanes in volcanic-hydrothermal fluids hosted by basaltic, andesitic, trachytic and rhyolitic rocks. We show that the bulk isotopic compositions of these gases follow trends that are characteristic of high temperature, open system degradation of organic matter. In sediment-free systems, organic matter is supplied by surface waters (seawater, meteoric water) circulating through the reservoir rocks. Our data set strongly implies that thermal degradation of organic matter is able to satisfy isotopic criteria previously classified as being indicative of abiogenesis. Further considering the ubiquitous presence of surface waters in Earth’s crust, abiotic hydrocarbon occurrences might have been significantly overestimated. Filho, J.F.A., Lacerda, V., Rom?o, W., 2019. Chapter 15 - Fourier transform mass spectrometry applied to forensic chemistry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 469-508. basis of Forensic Chemistry is the chemical characterization of an evidence or illegal substance for the purpose to determine or demonstrate the occurrence of a crime or an illegal practice. The broad of samples which are analyzed in Forensic Chemistry can be innumerous, e.g., hair, blood, urine, saliva, drugs, food, beverages, fraudulent documents, false banknotes, gunshot residue, explosives, fire residue, pharmaceuticals, and agrochemicals, among others. The combination of high resolution mass spectrometry (HRMS) based on Fourier transform mass analyzers with ambient ionization sources allows to reach reliable results with the specificity, which is mostly required in a wide diversity, reaching high complexity of forensic samples. In this chapter, the main studies using HRMS will be presented and discussed based on Fourier transform spectrometers applied in Forensic Chemistry (illicit abuse drugs, i.e., cocaine, marijuana; hallucinogens; and new psychoactive substances; food chemistry; agrochemicals; documentoscopy; and gunshot residues analysis).Finch, B.E., Stubblefield, W.A., 2019. Phototoxicity assessments of field sites in Barataria Bay, Louisiana, USA, and heavily weathered Macondo crude oil: Four years after the Deepwater Horizon oil spill. Environmental Toxicology and Chemistry 38, 1811-1819. Deepwater Horizon oil spill resulted in the release of large amounts of crude oil into waters of the Gulf of Mexico (USA). A significant portion of the oil reached coastal waters and shorelines where aquatic organisms reside. Four years after the spill, oil remains in small quantities along the coast. Given the high volume of oil coupled with the high ultraviolet light intensities of the Gulf of Mexico, continued polycyclic aromatic hydrocarbon phototoxicity may be occurring in the Gulf region. The objective of the present study was to determine the potential for phototoxicity at 5 field sites (oiled, remediated, and unoiled) in Barataria Bay (LA, USA) to caged mysid shrimp and sheepshead minnows and to evaluate the phototoxic potential of field‐collected oil water accommodated fractions (WAFs). Water chemistries were similar between field‐collected oil WAFs and ambient waters, excluding the most oiled field site. Field bioassays indicated no phototoxic risk of heavily weathered crude oil under the highly turbid conditions present during the study. Laboratory WAFs of field‐collected oil resulted in phototoxicity to mysid shrimp, suggesting a potential for phototoxicity of heavily weathered crude oil remaining in the Gulf of Mexico. Floc’h, K., Lacroix, F., Servant, P., Wong, Y.-S., Kleman, J.-P., Bourgeois, D., Timmins, J., 2019. Cell morphology and nucleoid dynamics in dividing Deinococcus radiodurans. Nature Communications 10, 3815. knowledge of bacterial nucleoids originates mostly from studies of rod- or crescent-shaped bacteria. Here we reveal that Deinococcus radiodurans, a relatively large spherical bacterium with a multipartite genome, constitutes a valuable system for the study of the nucleoid in cocci. Using advanced microscopy, we show that D. radiodurans undergoes coordinated morphological changes at both the cellular and nucleoid level as it progresses through its cell cycle. The nucleoid is highly condensed, but also surprisingly dynamic, adopting multiple configurations and presenting an unusual arrangement in which oriC loci are radially distributed around clustered ter sites maintained at the cell centre. Single-particle tracking and fluorescence recovery after photobleaching studies of the histone-like HU protein suggest that its loose binding to DNA may contribute to this remarkable plasticity. These findings demonstrate that nucleoid organization is complex and tightly coupled to cell cycle progression in this organism.Floris, F., O'Connor, P.B., 2019. Chapter 7 - Fundamentals of two dimensional Fourier transform mass spectrometry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 187-232. dimensional mass spectrometry (2D-MS) is a data-independent tandem mass spectrometry technique able to obtain information about the fragmentation patterns of all the analytes in a mixture in a single experiment, by correlating the in-cell generated fragments with their precursor ions. The amount of information generated by a single 2D-MS run is the equivalent of multiple tandem mass spectrometry studies on the entire sample, but without the necessity to isolate every single ion in the mixture before fragmentation, hence without any loss in sensitivity, and with the possibility to fragment ions otherwise impossible to isolate with standard 1D MS. From its conception in the 1980s, 2D-MS suffered an arrested development due to the required computational capacities of the technique, but it made its comeback in 2010, with implementation in the new-generation FT-ICR mass spectrometers. Subsequent developments in computer capabilities, FT-ICR technology, and the algorithms applied to the processing of 2D-MS data allowed two dimensional Fourier transform ion cyclotron resonance mass spectrometry (2D FT-ICR MS) to become a useful analytical technique. Since then, 2D-MS found its applications in the analysis of small molecules, top-down and bottom-up proteomics, and polymer analysis. The technique has also been exported to other mass analyzers, such as LITs, in a simulation study with SIMION. In this review, the history of 2D FT-ICR MS is revisited under the light of the recent improvements, the acquisition of 2D-MS data using contemporary FT-ICR mass spectrometers and processing software is explained, and the most recent applications of the technique are reported.Frank, A.B., Klaebe, R.M., Xu, L., Frei, R., 2019. Redox fluctuations during the Ediacaran-Cambrian transition, Nanhua Basin, South China: Insights from Cr isotope and REE+Y data. Chemical Geology 525, 321-333. fluctuations in marine and atmospheric redox conditions during the late Precambrian/Early Cambrian is essential to better our understanding of the link between oxygen and biological evolution. This study presents REE+Y and Cr isotopic data together with TOC data and redox-sensitive trace metal concentrations of marine black shales and cherts from the Cambrian Jiumenchong Formation and Ediacaran Liuchapo Formation from South China, in order to improve our understanding of the redox conditions in the Nanhua basin during this critical time period. The Liuchapo Formation records negative Ce anomalies and highly fractionated δ53Cr values of up to 1.06?±?0.09‰, suggesting deposition under oxic conditions and implying high oxidative weathering rates during the end of the Ediacaran. The overlying Jiumenchong Formation is characterised by a stratigraphic upward decrease in δ53Cr values to typical igneous values as well as a decrease in negative Ce anomalies and an increase in positive Eu anomalies, suggesting an increase in detrital content due to more aeolian weathering and deposition under anoxic conditions at the beginning of the Cambrian. The latter is also confirmed by the trends in V/Cr and Th/U ratios, which further indicate an eventual return to (dys-)oxic seawater conditions during the Early Cambrian.Frings, P.J., 2019. Palaeoweathering: How do weathering rates vary with climate? Elements 15, 259-265. feedback between Earth surface weathering and climate is thought to be fundamental in maintaining Earth's habitability over long times-cales, but investigating this control in the modern world is difficult. The geologic record of cycles between glacial and interglacial conditions of the last 2.6 million years allows us to study weathering feedback in action. A suite of mineral, element and isotope proxies have been applied to address how weathering rates have varied over glacial cycles. Despite evidence for substantial local changes, the emerging answer at a global scale seems to be, “not very much”.Frings, P.J., Buss, H.L., 2019. The central role of weathering in the geosciences. Elements 15, 229-234. is the chemical and physical alteration of rock at the surface of the Earth, but its importance is felt well beyond the rock itself. The repercussions of weathering echo throughout the Earth sciences, from ecology to climatology, from geomorphology to geochemistry. This article outlines how weathering interacts with various geoscience disciplines across a huge range of scales, both spatial and temporal. It traces the evolution of scientific thinking about weathering and man's impact on weathering itself—for better and for worse. Future computational, conceptual and methodological advances are set to cement weathering's status as a central process in the Earth sciences.Galili, N., Shemesh, A., Yam, R., Brailovsky, I., Sela-Adler, M., Schuster, E.M., Collom, C., Bekker, A., Planavsky, N., Macdonald, F.A., Préat, A., Rudmin, M., Trela, W., Sturesson, U., Heikoop, J.M., Aurell, M., Ramajo, J., Halevy, I., 2019. The geologic history of seawater oxygen isotopes from marine iron oxides. Science 365, 469-473.: The oxygen isotope composition (δ18O) of marine sedimentary rocks has increased by 10 to 15 per mil since Archean time. Interpretation of this trend is hindered by the dual control of temperature and fluid δ18O on the rocks’ isotopic composition. A new δ18O record in marine iron oxides covering the past ~2000 million years shows a similar secular rise. Iron oxide precipitation experiments reveal a weakly temperature-dependent iron oxide–water oxygen isotope fractionation, suggesting that increasing seawater δ18O over time was the primary cause of the long-term rise in δ18O values of marine precipitates. The 18O enrichment may have been driven by an increase in terrestrial sediment cover, a change in the proportion of high- and low-temperature crustal alteration, or a combination of these and other factors.Editor's summary: Not as hot as we thought. Earth's early oceans appear not to have been as hot as some have suggested. The oxygen isotope composition of marine carbonates has changed markedly over the past 3.5 billion years. However, it has been difficult to determine whether that is because of a cooling of the seawater (from temperatures as high as 70°C) or an actual change in the isotope composition of the water. Galili et al. calibrated the temperature-dependent oxygen isotope fractionation between iron oxides and aqueous solutions and constructed an oxygen isotope record in marine iron oxides covering the past 2 billion years. Their findings suggest that a change in the isotope composition of the water, rather than its cooling, underlies the observed geological trend.Gan, Y., Cheng, Q., Wang, Z., Yang, J., Sun, W., Liu, Y., 2019. Molecular dynamics simulation of the nucleation and gelation process for a waxy crude oil multiphase system under different physical–chemical influencing factors. Energy & Fuels 33, 7305-7320. molecular dynamics model was established to characterize the homogeneous and heterogeneous nucleation processes for a waxy crude oil multiphase system at the nanoscale. Using the established model, the homogeneous and heterogeneous nucleation processes were numerically simulated, and the accuracy of the model was verified by comparing the simulation results with those of classic nucleation theory. On this basis, the micromechanism for the effect of different cooling rates on the nucleation process was studied, and it was determined that the homogeneous and heterogeneous nucleation would coexist and compete with each other in the initial stage and, at last, a large spherical cluster would form. Furthermore, the calculation model for the interfacial free energy was proposed, the interfacial free energy with nucleation centers of different specific area factors were numerically calculated, and the influence rules of the interface effects on the nucleation process were clarified. Besides, the heterogeneous nucleation process of different nucleation center materials was simulated, and the aggregation degree and element composition of nucleation clusters were analyzed. Finally, the influence mechanism of doping ions on the nucleation process was investigated. The investigations in this study provided a theoretical basis for ensuring a safe and economic operation of waxy crude oil production.Gao, Y., Cai, X., Zhang, P., He, G., Gao, Q., Wan, J., 2019. Pore characteristics and evolution of Wufeng–Longmaxi Fms shale gas reservoirs in the basin-margin transition zone of SE Chongqing. Natural Gas Industry B 6, 323-332. present, researches on the pore evolution of shale reservoir and its evolution mechanism are still at such a groping stage that a consensus has not yet reached. Based on core analysis and thermal simulation experiments, the pore types, pore structures and pore-size change rules of shale gas reservoirs of Upper Ordovician Wufeng–Lower Silurian Longmaxi Fms in the southeastern (SE) Sichuan Basin and its basin-margin transition zone (hereinafter referred to as the basin-margin transition zone of SE Chongqing) were studied by means of argon ion polishing–scanning electron microscopy (SEM) and atomic force microscopy. Then, the evolution characteristics of organic pores were discussed, and the influence of associated minerals on pore evolution was analyzed. Finally, a pore evolution model for the shale gas reservoirs in this area was established. And the following research results were obtained. First, three types of reservoir spaces are mainly developed in the high-quality shale reservoirs of Wufeng–Longmaxi Fms in this area, including fracture, inorganic pore and organic pore. And the organic pores provide the primary reservoir space of shale gas, which can be divided into four categories, i.e., amorphous kerogen pores, structured kerogen pores, asphaltene pores and paleontology fossil pores. Second, organic contracted fractures are related to the contraction of organic matters, first appearing on one side of the organic matters and then becomes wider and wider with the increase of temperatures. Third, organic pores are mostly the “spongy” pores distributed densely inside the organic matters. When Ro is in the range of 1.56–3.50%, macropores and mesopores are dominant. And when Ro exceeds 3.50%, macropores decrease while mesopores and micropores increase. Fourth, the types of organic matters and the content of associated minerals (e.g. clay minerals, siliceous particles and pyrite) play an important role in the development of pores. In conclusion, the pore evolution law of Wufeng–Longmaxi shale in the basin-margin transition zone of SE Chongqing is that with the increase of burial depth, inorganic porosity decreases significantly, organic porosity increases first and then decreases, and the total porosity shows a change trend of decreasing first, then increasing and finally decreasing continuously.Gawryluk, R.M.R., Tikhonenkov, D.V., Hehenberger, E., Husnik, F., Mylnikov, A.P., Keeling, P.J., 2019. Non-photosynthetic predators are sister to red algae. Nature 572, 240-243. (red algae) is one of three lineages of Archaeplastida, a supergroup that is united by the primary endosymbiotic origin of plastids in eukaryotes. Red algae are a diverse and species-rich group, members of which are typically photoautotrophic, but are united by a number of highly derived characteristics: they have relatively small intron-poor genomes, reduced metabolism and lack cytoskeletal structures that are associated with motility, flagella and centrioles. This suggests that marked gene loss occurred around their origin4; however, this is difficult to reconstruct because they differ so much from the other archaeplastid lineages, and the relationships between these lineages are unclear. Here we describe the novel eukaryotic phylum Rhodelphidia and, using phylogenomics, demonstrate that it is a closely related sister to red algae. However, the characteristics of the two Rhodelphis species described here are nearly opposite to those that define red algae: they are non-photosynthetic, flagellate predators with gene-rich genomes, along with a relic genome-lacking primary plastid that probably participates in haem synthesis. Overall, these findings alter our views of the origins of Rhodophyta, and Archaeplastida evolution as a whole, as they indicate that mixotrophic feeding—that is, a combination of predation and phototrophy—persisted well into the evolution of the group.Gilbert, P.U.P.A., Porter, S.M., Sun, C.-Y., Xiao, S., Gibson, B.M., Shenkar, N., Knoll, A.H., 2019. Biomineralization by particle attachment in early animals. Proceedings of the National Academy of Sciences, 201902273.: The mechanisms by which organisms form mineralized skeletons have been a major research focus for the last 50 y and remain so today. Among the most surprising discoveries is the recent observation that different animals use the same mechanisms, and precisely the same amorphous precursors, to form biomineralized structures as diverse as coral skeletons, molluscan shells, and sea urchin spines. In living animals, skeletal biomineralization from amorphous precursors correlates with a distinctive nanoparticulate texture that can be preserved in fossils, enabling us to probe mechanisms of skeletal formation in early animals. We document nanoparticulate texture in some of the oldest known carbonate skeletons, which strongly suggests that skeletons formed from amorphous precursors throughout the recorded history of animals.Abstract: Crystallization by particle attachment (CPA) of amorphous precursors has been demonstrated in modern biomineralized skeletons across a broad phylogenetic range of animals. Precisely the same precursors, hydrated (ACC-H2O) and anhydrous calcium carbonate (ACC), have been observed spectromicroscopically in echinoderms, mollusks, and cnidarians, phyla drawn from the 3 major clades of eumetazoans. Scanning electron microscopy (SEM) here also shows evidence of CPA in tunicate chordates. This is surprising, as species in these clades have no common ancestor that formed a mineralized skeleton and appear to have evolved carbonate biomineralization independently millions of years after their late Neoproterozoic divergence. Here we correlate the occurrence of CPA from ACC precursor particles with nanoparticulate fabric and then use the latter to investigate the antiquity of the former. SEM images of early biominerals from Ediacaran and Cambrian shelly fossils show that these early calcifiers used attachment of ACC particles to form their biominerals. The convergent evolution of biomineral CPA may have been dictated by the same thermodynamics and kinetics as we observe today.Gillibert, R., Balakrishnan, G., Deshoules, Q., Tardivel, M., Magazzù, A., Donato, M.G., Maragò, O.M., Lamy de La Chapelle, M., Colas, F., Lagarde, F., Gucciardi, P.G., 2019. Raman tweezers for small microplastics and nanoplastics identification in seawater. Environmental Science & Technology 53, 9003-9013. understanding of the fate and distribution of micro- and nano- plastics in the marine environment is limited by the intrinsic difficulties of the techniques currently used for the detection, quantification, and chemical identification of small particles in liquid (light scattering, vibrational spectroscopies, and optical and electron microscopies). Here we introduce Raman Tweezers (RTs), namely optical tweezers combined with Raman spectroscopy, as an analytical tool for the study of micro- and nanoplastics in seawater. We show optical trapping and chemical identification of sub-20 μm plastics, down to the 50 nm range. Analysis at the single particle level allows us to unambiguously discriminate plastics from organic matter and mineral sediments, overcoming the capacities of standard Raman spectroscopy in liquid, intrinsically limited to ensemble measurements. Being a microscopy technique, RTs also permits one to assess the size and shapes of particles (beads, fragments, and fibers), with spatial resolution only limited by diffraction. Applications are shown on both model particles and naturally aged environmental samples, made of common plastic pollutants, including polyethylene, polypropylene, nylon, and polystyrene, also in the presence of a thin eco-corona. Coupled to suitable extraction and concentration protocols, RTs have the potential to strongly impact future research on micro and nanoplastics environmental pollution, and enable the understanding of the fragmentation processes on a multiscale level of aged polymers.Gogoi, S., Gogoi, S.B., 2019. Review on microfluidic studies for EOR application. Journal of Petroleum Exploration and Production Technology 9, 2263-2277. the time the flow of fluids happens below the surface of the earth. These flow processes can only be imagined, but not be fully visualised on how fluid flow behaviour occurs though the porous medium of the rocks. Hence comes the play of microfluidic micromodels. These are a transparent version of slices (2 dimensional) porous structure of rocks such as sandstone duplicated onto materials such as glass, polymers and silicon wafers. Fluids such as crude oil, surfactant and polymer solutions and gases such as carbon dioxide (CO2) are injected through special pumps into these transparent micromodels. The flow patterns and behaviours hence developed inside the micromodels are studied and analysed. Micromodels have helped in different branches of science such as medicine, genetics, liquid channelling and enhanced oil recovery (EOR). The concern of this paper is to study the flow behaviour and EOR in micromodels. Micromodels can be made to represent a micro version of a partially saturated rock with crude oil. The various chemical EOR processes such as surfactant flooding, polymer flooding, gas flooding injected into crude oil filled micromodels with water saturation is studied. The advancement of front developed between displacing and displaced fluids, the fingering effect, the presence of high permeability streaks is observed. Also the breakthrough of the flood front is analysed from the various experiments reviewed. This review paper is undertaken so as to help researchers find a consolidated and concise literature of the trends and developments in microfluidics especially in EOR.Gomez, M.G., Graddy, C.M.R., DeJong, J.T., Nelson, D.C., 2019. Biogeochemical changes during bio-cementation mediated by stimulated and augmented ureolytic microorganisms. Scientific Reports 9, 11517. Induced Calcite Precipitation (MICP) is a bio-mediated cementation process that can improve the engineering properties of granular soils through the precipitation of calcite. The process is made possible by soil microorganisms containing urease enzymes, which hydrolyze urea and enable carbonate ions to become available for precipitation. While most researchers have injected non-native ureolytic bacteria to complete bio-cementation, enrichment of native ureolytic microorganisms may enable reductions in process treatment costs and environmental impacts. In this study, a large-scale bio-cementation experiment involving two 1.7-meter diameter tanks and a complementary soil column experiment were performed to investigate biogeochemical differences between bio-cementation mediated by either native or augmented (Sporosarcina pasteurii) ureolytic microorganisms. Although post-treatment distributions of calcite and engineering properties were similar between approaches, the results of this study suggest that significant differences in ureolysis rates and related precipitation rates between native and augmented microbial communities may influence the temporal progression and spatial distribution of bio-cementation, solution biogeochemical changes, and precipitate microstructure. The role of urea hydrolysis in enabling calcite precipitation through sustained super-saturation following treatment injections is explored.Gonglach, S., Paul, S., Haas, M., Pillwein, F., Sreejith, S.S., Barman, S., De, R., Müllegger, S., Gerschel, P., Apfel, U.-P., Coskun, H., Aljabour, A., Stadler, P., Sch?fberger, W., Roy, S., 2019. Molecular cobalt corrole complex for the heterogeneous electrocatalytic reduction of carbon dioxide. Nature Communications 10, 3864. conversion of CO2 to alcohols is one of the most challenging methods of conversion and storage of electrical energy in the form of high-energy fuels. The challenge lies in the catalyst design to enable its real-life implementation. Herein, we demonstrate the synthesis and characterization of a cobalt(III) triphenylphosphine corrole complex, which contains three polyethylene glycol residues attached at the meso-phenyl groups. Electron-donation and therefore reduction of the cobalt from cobalt(III) to cobalt(I) is accompanied by removal of the axial ligand, thus resulting in a square-planar cobalt(I) complex. The cobalt(I) as an electron-rich supernucleophilic d8-configurated metal centre, where two electrons occupy and fill up the antibonding dz2 orbital. This orbital possesses high affinity towards electrophiles, allowing for such electronically configurated metals reactions with carbon dioxide. Herein, we report the potential dependent heterogeneous electroreduction of CO2 to ethanol or methanol of an immobilized cobalt A3-corrole catalyst system. In moderately acidic aqueous medium (pH?=?6.0), the cobalt corrole modified carbon paper electrode exhibits a Faradaic Efficiency (FE%) of 48 % towards ethanol production.Gonsior, M., 2019. Chapter 13 - FT-ICR MS and Orbitrap mass spectrometry approaches in environmental chemistry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 407-423. chapter will address non-target ultrahigh resolution mass spectrometric approaches currently implemented in aquatic and sediment environmental chemistry with a focus on drinking water, wastewater and emerging pollutant screening in aquatic/sediment systems. How to discover new and previously unknown DBPs will be described in drinking water. Non-target screening for unknown contaminants in wastewater is also an emerging field and examples are given describing approaches used in hydraulic fracturing (fracking) fluids and secondary treated effluent. Non-targeted screening for known and unknown contaminants in surface, groundwater and also sediments is discussed and approaches are summarized.Gooya, R., Silvestri, A., Moaddel, A., Andersson, M.P., Stipp, S.L.S., S?rensen, H.O., 2019. Unstable, super critical CO2–water displacement in fine grained porous media under geologic carbon sequestration conditions. Scientific Reports 9, 11272. this study we investigated fluid displacement water with supercritical (sc) CO2 in chalk under conditions close to those used for geologic CO2 sequestration (GCS), to answer two main questions: How much volume is available for scCO2 injection? And what is the main mechanism of displacement over a range of temperatures? Characterization of immiscible scCO2 displacement, at the pore scale in the complex microstructure in chalk reservoirs, offers a pathway to better understand the macroscopic processes at the continuum scale. Fluid behavior was simulated by solving the Navier-Stokes equations, using finite-volume methods within a pore network. The pore network was extracted from a high resolution 3D image of chalk, obtained using X-ray nanotomography. Viscous fingering dominates scCO2 infiltration and pores remain only partially saturated. The unstable front, developed with high capillary number, causes filling of pores aligned with the flow direction, reaching a maximum of 70% scCO2 saturation. The saturation rate increases with temperature but the final saturation state is the same for all investigated temperatures. The higher the saturation rate, the higher the dynamic capillary pressure coefficient. A higher dynamic capillary pressure coefficient indicates that scCO2 needs more time to reach capillary equilibrium in the porous medium.Gopalapillai, Y., Kirk, J.L., Landis, M.S., Muir, D.C.G., Cooke, C.A., Gleason, A., Ho, A., Kelly, E., Schindler, D., Wang, X., Lawson, G., 2019. Source analysis of pollutant elements in winter air deposition in the Athabasca oil sands region: A temporal and spatial study. ACS Earth and Space Chemistry 3, 1656-1668. extraction and upgrading of bitumen have been identified as sources of enhanced atmospheric deposition of pollutant elements to ecosystems in the Athabasca Oil Sands Region (AOSR) in northern Alberta, Canada. Bitumen extraction became increasingly efficient, and oil prices surged in the 1990s, resulting in rapid expansion and increased production over the last two decades. Here, we examine temporal and spatial trends in wintertime atmospheric deposition of pollutant elements in 1978, 1981, 2008, and 2011–2016 at broad spatial scales using snowpack measurements. A hybrid source analysis was conducted, including (i) simple and multiple linear regression (MLR) of identified source locations and elemental deposition, (ii) spatially resolved aluminum enrichment factors (Al EFs), and (iii) positive matrix factorization (PMF) to determine source profiles. Temporal trends revealed a general decrease in atmospheric loadings; however, near-field V, Ti, and Al loadings in 2016 were an order of magnitude greater than at reference sites in the Peace Athabasca Delta. MLRs demonstrated that the two largest bitumen producers were major contributors of key pollutant elements (e.g., V, Al, Ti, W, Ga, Fe, Be, Cs, Co, Mo, Rb, Pb, As, U, and Ba) including rare earth elements (Y, Ce, and La). Using Al EFs, fugitive (geogenic) dust was identified as the main contributor for most elements, except for V and W, which were directly introduced by industrial sources. Results strongly suggest that fugitive dusts from petcoke piles and roads are important wintertime pollution vectors in the AOSR.Gornik, G.S., Hu, I., Lassadi, I., Waller, F.R., 2019. The biochemistry and evolution of the dinoflagellate nucleus. Microorganisms 7, DOI: 10.3390/microorganisms7080245. are known to possess a highly aberrant nucleus&mdash;the so-called dinokaryon&mdash;that exhibits a multitude of exceptional biological features. These include: (1) Permanently condensed chromosomes; (2) DNA in a cholesteric liquid crystalline state, (3) extremely large DNA content (up to 200 pg); and, perhaps most strikingly, (4) a deficit of histones&mdash;the canonical building blocks of all eukaryotic chromatin. Dinoflagellates belong to the Alveolata clade (dinoflagellates, apicomplexans, and ciliates) and, therefore, the biological oddities observed in dinoflagellate nuclei are derived character states. Understanding the sequence of changes that led to the dinokaryon has been difficult in the past with poor resolution of dinoflagellate phylogeny. Moreover, lack of knowledge of their molecular composition has constrained our understanding of the molecular properties of these derived nuclei. However, recent advances in the resolution of the phylogeny of dinoflagellates, particularly of the early branching taxa; the realization that divergent histone genes are present; and the discovery of dinoflagellate-specific nuclear proteins that were acquired early in dinoflagellate evolution have all thrown new light nature and evolution of the dinokaryon.Goudemand, N., Romano, C., Leu, M., Bucher, H., Trotter, J.A., Williams, I.S., 2019. Dynamic interplay between climate and marine biodiversity upheavals during the early Triassic Smithian-Spathian biotic crisis. Earth-Science Reviews 195, 169-178. the aftermath of the Permian-Triassic boundary mass extinction (~252?Ma) ― the most dramatic biotic crisis of the Phanerozoic ― changes in climate, the carbon cycle, and biodiversity patterns remained extremely variable for several million years. In particular, the Smithian-Spathian boundary crisis, which occurred ca. 1.5?Ma after the Permian-Triassic boundary, coincided with drastic changes in global climate, a major extinction of nektonic organisms, and major shifts in the carbon and oxygen isotope compositions of marine carbonates and phosphates. However, the timing of these events and their interrelationships remain controversial. Previous studies concluded that the latest Smithian-earliest Spathian interval was a time of extremely high temperatures, which would have precluded marine (macro)-vertebrates from inhabiting the equatorial realm. Conversely, based on oxygen isotope measurements of conodont elements collected at high temporal resolution from the Salt Range record (Pakistan), we report a major cooling event during that time interval. These results suggest that the interplay between climate and biodiversity patterns is more complex than usually portrayed.Gray, M.R., 2019. Fundamentals of partial upgrading of bitumen. Energy & Fuels 33, 6843-6856. the past, transportation of heavy and bitumen to downstream refineries has been accomplished by either adding a diluent or converting the vacuum residue to produce a synthetic crude oil. In Canada, partial upgrading of bitumen to enhance its transportation to downstream refineries is becoming more attractive as production increases from both in situ and mining operations. Similar opportunities exist for inland production elsewhere in the world. This review discusses the relationship between the key properties for transport, which are viscosity and density, and the composition of a crude oil. The potential process pathways to achieve low-cost reduction in viscosity and density are discussed, particularly thermal cracking and partial deasphalting. Thermal cracking is effective for reducing the viscosity, but it is limited by the stability of the processed asphaltenes in the product blend. While thermal cracking has a long history in refining, the lower levels of asphaltene removal to achieve partial upgrading require removal of solid asphaltenes, rather than the viscous liquids produced in current refinery deasphalting plants. The benefits of combinations of reaction and separation approaches are discussed, particularly combinations of thermal cracking, addition of reduced amounts of diluent, and partial deasphalting.Griepentrog, M., De Wispelaere, L., Bauters, M., Bodé, S., Hemp, A., Verschuren, D., Boeckx, P., 2019. Influence of plant growth form, habitat and season on leaf-wax n-alkane hydrogen-isotopic signatures in equatorial East Africa. Geochimica et Cosmochimica Acta 263, 122-139. n-alkanes are produced by terrestrial plants, and through long-term preservation in sediments their stable hydrogen-isotopic signature (δ2Hwax) provides useful information on past hydrological variation for paleoclimate reconstructions. However, gaps remain in our understanding of the relationships between the isotopic signatures of leaf waxes and the plants’ source water. In this study, we investigated the influence of plant growth form, habitat and season on the distribution patterns and δ2Hwax values of 14 plant species (among which are two grasses, five trees and seven shrubs) sampled during four successive dry and wet seasons in three distinct habitats around Lake Chala in equatorial East Africa. Variation in δ2Hwax was analyzed with linear mixed-effect models and compared with the associated values of xylem water (δ2Hxylem), leaf water (δ2Hleaf) and biosynthetic hydrogen fractionation (εbio). Our results show that plant growth form was the most important driver of modern-day δ2Hwax variability in the study area, and that differences in δ2Hwax among habitats to a large extent reflect how each major growth forms is represented in those habitats. Individual plant species appear to express substantial species-specific isotopic fractionation that cannot be attributed to the tested external factors but rather seem to depend on intrinsic (e.g., plant phenological and biosynthesis-related) factors. For the purpose of calibrating δ2Hwax signatures against vegetation types, it is thus crucial to analyze representative samples of the plant communities present in the study area. Our results further indicate that paleohydrological studies in regions receiving rain from multiple moisture sources must take into account possible seasonal bias in the δ2Hwax signature relative to annual rainfall, due to unequal use of those moisture sources by the plants. Finally, the strong influence of plant growth form on δ2Hwax values argues for δ2Hwax variation in paleo-records being evaluated in conjunction with independent proxy data on changes in vegetation composition. Differences in n-alkane distribution patterns among trees, shrubs and grasses (e.g., average chain length, carbon preference index and C31/(C29?+?C31) ratio) may provide such proxies, and can be produced from the same leaf-wax n-alkane dataset used to determine δ2Hwax.Griffis, N.P., Monta?ez, I.P., Fedorchuk, N., Isbell, J., Mundil, R., Vesely, F., Weinshultz, L., Iannuzzi, R., Gulbranson, E., Taboada, A., Pagani, A., Sanborn, M.E., Huyskens, M., Wimpenny, J., Linol, B., Yin, Q.-Z., 2019. Isotopes to ice: Constraining provenance of glacial deposits and ice centers in west-central Gondwana. Palaeogeography, Palaeoclimatology, Palaeoecology 531, 108745. timing and geographic distribution of glaciers in high-latitude southern Gondwana during the Late Paleozoic Ice Age remain poorly constrained, ultimately precluding our ability to estimate ice volume and associated climate teleconnections and feedbacks during Earth's penultimate icehouse. Current aerial extents of glaciers, constrained by sedimentary flow directions, near exclusively infer paleo-glaciation to be highland-driven and may underestimate potential ice sources in continental regions from which ice sheets may have emanated. Here, we report new U-Pb ages and Hf isotope compositions of detrital zircons recovered from diamictites in two key mid- to high-latitude Gondwanan basins (Paraná, Brazil and Tepuel, Argentine Patagonia). The results indicate regional sediment sources for both basins during the early period of late Paleozoic glaciation evolving into more distal sources during the final deglaciation along southern and western Gondwana. Similar age sediment sourced from diamictites in the Congo Basin, that require an ice center in eastern Africa suggest the possibility of a large ice sheet in this area of Africa proximal to the Carboniferous-Permian boundary, which may have sourced sediments to the Paraná Basin. An inferred distal southern source of glacial sediment for the Tepuel Basin argues for the presence of an ice sheet(s) in the Ellsworth Block of Antarctica towards the end of the glaciation history in Patagonia. These findings indicate an evolution during the Late Paleozoic Ice Age from proximally to extrabasinally sourced sediment reflecting continental-scale glaciation and subsequent drainage from the Windhoek Highlands, Ellsworth Block and an east African source in west-central Gondwana. Coincidence with a long-term fall in atmospheric pCO2 during the Pennsylvanian to a minimum across the Carboniferous-Permian boundary and a subsequent rise in the early Permian suggests a primary CO2-driver for deglaciation in the Paraná Basin. Additional boundary conditions including availability of moisture and paleogeography likely further contributed to the timing of nucleation, growth and demise of these Gondwanan glaciers.Guido, D.M., Campbell, K.A., Foucher, F., Westall, F., 2019. Life is everywhere in sinters: examples from Jurassic hot-spring environments of Argentine Patagonia. Geological Magazine 156, 1631-1638. siliceous hot-spring (sinter) deposits from Argentine Patagonia were evaluated to determine the distribution and preservation quality of their entombed microbial fabrics. Detailed study showed that the Claudia palaeo-geothermal field hosts the best-preserved sinter apron in the Deseado Massif geological province, where we also found hot-spring silica–biotic interactions extending into hydrothermally influenced fluvial and lacustrine settings. Carbonaceous material was identified by petrography and Raman spectroscopy mapping; it is inter-laminated with silica across proximal vent to distal marsh facies. The ubiquitous presence of microbial biosignatures has application to studies of hydrothermal settings of early life on Earth and potentially Mars.Gullapalli, S., Dewangan, P., Kumar, A., Dakara, G., Mishra, C.K., 2019. Seismic evidence of free gas migration through the gas hydrate stability zone (GHSZ) and active methane seep in Krishna-Godavari offshore basin. Marine and Petroleum Geology 110, 695-705. amplitude versus offset (AVO) analysis was performed on the multichannel seismic data in the vicinity of Site NGHP-01-10, where thick fracture-filled gas hydrate is reported, to understand the fluid migration in fracture dominated gas hydrate system. Amplitude preserved common image gathers (CIG) are used in extracting the seismic amplitude with offset for seafloor, bottom simulating reflectors (BSR), and different horizons within the gas hydrate stability zone (GHSZ). The extracted amplitudes are fitted with three-term Shuey's AVO approximation to estimate the intercept and gradient values. Based on the intercept and gradient values, two distinct classes of seismic AVO responses are observed; class IV AVO (decreasing negative amplitudes with increasing offsets) and class III AVO (increasing negative amplitudes with increasing offsets) for the BSR and other horizons above the BSR. The large negative intercept and gradient values which indicate class III AVO ranges from ?0.2 to ?1.8 for the inline seismic profile and from ?0.01 to ?0.3 for the crossline profile. The presence of class III AVO anomaly within the gas hydrate stability zone (GHSZ) provides evidence of existence of free gas which may be migrating along the fault system. Some of the active faults are exposed on the surface and show gas venting signatures such as gas-flares and pockmarks in the multibeam data.Guo, S., Mao, W., 2019. Division of diagenesis and pore evolution of a Permian Shanxi shale in the Ordos Basin, China. Journal of Petroleum Science and Engineering 182, 106351. research analyzed the pore evolution and diagenesis in a Permian Shanxi shale from the Ordos Basin. Thermal simulation method simulated the thermal evolution of organic matter in a sample from mature (Ro?=?0.96%) to overmature (Ro?=?3.05%). Gas adsorption and mercury intrusion capillary pressure techniques were used to analyze pore-size distribution across a maturation gradient. X-ray diffraction, Focused Ion Beam-Scanning Electron Microscopy and rock pyrolysis techniques were used to divide the stages of diagenesis and pore evolution. Results showed that mesopores and macropores dominate pore volume while micropores and mesopores dominate surface area. Pore volume and surface area initially decreased and then increased with maturity. Kaolinite is converted to illite and illite-smectite mixedlayer in the middle to late diagenesis stage. Pore evolution and diagenesis can be divided into four stages in a sample from mature to overmature. Factors influencing pore-size distribution are different in four stages.Guo, X., 2019. Major factors controlling the shale gas accumulations in Wufeng-Longmaxi Formation of the Pingqiao Shale Gas Field in Fuling Area, Sichuan Basin, China. Journal of Natural Gas Geoscience 4, 129-138. Shale Gas Field in Fuling Area of Sichuan Basin in China is located in a narrow-abrupt fault anticline of the Fenglai Syncline. Presently, the proven geological reserves of shale gas are 138.917 × 109 m3 in the Pingqiao Shale Gas Field, suggesting good potential for shale gas exploration in the Pingqiao Shale Gas Field. According to the drilling, logging, as well as the seismic and experimental data, the basic features of the Pingqiao Shale Gas Field with the narrow-abrupt fault anticline structure is outlined. Herein, the major factors controlling the accumulation and the high productivity, as well as the reasons for the differences in the production in the Pingqiao Shale Gas Field are also analyzed. The studies show the following: (1) The thickness of the shale gas layers (TOC ≥ 1%) is 115–155 m, the thickness of quality shale layers (TOC ≥ 3%) at the bottom of Wufeng-Longmaxi Formation in the Pingqiao Shale Gas Field is 36–40 m, which is featured by the high abundance in reserves (1.268 × 109 m3/km2), high pressure of shale gas accumulation (pressure ratio 1.56) and the high production value (average testing production 219.9 × 103 m3/d). (2) Main factors controlling shale gas accumulation and production in the Pingqiao Shale Gas Field include developed quality shales in the deep shelf, no faults stretching to the surface, weak slipping, good sealing, no outcrops and no obvious pressure-released belts in the surrounding area. (3) The development degree of the micro-fractures, structure position and depth are the key factors for the differences in production when shale gas layers have similar enrichment conditions.Gutiérrez, D., Moore, R.G., Mehta, S.A., Ursenbach, M., Bernal, A., 2019. Phase-behavior modeling of oils in terms of saturates/aromatics/resins/asphaltenes fractions. SPE Reservoir Evaluation & Engineering 22, 1015-1029. of the key steps toward improving the predictability of air-injection-based processes relies on the development of accurate phase-behavior models of the oil.Historically, for in-situ combustion (ISC) in heavy oils and bitumens, phase behavior was often ignored because the physical aspects of the process (e.g., distillation) were not considered to be as significant as the oxidation reactions. However, this step is important for several reasons. First, the compositional model should reflect the phase behavior of the original fluids. Second, reaction rates are dependent on the concentrations of the reactants, which in turn are affected by the volatility of the components. This is particularly important for lighter oils (but not unimportant for heavier oils), where the phase equilibrium between the liquid and vapor can have a significant effect on the flammability range for vapor-phase combustion at given temperature and pressure conditions. Finally, for the case of lighter oils, a good phase-behavior model is required to capture the compositional effects of the resulting flue-gas drive.This study presents a practical work flow to develop a phase-behavior model in terms of saturates/aromatics/resins/asphaltenes (SARA) fractions that is aligned with the reaction-modeling approach used in most kinetic models. The methodology requires conventional-oil-characterization (i.e., dependent on distillation cuts) and conventional-phase-behavior experiments (e.g., differential liberation), as well as oil characterization in terms of SARA fractions.The first step of the method consists of splitting the heaviest oil fraction (i.e., plus fraction), followed by lumping all of the single-carbon-number (SCN) components, in such a way that the new oil characterization honors the SARA data available, such as composition and the physical properties of each fraction (e.g., molecular weight). In addition, the gas components (e.g., methane) would be treated as additional components as necessary. The second step is to tune an equation of state (EOS), in terms of the SARA-based model, to match the relevant laboratory experiments. Finally, the tuned EOS would be used to export the equilibrium constants (K-value tables) to the thermal numerical simulator.Different examples on the application of the phase-behavior-modeling work flow are presented and discussed in detail for heavy and light oils. This work opens up opportunities to model the ISC process for any oil (i.e., light or heavy) using the currently available kinetic models, which in turn is an important step toward improving the predictability of ISC processes using reservoir simulation.Hajny, K.D., Salmon, O.E., Rudek, J., Lyon, D.R., Stuff, A.A., Stirm, B.H., Kaeser, R., Floerchinger, C.R., Conley, S., Smith, M.L., Shepson, P.B., 2019. Observations of methane emissions from natural gas-fired power plants. Environmental Science & Technology 53, 8976-8984. research efforts on the atmospheric impacts of natural gas (NG) have focused heavily on the production, storage/transmission, and processing sectors, with less attention paid to the distribution and end use sectors. This work discusses 23 flights at 14 natural gas-fired power plants (NGPPs) using an aircraft-based mass balance technique and methane/carbon dioxide enhancement ratios (ΔCH4/ΔCO2) measured from stack plumes to quantify the unburned fuel. By comparing the ΔCH4/ΔCO2 ratio measured in stack plumes to that measured downwind, we determined that, within uncertainty of the measurement, all observed CH4 emissions were stack-based, that is, uncombusted NG from the stack rather than fugitive sources. Measured CH4 emission rates (ER) ranged from 8 (±5) to 135 (±27) kg CH4/h (±1σ), with the fractional CH4 throughput lost (loss rate) ranging from ?0.039% (±0.076%) to 0.204% (±0.054%). We attribute negative values to partial combustion of ambient CH4 in the power plant. The average calculated emission factor (EF) of 5.4 (+10/–5.4) g CH4/million British thermal units (MMBTU) is within uncertainty of the Environmental Protection Agency (EPA) EFs. However, one facility measured during startup exhibited substantially larger stack emissions with an EF of 440 (+660/–440) g CH4/MMBTU and a loss rate of 2.5% (+3.8/–2.5%).Haliki, E., 2019. Broadcast network model of pulsars as beacons of extraterrestrial civilizations. International Journal of Astrobiology 18, 455-462. to the Kardashev scale, likely extraterrestrial civilizations above Type-I might use natural energy sources of the Universe, which is also true for transmitting their signals out to distances. A variety of studies have shown that radio pulsars are most likely candidates for this. First, the current study examined how the radio beams of pulsars scan across their environment. Later when the radio beams of pulsars have been modulated, a network model has been proposed on how many habitable planets possible to be home for other assumed advanced civilizations could be reached. It has been found that size of each pulsar's broadcast network depends on the inclination angle. If a civilization controls multiple pulsars, it could comb a considerable fraction of their own celestial sphere and pulsars share their signals in a decentralized fashion as in the mail servers. Moreover, it is briefly cited how beam-modulating mechanisms can be built and searched around pulsars.? It has been shown how pulsars would behave like beacons only when they have been used by modulating their radio signals.? It has also been indicated how each pulsar could constitute an increasingly growing broadcast network by sweeping geometries and in what way it would emerge as number of controlled pulsars increases.? It has been interpreted how a modulation mechanism could be established and searched under basic physical principles.Hamdan, H.Z., Salam, D.A., Saikaly, P.E., 2019. Characterization of the microbial community diversity and composition of the coast of Lebanon: Potential for petroleum oil biodegradation. Marine Pollution Bulletin 149, 110508. this study, the shoreline of Lebanon, which extends over 225?km along the eastern side of the Mediterranean Sea, was characterized for its sediment microbial community diversity and composition using 16S rRNA gene sequencing with Illumina MiSeq technology. Non-metric multidimensional scaling (NMDS) analysis showed no clear grouping among nearby sampled sites along the shoreline. Insignificant diversion between the wet and dry season microbial communities was observed along the coast at each sampling site. A high variation at the genus level was observed, with several novel genera identified at high relative abundance in certain locations, such as JTB255 marine benthic groups OTU_4 (5.4%) and OTU_60 (3.2%), and BD7-8 marine group OTU_5 (2.9%).Hammer, ?., Jones, M.T., Schneebeli-Hermann, E., Hansen, B.B., Bucher, H., 2019. Are Early Triassic extinction events associated with mercury anomalies? A reassessment of the Smithian/Spathian boundary extinction. Earth-Science Reviews 195, 179-190. concentrations of mercury, possibly connected with widespread volcanism of the Siberian Traps, have previously been associated with the Smithian/Spathian (Early Triassic) boundary (SSB) in the Sverdrup Basin, Tethyan sections in India and China, as well as with a shallow-water record in western Spitsbergen. We confirm this Hg/TOC anomaly in the deeper water record at Wallenbergfjellet, central Spitsbergen. However, both paleontological age control and carbon isotopes indicate that the Hg anomaly occurred mainly within strata of middle Smithian age. Therefore, this Hg anomaly is unlikely to be directly and causally related to mechanisms contributing to the late Smithian global extinction of nektonic faunas. The TOC and trace element data suggest generally more oxygenated conditions during the Smithian compared to the Spathian, which is at odds with the hypothesis that oxygen depletion may have been a global kill mechanism for the SSB extinction. Further work is needed to assess if precise timing and paleogeographic distribution of anoxia shows any consistent pattern or not during the Smithian and Spathian. The very abrupt lower limb of the positive carbon isotope excursion (CIE) and the coarser grain size immediately below the boundary between the Lusitaniadalen Member and the Vendomdalen Member indicate a substantial stratigraphic gap of latest Smithian age, a previously neglected signal shared with many other boreal SSB sections. Ammonoid age control also indicates that the onset of the late Smithian gap in the high latitudes was earlier than in the Tropics. The gradual end of the positive CIE contrasts with the frequent spike shape observed in tropical shelf records and is definitively earliest Spathian in age. The middle Smithian Hg anomaly in the Boreal record is only visible in the Hg/TOC values, and is associated with a possible shift in organic matter type from terrestrial to marine in the case of Spitsbergen. This suggests that the middle Smithian Hg/TOC anomaly in Spitsbergen may not unequivocally originate from volcanism, and calls for additional caution before interpreting Hg spikes as a volcanic proxy.Han, Y., Horsfield, B., Mahlstedt, N., Wirth, R., Curry, D.J., LaReau, H., 2019. Factors controlling source and reservoir characteristics in the Niobrara shale oil system, Denver Basin. American Association of Petroleum Geologists Bulletin 103, 2045-2072. paper clarifies the controls of oil retention in the Niobrara Formation, Denver Basin, in the western United States. Sweet spots have been recognized using a total of 98 core samples from 5 wells with maturities covering the oil window.Oil retention in the source rock samples (carbonate content <70 wt. %) is controlled by organic matter richness and thermal maturity. In general, the vaporizable hydrocarbon (HC) yield at nominal temperatures at 300°C ([S1]; Rock-Eval) is positively correlated to total organic carbon (TOC). With increasing maturity, the so-called oil saturation index (S1/TOC × 100) first increases until a maximum retention capacity (100 mg HC/g TOC) is exceeded at the temperature at the maximum rate of petroleum generation by Rock-Eval pyrolysis (Tmax) of approximately 445°C and subsequently decreases. The depletion in oil retention capacity is believed to be associated with the appearance of organic nanopores.Oil retention in samples with distinct reservoir potential (carbonate >30 wt. %) is controlled by carbonate content, which is positively related to the amount of retained oil. Petrographic features indicate that oil or bitumen is stored in porous calcite fossils (i.e., coccolith and foraminifera), which provide additional space for petroleum storage. Chalk samples (carbonate >85 wt. %) are characterized by anomalously low Tmax values caused by the influence of heavy petroleum or bitumen. The amount of this bitumen is higher than the initial petroleum potential of kerogen in A and B chalks and thus must have been emplaced here. The most likely sources are juxtaposed organic-rich marl layers.Thus, sweet spots occur where carbonate content is either low (high TOC) or high (low TOC), whereas production of petroleum from the pore space of presumably brittle chalk seems more attractive than production from organic- and clay-rich rocks.Haq, B., Liu, J., Liu, K., Malaki, E., Al-Shehri, D., 2019. Modification of Eclipse simulator for microbial enhanced oil recovery. Journal of Petroleum Exploration and Production Technology 9, 2247-2261. widely used reservoir simulators include an EOR option, but there is no feature available in a commercial simulator in the oil industry that simulates microbial enhanced oil recovery (MEOR) process. Eclipse, one of the popular reservoir simulators, does not have this option. In this study the Eclipse reservoir simulator has been modified and used to simulate MEOR core-flooding experiments. The combined effects on oil recovery of anionic surfactants and alcohol, nonionic surfactants and alcohol, and anionic and nonionic surfactants blended with alcohol are examined. A commercial Eclipse simulator was modified to add the option to simulate a MEOR process as this was not available. The modified simulator was used to simulate three core-flood experiments with three formulations. The JF-2 bio-surfactant and butanol solution core-flood test was simulated. The result was slightly higher than the experimental result but compared reasonably well. The simulated tertiary and total oil recoveries of the APG and butanol solution were similar to the experimental values: the simulated TOR and total recovery were 41% and 81%, respectively, while the core-flooding TOR and total recovery were 41% and 82%. The APG, bio-surfactant and butanol combination core-flood experiment, when simulated, produced an oil recovery curve that was a reasonable match with the experimental curve.Harney, ?., Nayak, A., Patterson, N., Joglekar, P., Mushrif-Tripathy, V., Mallick, S., Rohland, N., Sedig, J., Adamski, N., Bernardos, R., Broomandkhoshbacht, N., Culleton, B.J., Ferry, M., Harper, T.K., Michel, M., Oppenheimer, J., Stewardson, K., Zhang, Z., Harashawaradhana, Bartwal, M.S., Kumar, S., Diyundi, S.C., Roberts, P., Boivin, N., Kennett, D.J., Thangaraj, K., Reich, D., Rai, N., 2019. Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India. Nature Communications 10, 3670. at over 5,000 meters above sea level in the Himalayan Mountains, Roopkund Lake is home to the scattered skeletal remains of several hundred individuals of unknown origin. We report genome-wide ancient DNA for 38 skeletons from Roopkund Lake, and find that they cluster into three distinct groups. A group of 23 individuals have ancestry that falls within the range of variation of present-day South Asians. A further 14 have ancestry typical of the eastern Mediterranean. We also identify one individual with Southeast Asian-related ancestry. Radiocarbon dating indicates that these remains were not deposited simultaneously. Instead, all of the individuals with South Asian-related ancestry date to ~800 CE (but with evidence of being deposited in more than one event), while all other individuals date to ~1800 CE. These differences are also reflected in stable isotope measurements, which reveal a distinct dietary profile for the two main groups.Harries, M.E., Huber, M.L., Bruno, T.J., 2019. A distillation approach to phase equilibrium measurements of multicomponent fluid mixtures. Energy & Fuels 33, 7908-7915. building on the Advanced Distillation Curve (ADC) approach to measuring the volatility of fuels and other fluid mixtures, the ADC with Reflux or ADCR technique was developed to address the difficulty of experimentally determining the vapor–liquid equilibrium of fluids containing many components. For fuels and other multicomponent mixtures, the ADCR collects data about the chemical compositions of both liquid and vapor phases across a range of temperatures, elucidating the two-phase region at constant pressure. Two simple mixtures were used to demonstrate the ADCR method: an n-decane/n-tetradecane binary and the Huber-Bruno surrogate, a ternary mixture designed to represent the volatility of an aviation turbine kerosene. These mixtures were chosen to test the method because they have been extensively studied and modeled in previous work. For both test fluids, the ADCR measurements of vapor–liquid equilibrium were in good agreement with model predictions. We conclude that the ADCR is a useful method for determining the T-P-x-y behavior of fluid mixtures with many components. The experimental approach presented may support the development of fuels, design of separations, and forensic sciences that use vapor analysis, especially arson fire debris analysis, by providing quantitative data with well-characterized uncertainty describing the relationships between the vapor and condensed phases of a fuel subjected to thermal weathering.Haslauer, K.E., Hemmler, D., Schmitt-Kopplin, P., Heinzmann, S.S., 2019. Guidelines for the use of deuterium oxide (D2O) in 1H NMR metabolomics. Analytical Chemistry. metabolomics, nuclear magnetic resonance (NMR) spectroscopy allows to identify and quantify compounds in biological samples. The sample preparation generally requires only few steps; however, an indispensable factor is the addition of a locking substance into the biofluid sample, such as deuterium oxide (D2O). While creatinine loss in pure D2O is well-described, the effects of different D2O concentrations on the signal profile of biological samples are unknown. In this work, we investigated the effect of D2O levels in the NMR buffer system in urine samples, in dependence on dwell time and temperature exposition. We reveal a decrease of the urinary creatinine peak area up to 35% after 24 h of dwell time at room temperature (RT) using 25% (v/v) D2O, but only 4% loss using 2.5% D2O. 1H, inverse-gated (IG) 13C, DEPT-HSQC NMR, and mass spectrometry (MS) experiments confirmed a proton–deuterium (H/D) exchange at the CH2. This leads to underestimation of creatinine levels and has an extensive effect when creatinine is used for normalization. This work offers a sample stability examination, depending on the D2O concentration, dwell time, and temperature and enables a method to correct for the successive loss. We propose an equation to correct the creatinine loss for samples prepared with various D2O concentrations and storage temperatures for dwell times up to 24 h. The correction function was validated against an external data set with n = 26 samples. To ensure sufficient creatinine stability in future studies, we suggest that a maximum of 10% D2O should be used at 4 °C or 2.5% D2O at RT, respectively.Hassan, I.A., Mohamedelhassan, E.E., Yanful, E.K., Weselowski, B., Yuan, Z.-C., 2019. Isolation and characterization of novel bacterial strains for integrated solar-bioelectrokinetic of soil contaminated with heavy petroleum hydrocarbons. Chemosphere 237, 124514. study investigated the isolation and characterization of three novel bacterial strains; Acinetobacter calcoaceticus, Sphingobacterium multivorum, and Sinorhizobium, isolated form agriculture land. From three hundred strains of bacteria, the three isolates were identified for their superior diesel degradation ability by a series of bench-scale tests. The isolates were further investigated in bench tests for their ability to grow in different diesel fuel concentrations, temperature and pH; degrade diesel fuel in?vitro; and for the identification of functional genes. Semi-pilot bioelectrokinetic tests were conducted in three electrokinetic cells. An innovative electrode configuration was adopted to stabilize the soil pH and water content during the test. The genes expressed in the diesel degradation process including Lipases enzymes Lip A, LipB, Alk-b2, rubA, P450, and 1698/2041 were detected in the three isolates. The results showed that the solar panel voltage output is in agreement with the trapezoid model. The temperatures in the cells were found to be 5–7?°C higher than the ambient temperature. The electrode configuration succeeded in stabilizing the soil pH and water content, preventing the development of a pH gradient, important progress for the survival of bacteria. The diesel degradation in the soil after bioelectrokinetic tests were 20–30%, compared to 10–12% in the controls. The study succeeded in developing environmentally friendly technology employing novel bacterial strains to degrade diesel fuel and utilizing solar panels to produce renewable energy for bioelectrokinetics during the winter season.Hatch, L.E., Jen, C.N., Kreisberg, N.M., Selimovic, V., Yokelson, R.J., Stamatis, C., York, R.A., Foster, D., Stephens, S.L., Goldstein, A.H., Barsanti, K.C., 2019. Highly speciated measurements of terpenoids emitted from laboratory and mixed-conifer forest prescribed fires. Environmental Science & Technology 53, 9418-9428. fires in the western United States are projected to increase in frequency, duration, and size. Characterized by widespread and diverse conifer forests, burning within this region may lead to significant terpenoid emissions. Terpenoids constitute a major class of highly reactive secondary organic aerosol (SOA) precursors, with significant structure-dependent variability in reactivity and SOA-formation potential. In this study, highly speciated measurements of terpenoids emitted from laboratory and prescribed fires were achieved using two-dimensional gas chromatography. Nearly 100 terpenoids were measured in smoke samples from 71 fires, with high variability in the dominant compounds. Terpenoid emissions were dependent on plant species and tissues. Canopy/needle-derived emissions dominated in the laboratory fires, whereas woody-tissue-derived emissions dominated in the prescribed fires. Such differences likely have implications for terpenoid emissions from high vs low intensity fires and suggest that canopy-dominant laboratory fires may not accurately represent terpenoid emissions from prescribed fires or wildland fires that burn with low intensity. Predicted SOA formation was sensitive to the diversity of emitted terpenoids when compared to assuming a single terpene surrogate. Given the demonstrated linkages between fuel type, fire terpenoid emissions, and the subsequent implications for plume chemistry, speciated measurements of terpenoids in smoke derived from diverse ecosystems and fire regimes may improve air quality predictions downwind of wildland fires.Hawthorne, S.B., Grabanski, C.B., Miller, D.J., Kurz, B.A., Sorensen, J.A., 2019. Hydrocarbon recovery from Williston Basin Shale and mudrock cores with supercritical CO2: 2. Mechanisms that control oil recovery rates and CO2 permeation. Energy & Fuels 33, 6867-6877. part 1 (10.1021/acs.energyfuels.9b01177), CO2 was used to recover oil from 51 source shale and reservoir mudrock cores collected from the Bakken Petroleum System in the Williston Basin. Oil hydrocarbon recoveries after 24 h exposures to CO2 at reservoir pressure and temperature were >94% for the reservoir mudrock cores and ranged from a few percent to as much as 80% for the source shales depending on the well location. In part 2, the experimental parameters that control oil recoveries were investigated, and the results show that exposed rock surface areas and CO2 contact times are primary factors controlling oil recovery at reservoir temperature and pressure. Compared to the 11.2 mm diameter rods used in part 1, increasing the surface area by splitting the rods into a stack of 2–3 mm thick “coins” doubled the oil recovery rates from both reservoir and source rocks, while further increasing the surface area using ground and sieved 1–3.4 mm samples at least tripled recovery rates. In addition, extending the exposure time for the 11.2 mm diameter source shale rods to 96 h yielded nearly complete oil recoveries (as did the 24 h exposures with the 1–3.4 mm samples), indicating that pore spaces in the source shales as well as the more permeable reservoir rocks can be accessed by the CO2 and the associated oil hydrocarbons recovered. Higher CO2 pressures yielded higher oil recoveries from both the reservoir rocks and source shales regardless of whether the exposure pressure was at or a little below, somewhat above, or substantially above the minimum miscibility pressure (MMP). Laboratory experiments also demonstrated that crude oil recoveries are based primarily on the ability of the CO2 to penetrate the rock matrix and dissolve the oil hydrocarbons via hydrocarbon vaporization into the CO2 phase rather than bulk physical processes (e.g., swelling, lowered viscosity, the physical “sweeping” effect) that are important in conventional CO2 floods. Lighter hydrocarbons (e.g., C7 to C14) were recovered at much faster rates than heavier hydrocarbons (e.g., >C20) from all rock samples and geometries as well as for all CO2 pressures tested, as might be expected because lighter hydrocarbons have both higher diffusion coefficients and higher solubilities in CO2 than heavier hydrocarbons. Limiting the amount of CO2 had little or no effect on the recovery rates of the lighter hydrocarbons but greatly reduced those of the heavier hydrocarbons. These two observations are consistent with a concentration-gradient-driven diffusion recovery mechanism. Laboratory results suggest that oil recovery in the Bakken play with CO2 will be enhanced by longer soak times, larger exposed rock surface areas, and higher pressures.Hawthorne, S.B., Miller, D.J., Grabanski, C.B., Azzolina, N., Kurz, B.A., Ardakani, O.H., Smith, S.A., Sanei, H., Sorensen, J.A., 2019. Hydrocarbon recovery from Williston Basin shale and mudrock cores with supercritical CO2: Part 1. Method validation and recoveries from cores collected across the basin. Energy & Fuels 33, 6857-6866. core samples (51) from multiple lithofacies and depths were collected from 10 wells located throughout the Bakken Petroleum System. Each 11.2 mm diameter core was exposed to CO2 for 24 h at reservoir conditions of 34.5 MPa (5000 psi) and 110 °C in a pressurized apparatus designed to mimic the fracture-dominated flow expected to occur during a CO2 injection into hydraulically fractured tight unconventional formations. The oil recovered from the rock samples was collected hourly by slowly depressurizing the CO2 into a collection solvent, while maintaining both CO2 pressure and temperature constant in the extraction chamber. Recoveries of light and heavy oils were validated by comparing rock samples before and after CO2 exposure using the extended slow heating Rock-Eval analysis. Extractions of replicate core samples from Middle Bakken (MB) tight nonshale, Upper Bakken shale (UBS), and Lower Bakken shale (LBS) gave reproducible results, demonstrating that the 11.2 mm diameter cores represent the original 10.2 cm (4 in.) core, and that the extraction and associated analysis procedures are reproducible. Recoveries of oil from the Three Forks (TF) and all MB cores ranged from 65 to >99% after 7 h of exposure and exceeded 94% for all cores at 24 h, despite median pore throat radii of only about 13 nm (MB) to 26 nm (TF). Surprisingly, significant oil was obtained from UBS and LBS cores despite the median pore throat radii of only ca. 3.5 nm, sizes that approach molecular dimensions. Although all TF and MB reservoir rocks showed high oil recoveries, the oil obtained in 24 h from UBS and LBS source rocks varied greatly for different well locations and ranged from as low as 11% to as high as 80%. Data analysis of mineralogical components, including clays, carbonates, evaporates, feldspars, and pyrite, showed that these factors were not useful to predict oil recoveries. Both total organic carbon (4–15 wt % for shales and 0.1–0.4 wt % for TF and MB) and the pore throat radii appear to control oil recovery, though they were not predictive for individual UBS and LBS cores. Results from the 51 rock core samples demonstrate that CO2 is capable of penetrating oil-bearing pores and displacing crude oil from the UBS and LBS source rocks as well as the MB and TF reservoir rocks.He, C., Lin, W., Zheng, X., Wang, C., Hu, Z., Wang, W., 2019. Synergistic effect of magnetite and zero-valent iron on anaerobic degradation and methanogenesis of phenol. Bioresource Technology 291, 121874. digestion is widely employed for treating phenol-containing wastewater, but there are still some drawbacks such as slow phenol degradation rate and vulnerable acetoclastic methanogens. Coupling of magnetite (Fe3O4) and zero valent iron (ZVI) was firstly used to enhance anaerobic digestion of phenol. The results indicated an obvious synergistic effect was generated with coupling of Fe3O4 and ZVI during the whole anaerobic digestion of phenol. The phenol degradation rate and methane production of Fe3O4/ZVI-added group were increased by 8.8–23.1% and 11.9–31.6%, respectively compared with Fe3O4-added group, and enhanced by 5.9–17.1% and 4.4–18.3%, respectively compared with ZVI-added group. ZVI improved the growth of hydrogenotrophic methanogens and Fe3O4 enhanced the growth of syntrophic acetate-oxidizing bacteria. Finally, the syntrophic interaction between acetate-oxidizing bacterium and hydrogenotrophic methanogens played a vital role on the synergistic effect of Fe3O4 and ZVI on the whole anaerobic phenol digestion.He, Q., Dong, T., He, S., Zhai, G., 2019. Methane adsorption capacity of marine-continental transitional facies shales: The case study of the Upper Permian Longtan Formation, northern Guizhou Province, Southwest China. Journal of Petroleum Science and Engineering 183, 106406. influencing the methane adsorption capacity (MAC) of marine-continental transitional facies shales have been identified applying a variety of techniques (e.g., total organic carbon (TOC) content, X-ray diffraction mineralogy, low-pressure CO2 and N2 adsorption, and methane adsorption analyses) on samples from the Upper Permian Longtan Formation, northern Guizhou Province, Southwest China. The TOC contents of the Longtan shale samples ranged between 1.2 and 9.9?wt% (average?=?3.5?wt%). The results of the bulk XRD analysis suggested that the mineralogical composition of the studied samples was different from that of typical marine shales: the samples primarily consisted of clay minerals, followed by quartz and feldspar. The Langmuir volumes (VL) of the 14 shale samples ranged from 1.02?ml/g to 5.25?ml/g (average?=?2.52?ml/g); moreover, their MAC was positively correlated with the pore volume, surface area, and TOC content, suggesting that organic matter and pore structure were the most critical factors influencing the adsorption capacity of these transitional shales. Our results showed that the MAC was not positively with the clay content; additionally, the MAC tended to increase with increasing pressure, but to decrease with increasing temperature. The presence of moisture greatly reduced the MAC. Overall, the MAC of the transitional Longtan Formation shales resulted to be quite different from that of typical marine shales (e.g., the Lower Silurian Longmaxi Formation in the Sichuan Basin) in terms of mineralogical component and abundance of organic pores. The particularly high abundance of (hydrophilic) clay minerals in the Longtan Formation transitional shales resulted in a higher number of adsorption sites occupied by water molecules than in the Longmaxi Formation and a lower MAC. Finally, the abundance of organic pores in marine shales resulted in a higher MAC than that of transitional shales.He, X., He, G., Gao, Y., Zhang, P., Lu, S., Wan, J., 2019. Geological characteristics and enrichment laws of normal-pressure shale gas in the basin-margin transition zone of SE Chongqing. Natural Gas Industry B 6, 333-346. southeastern Sichuan Basin and its basin-margin transition zone (hereinafter referred to as “the basin-margin transition zone of SE Chongqing”) is the focus of normal-pressure shale gas exploration in China. In order to summarize the geological characteristics and enrichment laws of shale gas in the basin-margin transition zone of SE Chongqing, we analyzed the geological characteristics of shale gas reservoirs in the Nanchuan–Wulong area of this transition zone from the aspects of sedimentary formation, tectonic reworking and production characteristics by using geophysical, drilling, logging and testing data, and then we compared it with the overpressure shale gas reservoirs in the Jiaoshiba Block. Finally, we explored the main factors controlling the enrichment & high yields of normal-pressure shale gas in this transition zone and their hydrocarbon accumulation patterns. And the following research results were obtained. (1) Different from the over-pressure shale gas reservoirs in Jiaoshiba Block, the normal-pressure shale gas reservoirs in this transition zone are characterized by lower organic porosities, more developed micro-fractures, higher ratios of adsorbed gas, greater differences of stresses in two directions, lower geothermal gradients, lower formation pressure coefficients, higher initial fluid production rates and higher fluid flowback rates. (2) The enrichment & high yields of normal-pressure shale gas in this area is mainly controlled by three factors, i.e., carbon-rich, silicate-rich and graptolite-rich shale, organic pores, and tectonic stress field, among which, the first factor controlled by deepwater continental shelf facies is the basis of shale gas enrichment, the second is the main controlling factor of shale gas enrichment, and the third is the key factor of high-yield shale gas. (3) The hydrocarbon accumulation patterns of normal-pressure shale gas reservoirs in the transition zone can be divided into four types, including the anticline type, the syncline type, the slope type and the reverse fault type. And the enrichment & high-yield characteristics of shale gas in different hydrocarbon accumulation patterns are also clarified. In conclusion, the research results enrich the geological theory of enrichment & high-yield laws of normal-pressure shale gas and provide a support for the exploration and development of normal-pressure shale gas in complex structures.Hegazi, A.H., Fathalla, E.M., Andersson, J.T., 2019. Organic geochemically significant high-molecular-mass sulfur compounds of North African crude oils. Energy & Fuels 33, 6995-7000. transform ion cyclotron resonance mass spectrometry was applied to the analysis of the complex distribution of sulfur compounds of North African crude oils. The sulfur compound distribution fingerprints were used for the characterization of crude oils from the Gulf of Suez and Western Desert of Egypt. Because a mass spectrometric technique was involved, the information supplied by high-molecular-mass sulfur compounds could be collected, in contrast to previous attempts that mainly used gas chromatography and low-molecular-mass sulfur compounds. The results showed large variations in the distribution of sulfur compounds in crude oils of different sources. The high relative abundance of double bond equivalent (DBE) of 6, the benzothiophene series, is associated with oil from a carbonate source rock, while a fairly equal DBE distribution was observed in a siliciclastic crude oil. A newly proposed parameter ∑DBEs/DBE of 6 is proposed and was found to be sensitive to changes in thermal maturity and correlate quite well with the American Petroleum Institute gravity. The parameter decreases with decreasing maturation.Henson, S., Le Moigne, F., Giering, S., 2019. Drivers of carbon export efficiency in the global ocean. Global Biogeochemical Cycles 33, 891-903. export of organic carbon from the surface ocean forms the basis of the biological carbon pump, an important planetary carbon flux. Typically, only a small fraction of primary productivity (PP) is exported (quantified as the export efficiency: export/PP). Here we assemble a global data synthesis to reveal that very high export efficiency occasionally occurs. These events drive an apparent inverse relationship between PP and export efficiency, which is opposite to that typically used in empirical or mechanistic models. At the global scale, we find that low PP, high export efficiency regimes tend to occur when macrozooplankton and bacterial abundance are low. This implies that a decoupling between PP and upper ocean remineralization processes can result in a large fraction of PP being exported, likely as intact cells or phytoplankton-based aggregates. As the proportion of PP being exported declines, macrozooplankton and bacterial abundances rise. High export efficiency, high PP regimes also occur infrequently, possibly associated with nonbiologically mediated export of particles. A similar analysis at a biome scale reveals that the factors affecting export efficiency may be different at regional and global scales. Our results imply that the whole ecosystem structure, rather than just the phytoplankton community, is important in setting export efficiency. Further, the existence of low PP, high export efficiency regimes imply that biogeochemical models that parameterize export efficiency as increasing with PP may underestimate export flux during decoupled periods, such as at the start of the spring bloom.Hernandez, H.W., Perrard, A., Mendoza Gonzalez, E., Ehlert, W., Trabelsi, S., 2019. Advantages of using a microemulsion to remove crude oil residue from solid surfaces, in: Rahimi, P., Ovalles, C., Zhang, Y., Adams, J.J. (Eds.), Chemistry Solutions to Challenges in the Petroleum Industry. American Chemical Society, Washington DC, pp. 23-36. often precipitate, because of changes in pressure, temperature, and composition, and then deposit on rock surfaces, altering the wettability and plugging formation pores. This deposition has a detrimental effect on relative permeability and oil production. This chapter shows the advantages of using a microemulsion to remove crude oil residue from solid surfaces using two innovative experimental techniques. The first technique consists of using the Shaken Bottle test to quantify the removal of asphaltenic residues from baked crude oil–coated sand. The second technique consists of using microfluidics to visualize asphaltene residue deposition into model two-dimensional porous media followed by application of a diluted microemulsion. Asphaltenes removal was quantified by analyzing images taken before and after microemulsion treatment using image analysis software. In both techniques, the diluted microemulsion removed a large amount of the asphaltenes deposited on the surface. The amount of removal was strongly dependent on microemulsion concentration, solvent type and content within the microemulsion, surfactant type, and soaking time. Both techniques can be used to effectively quantify removal of asphaltenes from solid surfaces. These results are expected to have a significant impact in completing and restimulating wells.Hertzog, J., Carré, V., Aubriet, F., 2019. Chapter 22 - Contribution of Fourier transform mass spectrometry to bio-oil study, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 679-733. obtained from the thermochemical conversion of the lignocellulosic biomass are potential sources of renewable materials (bio-fuels, chemicals, …). However, their high chemical complexity and the high amount of oxygenated compounds limit their ready-to-use capacity. Upgrading treatments, such as deoxygenation and/or cracking, have to be applied. In order to assess the most suited and the most efficient upgrading process, it is necessary to obtain an extensive composition description of the bio-oils at all processing stages. In this respect, the non-targeted approach, using Fourier transform high-resolution mass spectrometry combined with different ionization sources, has demonstrated its great abilities to characterize thousands of bio-oil components over a large range of mass and polarity. In this chapter, an exhaustive review of the studies performed in this field will be presented. To define the main challenges related to the bio-oil characterization, some relevant information will be briefly given in regards to the biomass composition and the used processes that ensure its conversion into bio-oils. Additionally, information achieved by “classical” analytical methods will be presented. This will allow demonstrating the contribution of high-resolution Fourier transform mass spectrometry (FTMS) analyses to characterization of bio-oils.Heuer, R.M., Galli, G.L.J., Shiels, H.A., Fieber, L.A., Cox, G.K., Mager, E.M., Stieglitz, J.D., Benetti, D.D., Grosell, M., Crossley II, D.A., 2019. Impacts of Deepwater Horizon crude oil on mahi-mahi (Coryphaena hippurus) heart cell function. Environmental Science & Technology 53, 9895-9904. Horizon crude oil is comprised of polycyclic aromatic hydrocarbons that cause a number of cardiotoxic effects in marine fishes across all levels of biological organization and at different life stages. Although cardiotoxic impacts have been widely reported, the mechanisms underlying these impairments in adult fish remain understudied. In this study, we examined the impacts of crude oil on cardiomyocyte contractility and electrophysiological parameters in freshly isolated ventricular cardiomyocytes from adult mahi-mahi (Coryphaena hippurus). Cardiomyocytes directly exposed to oil exhibited reduced contractility over a range of environmentally relevant concentrations (2.8–12.9 μg l–1∑PAH). This reduction in contractility was most pronounced at higher stimulation frequencies, corresponding to the upper limits of previously measured in situ mahi heart rates. To better understand the mechanisms underlying impaired contractile function, electrophysiological studies were performed, which revealed oil exposure prolonged cardiomyocyte action potentials and disrupted potassium cycling (9.9–30.4 μg l–1∑PAH). This study is the first to measure cellular contractility in oil-exposed cardiomyocytes from a pelagic fish. Results from this study contribute to previously observed impairments to heart function and whole-animal exercise performance in mahi, underscoring the advantages of using an integrative approach in examining mechanisms of oil-induced cardiotoxicity in marine fish.Higgs, B., Mountjoy, J.J., Crutchley, G.J., Townend, J., Ladroit, Y., Greinert, J., McGovern, C., 2019. Seep-bubble characteristics and gas flow rates from a shallow-water, high-density seep field on the shelf-to-slope transition of the Hikurangi subduction margin. Marine Geology 417, 105985. analyse an area of high density submarine methane gas seeps situated on the shelf to slope transition (130–420?m water depth) on the northern region of New Zealand's Hikurangi margin, off Poverty Bay. Multibeam and singlebeam echo sounder data collected in 2014 and 2015 revealed >600 seeps, at much greater density than any previously mapped areas of seepage on the Hikurangi margin. To broadly constrain the output of methane from these seeps, we have estimated the flow of methane at individual seeps, utilising perspective-measurements applied to still frames from a deep towed camera system to measure the dimensions of rising bubbles. We combine bubble size and rise-rate distributions with singlebeam acoustic data to estimate gas flow rates at six selected seeps sites. Our results predict a wide range (3.0–2249?mL/min) of methane release into the water column. If we assume that the six seeps we analysed are representative of the entire seep population, and that gas flow is constant, we can extrapolate across the seep field and infer a gas release of 30 to 2415?t of methane per year into the ocean.Hill, A.H., Fu, D., 2019. Cellular imaging using stimulated Raman scattering microscopy. Analytical Chemistry 91, 9333-9342. imaging is an active area of research that enables researchers to monitor cellular dynamics, as well as responses to various external stimuli (physiological stress, exogenous compounds, etc.). Stimulated Raman scattering (SRS) microscopy is one popular experimental tool used to image cells, largely because of its chemical specificity, high spatial resolution, and high image acquisition speed. In this Perspective, the theoretical background and experimental implementation of SRS microscopy are discussed and recent developments in the field of cellular imaging with SRS are highlighted and summarized.Hines, S.K.V., Eiler, J.M., Southon, J.R., Adkins, J.F., 2019. Dynamic intermediate waters across the late glacial revealed by paired radiocarbon and clumped isotope temperature records. Paleoceanography and Paleoclimatology 34, 1074-1091. radiocarbon and clumped isotope temperature records from U/Th‐dated Desmophyllum dianthus corals in the North Atlantic and Southern Ocean provide unique information about the history of intermediate waters (～1,500–1,700 m) across the late glacial and deglaciation (～35–10 ka). These measurements allow for the construction of radiocarbon‐temperature crossplots, which help to identify water mass endmembers at different times across the deglaciation. Radiocarbon and temperature values from the late glacial fall outside the range of modern ocean data from near the sample collection sites. In the North Atlantic, radiocarbon values tend to be much older than the modern, while in the Southern Ocean, they are more often younger than the modern. Reconstructed temperatures vary around respective modern ocean values; however, warm waters are observed at the Last Glacial Maximum and across the deglaciation in the north and south. We interpret our data in the context of the modern hydrography of the Western North Atlantic and Southern Ocean, and we draw upon direct comparisons between sediment core‐derived reconstructions of ocean circulation from the South Indo‐Pacific and our deep‐sea coral data from the Southern Ocean. Our North Atlantic data support accepted patterns of reduced North Atlantic Deep Water formation during Heinrich Stadials 1 and 2. In the Southern Ocean, deep‐sea coral populations respond to changes in ocean structure that are also reflected in a depth profile of δ13C data from New Zealand, and data indicate that there was less influence of Pacific Deep Water between 1,500 and 1,700 m south of Tasmania across much of the deglaciation.Hippke, M., 2019. Spaceflight from Super-Earths is difficult. International Journal of Astrobiology 18, 393-395. rocky exoplanets are heavier and larger than the Earth and have higher surface gravity. This makes space-flight on these worlds very challenging because the required fuel mass for a given payload is an exponential function of planetary surface gravity, exp(g0). We find that chemical rockets still allow for escape velocities on Super-Earths up to 10× Earth mass. More massive rocky worlds, if they exist, would require other means to leave the planet, such as nuclear propulsion. This is relevant for space colonization and the search for extraterrestrial intelligence.Hoepfner, M.P., Yang, Y., 2019. Ultra-small-angle X-ray scattering as a probe of petroleum heterogeneities from the nano- to the macroscale, in: Rahimi, P., Ovalles, C., Zhang, Y., Adams, J.J. (Eds.), Chemistry Solutions to Challenges in the Petroleum Industry. American Chemical Society, Washington DC, pp. 67-87. techniques are invaluable for the study of self-association and structure of soft systems. The properties and phase behavior of petroleum asphaltenes have long been investigated using small-angle X-ray and neutron scattering. However, these techniques conventionally fail to assess structures >50 nm, and significant uncertainty about the mechanisms of asphaltene phase transitions persists. Recently, ultra-small-angle X-ray scattering (USAXS) was applied to precipitating asphaltene systems to characterize the size and morphology of growing asphaltene insoluble particles. USAXS is a powerful technique that allows researchers to probe the size and structure of matter up to sizes of 5 μm. When paired with traditional pinhole small-angle X-ray scattering, a single experiment can characterize structures spanning 1 nm to 5 μm with time resolution on the order of minutes. This powerful combination has to date only been applied to a few petroleum systems, but the findings have been significant. Specifically, it has long been unclear how asphaltenes precipitate. Colloidal aggregation, liquid–liquid transitions, and solid–liquid transitions have all been used to model the process. Recent USAXS experiments have revealed that the open fractal structure of soluble asphaltenes collapses and a new liquid–liquid interface slowly forms. These new asphaltene-rich droplets flocculate into structures >1 μm in size and are what is conventionally viewed under optical microscopy. The power of USAXS and other scattering techniques is the ability not only to assess the size of heterogeneities in liquid environments, but also to probe the internal structure, overall shape, and surface morphology. The capabilities of this powerful new approach are now being applied to understand the influence of chemical inhibitors to alter the structure and rate of the precipitation process. The unmatched capabilities of USAXS on probing insoluble asphaltene properties and other heterogeneities in petroleum may usher in a new era of understanding in traditionally challenging fields.Holder, R.M., Viete, D.R., Brown, M., Johnson, T.E., 2019. Metamorphism and the evolution of plate tectonics. Nature 572, 378-381.’s mantle convection, which facilitates planetary heat loss, is manifested at the surface as present-day plate tectonics. When plate tectonics emerged and how it has evolved through time are two of the most fundamental and challenging questions in Earth science. Metamorphic rocks—rocks that have experienced solid-state mineral transformations due to changes in pressure (P) and temperature (T)—record periods of burial, heating, exhumation and cooling that reflect the tectonic environments in which they formed. Changes in the global distribution of metamorphic (P, T) conditions in the continental crust through time might therefore reflect the secular evolution of Earth’s tectonic processes. On modern Earth, convergent plate margins are characterized by metamorphic rocks that show a bimodal distribution of apparent thermal gradients (temperature change with depth; parameterized here as metamorphic T/P) in the form of paired metamorphic belts, which is attributed to metamorphism near (low T/P) and away from (high T/P) subduction zones. Here we show that Earth’s modern plate tectonic regime has developed gradually with secular cooling of the mantle since the Neoarchaean era, 2.5 billion years ago. We evaluate the emergence of bimodal metamorphism (as a proxy for secular change in plate tectonics) using a statistical evaluation of the distributions of metamorphic T/P through time. We find that the distribution of metamorphic T/P has gradually become wider and more distinctly bimodal from the Neoarchaean era to the present day, and the average metamorphic T/P has decreased since the Palaeoproterozoic era. Our results contrast with studies that inferred an abrupt transition in tectonic style in the Neoproterozoic era (about 0.7 billion years ago) or that suggested that modern plate tectonics has operated since the Palaeoproterozoic era (about two billion years ago) at the latest.Horai, S., Yamauchi, N., Naraoka, H., 2019. Simultaneous total analysis of core and polar membrane lipids in archaea by high-performance liquid chromatography/high-resolution mass spectrometry coupled with heated electrospray ionization. Rapid Communications in Mass Spectrometry 33, 1571-1577.: Archaea have characteristic membrane lipids including diether and/or tetraether isoprenoidal core lipids with various polar head groups. Since the polar group is removed soon after the end of archaeal activity, the occurrences of core and polar lipids are regarded as dead and active signals, respectively. The core and polar lipids have generally been analyzed separately using atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI), respectively, coupled with mass spectrometry.Methods: In this study, simultaneous analyses of core and polar archaeal lipids have been examined using heated electrospray ionization (HESI) by high‐performance liquid chromatography/high‐resolution mass spectrometry (HPLC/HRMS).Results: Both core and intact polar lipids can be analyzed simultaneously by HESI with good sensitivity (sub ng to 100?ng) and separation using a semi‐bore diol column by normal‐phase chromatography. The core lipids eluted firstly to separate archeaol, then glycerol dibiphytanyl glycerol tetraethers (GDGTs), followed by the polar lipids with glycosides and glycophosphates. The relative GDGT composition is identical between HESI and APCI methods.Conclusions: The simultaneous analysis has the benefit of minimizing sample amount and elution solvent as well as preparation work. The method can also be applied to a compound class fractionation for compound‐specific carbon and hydrogen isotope analysis.Horan, K., Hilton, R.G., Dellinger, M., Tipper, E., Galy, V., Calmels, D., Selby, D., Gaillardet, J., Ottley, C.J., Parsons, D.R., Burton, K.W., 2019. Carbon dioxide emissions by rock organic carbon oxidation and the net geochemical carbon budget of the Mackenzie River Basin. American Journal of Science 319, 473-499. exposure of organic carbon in rocks to oxidative weathering can release carbon dioxide (CO2) to the atmosphere and consume atmospheric oxygen. Alongside volcanism, metamorphism, and the weathering of carbonate minerals by sulfuric acid, this is a major source of atmospheric CO2 over million year timescales. The balance between CO2 release and CO2 drawdown by silicate weathering and organic carbon burial sets the net geochemical carbon budget during weathering and erosion. However, the rates of rock-derived organic carbon (petrogenic organic carbon, OCpetro) oxidation remain poorly constrained. Here, we use rhenium as a proxy to trace and quantify CO2 release by OCpetro oxidation in the Mackenzie River Basin, Canada, where the other carbon fluxes have been well constrained previously. River water and sediment samples were collected between 2009 and 2013 at gauging stations along the Mackenzie River and its main tributaries (Liard, Peel and Arctic Red). To assess rhenium inputs from silicate, sulfide and OCpetro mineral phases we normalize dissolved rhenium concentrations, [Re]diss, to sodium and sulfate ion concentrations. This approach suggests that >85 percent of [Re]diss is derived from OCpetro in the main river channels. [Re]diss and water discharge measurements are used to quantify dissolved Re yields. River sediments provide a measure of the Re to OCpetro ratio of materials undergoing weathering in the basin, and agree well with published rock samples. Dissolved Re yields are combined with river sediment [Re]/[OCpetro] ratios to estimate the CO2 emissions by OCpetro weathering. These are 0.45 +0.19/?0.11 metric tonnes of carbon, tC km?2 yr?1for the Mackenzie River at Tsiigehtchic (3.8 +1.5/?0.9 × 104 moles km?2 yr?1), and 0.94 +0.41/?0.26 tC km?2 yr?1, 0.78 +0.35/?0.21 tC km?2 yr?1 and 1.01 +0.42/?0.25 tC km?2 yr?1 for the Peel, Arctic Red and Liard catchments, respectively. When considered alongside published silicate and carbonate weathering rates and the sedimentary burial of biospheric organic carbon, these data suggest that the upper part of the Mackenzie River Basin presently acts as an atmospheric CO2 sink of ～1 tC km?2 yr?1 (～8 × 104 moles km?2 yr?1) as a result of the carbon transfers by weathering and erosion. During the Last Glacial Maximum, it is possible that the net geochemical carbon balance may have been very different: potential increases in CO2 emissions from oxidative weathering of OCpetro and carbonate minerals, coupled with reduced biospheric carbon burial, may have tipped the balance to a net source of CO2.Horst, A., Bonifacie, M., Bardoux, G., Richnow, H.H., 2019. Isotopic characterization (2H, 13C, 37Cl, 81Br) of abiotic degradation of methyl bromide and methyl chloride in water and implications for future studies. Environmental Science & Technology 53, 8813-8822. bromide (CH3Br) and methyl chloride (CH3Cl) significantly contribute to stratospheric ozone depletion. The atmospheric budgets of both compounds are unbalanced with known degradation processes outweighing known emissions. Stable isotope analysis may be capable to identify and quantify emissions and to achieve a balanced budget. Degradation processes do, however, cause isotope fractionation in methyl halides after emission and hence knowledge about these processes is a crucial prerequisite for any isotopic mass balance approach. In the current study, triple-element isotope analysis (2H, 13C, 37Cl/81Br) was applied to investigate the two main abiotic degradation processes of methyl halides (CH3X) in fresh and seawater: hydrolysis and halide exchange. For CH3Br, nucleophilic attack by both H2O and Cl– caused significant primary carbon and bromine isotope effects accompanied by a secondary inverse hydrogen isotope effect. For CH3Cl only nucleophilic substitution by H2O was observed at significant rates causing large primary carbon and chlorine isotope effects and a secondary inverse hydrogen isotope effect. Observed dual-element isotope ratios differed slightly from literature values for microbial degradation in water and hugely from radical reactions in the troposphere. This bodes well for successfully distinguishing and quantifying degradation processes in atmospheric methyl halides using triple-element isotope analysis.Hou, M., Wu, W., Cohen, D.J., Zhou, Y., Zeng, Z., Huang, H., Zheng, H., Ge, Q., 2019. Evidence for a widespread climatic anomaly at around 7.5-7.0 cal ka BP. Climate of the Past Discussions 2019, 1-50. climate event at 7.5–7.0?cal?ka?BP (thousand calibrated years before present) has been recognized. This event is important for foreseeing the possible response of the climate system to global warming and for interpreting considerable societal change, but it has heretofore lacked a systematic review. Here, we summarize previously published paleoclimate records spanning this event from 47 sites around the world. The proxy evidence from a variety of paleo-archives, including lake sediments, speleothems, marine sediments, and ice cores, provides a clear picture of this climate change. The synthesis results show a weaker Asian summer monsoon, in contrast to a stronger South American summer monsoon during the event. The event also involves dramatic cooling and wetter conditions in north-central Europe and in western North America, widespread aridity across Africa, contrasting patterns of precipitation variability throughout the Mediterranean, and notable cooling over the polar region, suggesting that it is a worldwide climate event. Comparison of paleoclimate records with climate-forcing time series gives likely climate controls for the event. The close correspondence in time of solar irradiance minima, strong volcanic eruptions, the meltwater flux into the North Atlantic, an orbitally induced decrease in solar insolation, and climate changes indicated by proxy data suggest possible linkages. More quantitative reconstructions and higher resolution climate records are needed to fully capture the magnitude, timing, duration, and nature of this event, which will be of considerable relevance to modeling.Hou, Y., Li, Y., Liu, Y., Li, G., Zhang, Z., 2019. Effects of polycyclic aromatic hydrocarbons on the UV-induced fluorescence spectra of crude oil films on the sea surface. Marine Pollution Bulletin 146, 977-984. the main fluorescent substances in oils, polycyclic aromatic hydrocarbons (PAHs) are the basis of ultraviolet (UV)-induced fluorescence spectroscopy methods to detect oil films on the sea surface. The relative contents of PAHs in six crude oil samples and their effects on ultraviolet fluorescence spectra were studied. The PAHs were divided into four categories according to their fluorescence characteristics. Naphthalene series dominated the fluorescence spectra, which led to a main peak at 320–350?nm, but this showed no relationship with PAH content. The six oil samples could not be distinguished by differences in the fluorescence spectra in this range, but could be distinguished by the fluorescence spectra in the 350–380?nm band. The relative contents of dibenzothiophene and phenanthrene series showed significant positive correlations (R2?=?0.96) with fluorescence intensity. Fluorescence spectroscopy combined with GC–MS can be used to distinguish and identify crude oils.Howarth, R.W., 2019. Ideas and perspectives: Is shale gas a major driver of recent increase in global atmospheric methane? Biogeosciences 16, 3033-3046. has been rising rapidly in the atmosphere over the past decade, contributing to global climate change. Unlike the late 20th century when the rise in atmospheric methane was accompanied by an enrichment in the heavier carbon stable isotope (13C) of methane, methane in recent years has become more depleted in 13C. This depletion has been widely interpreted as indicating a primarily biogenic source for the increased methane. Here we show that part of the change may instead be associated with emissions from shale-gas and shale-oil development. Previous studies have not explicitly considered shale gas, even though most of the increase in natural gas production globally over the past decade is from shale gas. The methane in shale gas is somewhat depleted in 13C relative to conventional natural gas. Correcting earlier analyses for this difference, we conclude that shale-gas production in North America over the past decade may have contributed more than half of all of the increased emissions from fossil fuels globally and approximately one-third of the total increased emissions from all sources globally over the past decade.Hu, X., Chen, L., Qi, L., Lei, Z., Luo, Y., 2019. Marine shale reservoir evaluation in the Sichuan Basin-A case study of the Lower Silurian Longmaxi marine shale of the B201 well in the Baoluan area, southeast Sichuan Basin, China. Journal of Petroleum Science and Engineering 182, 106339. on the total organic matter (TOC) content, brittle minerals (quartz?+?feldspar) content, total gas content, porosity and production data of eight vertical and twenty-three horizontal shale gas wells in the Sichuan Basin, a new reservoir evaluation method for the marine shale reservoirs of the Sichuan Basin is developed. In this study, based on the analytic hierarchy process (AHP) and deviation method, a comprehensive evaluation index (CEI) was proposed to evaluate the marine shale reservoir. According to the CEI and the production data, three type marine shale reservoirs were proposed. The CEI was applied to evaluate the Wufeng-Longmaxi marine shale of the B201 well. The results show that the Wufeng-Longmaxi marine shale is the low quality shale reservoir. The comprehensive evaluation criteria proposed in this study can also be applied to evaluate the marine shale reservoirs in other areas in the Sichuan Basin through the verification of several other shale gas wells in the Sichuan Basin.Hu, Y., Hao, M., Chen, G., Sun, R., Li, S., 2019. Technologies and practice of CO2 flooding and sequestration in China. Petroleum Exploration and Development 46, 753-766. latest advancement of CO2 flooding and sequestration theory and technology in China is systematically described, and the future development direction is put forward. Based on the geological characteristics of continental reservoirs, five theories and key technologies have been developed: (1) Enriched the understandings about the mass transfer characteristics of components between CO2 and crude oil in continental reservoirs, micro-flooding mechanism and sequestration mechanism of different geological bodies. (2) Established the design method of reservoir engineering parameters, injection-production control technology and development effect evaluation technology of CO2 flooding, etc. (3) Developed a series of production engineering technologies such as separated layer CO2 injection technology, high efficiency lifting technology, on-line wellbore corrosion monitoring and protection technology. (4) Innovated a series of surface engineering technology including CO2 capture technology, pipeline CO2 transportation, CO2 surface injection, and production gas circulation injection, etc. (5) Formed a series of supporting technologies including monitoring, and safety and environmental protection evaluation of CO2 flooding reservoir. On this basis, the technological development directions in the future have been put forward: (1) Breakthrough in low-cost CO2 capture technology to provide cheap CO2 gas source; (2) Improve the miscibility technology between CO2 and crude oil to enhance oil displacement efficiency; (3) Improve CO2 sweeping volume; (4) Develop more effective lifting tools and technologies; (5) Strengthen the research of basic theory and key technology of CO2 storage monitoring. CO2 flooding and sequestration in the Jilin Oilfield shows that this technology has broad application prospects in China.Huang, T., Chen, D., Fu, Y., Yeasmin, R., Guo, C., 2019. Development and evolution of a euxinic wedge on the ferruginous outer shelf of the early Cambrian Yangtze sea. Chemical Geology 524, 259-271. early Cambrian was a critical interval in geological history and featured profound oceanic and biotic changes. To unravel the oceanic redox conditions, high-resolution analyses of iron speciation and redox-sensitive trace elements (Mo and U) within the framework of sequence stratigraphy were carried out on the Niutitang Formation (~528–521?Ma). The two examined sections, the Daotuo and Bahuang sections, were respectively located in a mid-upper slope setting and a lower slope to basin settings behind a seaward submerged sill on the middle Yangtze Block, South China. At Daotuo, the Fepy/FeHR values display moderate positive covariances with the total organic carbon contents (TOC) and the Mo/TOC ratios, notably in the basal part of the Niutitang Formation. Therefore, at this locality the euxinic water mass wedge was developed in association with a high primary organic productivity/burial rate, likely within a high-productivity zone. In contrast, at Bahuang, the Fepy/FeHR values show weak to negative covariances with the Mo/TOC ratios and TOC contents in the basal part, indicating that the biogeochemical cycles of Fe, Mo with C were decoupled in a lower-productivity, ferruginous deeper basinal setting. These spatial changes in marine redox structures and biogeochemical cycles can be reasonably explained by the existence of oceanic upwelling in the presence of strong offshore currents and a seaward submarine sill, reconciling the oxygen minimum zone (OMZ) in modern oceanic margins to some extent. This spatial redox pattern also accounts well for previous data based on which the euxinic state intermittently invaded upward onto the shelf margin and evolved into a ferruginous-dominant anoxia in the inner shelf subbasins. In addition, the euxinic wedge dynamically fluctuated upslope and downslope along the transect from the ferruginous outer shelf slope to the basin in response to rise and fall of sea-level. Consequently, the temporal evolution of the redox conditions was driven in part by eustatic variations. Moreover, the paleogeographic position of the Yangtze Block in the mid-lower latitudes suggests that the block was associated with relatively strong offshore currents induced by trade winds, which notably enhanced the oceanic upwelling near the transgression maximum. On the other hand, the dominance of deep ferruginous waters with the local occurrence of a euxinic wedge on the outer shelf slope indicates relatively low concentrations of seawater sulfate and atmospheric oxygen during the deposition of the Niutitang black shales. This redox model thus highlights the important roles of paleogeographic, paleoclimatic and eustatic sea-level changes in controlling the spatiotemporal fluctuations in marine redox conditions and biogeochemical cycling in the early Cambrian ocean.Huang, X., Jiang, J., Zhang, Y., Zhan, L., Liu, C., Xiong, C., Nie, Z., 2019. A miniature particle mass spectrometer. Analytical Chemistry 91, 9393-9397. play important roles in our life. Besides chemical compositions and morphology, the size of microparticles will also decide their behavior in the environment or in organisms. Weighing the mass of microparticles by mass spectrometry is a useful method to characterize their size. In this technical note, a miniature particle mass spectrometer with an aerodynamic desorption/ionization ion source has been developed. We used a compact main control board to produce an ac voltage for trapping and ejecting the particles. The sampling process and data acquisition were also controlled by this board. We utilized this instrument to measure polystyrene spheres, silica particles, and mice red blood cells. Mass distributions of these particles were obtained rapidly with good accuracy.Huang, X., Li, A., Li, X., Liu, Y., 2019. Influence of typical core minerals on tight oil recovery during CO2 flooding using the nuclear magnetic resonance technique. Energy & Fuels 33, 7147-7154. flooding is widely recognized as an efficient way of developing tight reservoirs. Multiple types of minerals in tight rocks may interact with introduced CO2, resulting in more complex mechanisms of tight reserve recovery from tight reservoirs. It is necessary to reveal the impact of core minerals on tight oil recovery, which is critical in understanding the fundamental mechanisms of CO2 flooding for enhanced tight reserve recovery. In this work, 18 tight core samples, retrieved from the Changqing oilfield, are characterized to obtain their mineral compositions. Three typical core samples are then selected to conduct CO2 flooding and investigate how the minerals contained in these tight cores affect the tight oil recovery during CO2 flooding using the nuclear magnetic resonance technique. On the basis of the characterization results, Changqing tight cores mainly contain three typical minerals, i.e., illite, montmorillonite, and quartz. With regard to illite-dominated cores, CO2 is not efficient in extracting oil from the smaller pores when the injection pressure is lower than the minimum miscible pressure (MMP); on the contrary, crude oil can be efficiently recovered from both the smaller and larger pores when the injection pressure is beyond the MMP. With regard to the montmorillonite-dominated core, oil saturation in the medium pores increases when CO2 is injected. However, with regard to the quartz-dominated core, oil residing in both the smaller and larger pores is significantly recovered after CO2 injection. This work may help understand the question of how the minerals residing in core samples affect oil recovery from a pore-scale perspective.Huang, Y., Zheng, L., 2019. Hydrocarbon accumulation in deep water areas of Angola in West Africa. Petroleum Research 4, 268-275. comprehensive analysis of source rocks and hydrocarbon geochemical data of several offshore blocks in Angola, two sets of source rocks in the Cretaceous Iabe Formation and Lower Oligocene Malembo Formation are developed in the suprasalt structures in deep water area. The source rocks in the Cretaceous Iabe Formation is dominated by Type I kerogen, while the source rocks in the Lower Oligocene Malembo Formation is dominated by Type II–III kerogen which mainly generate gas. In the extensional zone, the source rocks in the Malembo Formation are mature and the source rocks in the Iabe Formation are post-matured; this zone undergo multi-stage filling, and the Oligocene paleoreservoirs experience high-temperature pyrolysis to form gas reservoirs; the Upper Miocene reservoirs undergo biodegradation due to poor storage condition. In the transitional zone, oil and gas in the drape anticline area are mainly from the Iabe Formation, and it mix with a small amount of oil and gas from the Malembo Formation in the later stage. In the compression zone, the crude oil is from the Iabe Formation at the mature stage, and contains a small amount of dissolved gas generated by thermal degradation.Huangfu, Y., Kang, Y., Deng, Z., Li, G., Mao, D., Liu, H., Zhao, Q., Sun, T., 2019. Low coal rank coalbed methane accumulation model and exploration direction. Acta Petrolei Sinica 40, 786-797. coal rank coalbed methane resources are rich in China, but are less known and explored; there is still insufficient understanding of the main controlling factors and enrichment laws of coalbed methane accumulation. Based on analyzing the variation trends in the gas content of low coal rank coalbed methane changing with depths in different basins and blocks worldwide, this paper explores the premise of low coal rank coalbed methane accumulation in terms of the present and ancient hydrogeological conditions, and also analyzes the impact of coal-forming environment on gas content. Research indicates:(1) Low rank coals (Ro<0.65%) are mainly distributed in the Mesozoic and Cenozoic coal measures strata with buried depth<1200 m, and low rank coalbed methane is mainly dominated by secondary biogenic gas. (2) The gas content of low rank coal tend to increase firstly and then decrease with the buried depth, generally showing an optimal depth. The present hydrogeological conditions of fresh water infiltration or paleo-fresh water infiltration are the preconditions for secondary biogas generation. (3) In addition to the formation and enrichment of low coal rank coalbed methane controlled by hydrogeological conditions for freshwater infiltration, the reservoir characteristics such as coal-rock component, coal seam thickness, coal-rock top lithology and coal-rock physical properties also have an important influence on gas content. (4) Low coal rank coalbed methane presents two accumulation modes, i.e., the Neogene hydrocarbon accumulation in marginal slope zone of the basin and the paleo-accumulation in small fault depressions, indicating two directions of low coal rank coalbed methane exploration.Huba, A.K., Mirabelli, M.F., Zenobi, R., 2019. Understanding and optimizing the ionization of polycyclic aromatic hydrocarbons in dielectric barrier discharge sources. Analytical Chemistry 91, 10694-10701. aspects of undoped and dopant-assisted dielectric barrier discharge ionization (DBDI) were here addressed to help overcome the suboptimal ionization efficiency of nonpolar species. In the absence of dopants, polycyclic aromatic hydrocarbons (PAHs) mostly form [M + H]+ rather than [M]+? ions. Humidity was shown to further increase the relative amount of protonated PAHs, while the introduction of other dopants, such as fluorobenzene and chlorobenzene, shifted the ionization toward radical cations. The source of the protons was clarified through the use of deuterated species and confirmed both water as well as dopants as potential sources. The type of plasma gas also influenced the ionization, with the relative amount of radical cations increasing from CO2, to N2, to air. The addition of SF6 gas and the relative amount of low-energy (0–11 eV) electrons in the source suggests that Penning ionization leads to the relatively high amount of radical cations in air plasma. Penning ionization of excess dopant to form radical dopant species, and subsequent charge exchange with the PAHs, is proposed as the principal ionization mechanism for the formation of radical cationic PAHs in dopant-assisted DBDI. Benzylamine “thermometer molecules” were used to evaluate the energy involved in the ionization process and showed that dopants can affect the internal energy (?39.4 kJ mol–1 with humidity in a nitrogen plasma and +15.7 kJ mol–1 with fluorobenzene in an air plasma). A deeper understanding of fundamental aspects, especially of dopant-assisted ionization in a dielectric barrier discharge source, will be vital for future method optimization, particularly with regards to difficult to ionize (e.g., nonpolar) species.Humborg, C., Geibel, M.C., Sun, X., McCrackin, M., M?rth, C.-M., Stranne, C., Jakobsson, M., Gustafsson, B., Sokolov, A., Norkko, A., Norkko, J., 2019. High emissions of carbon dioxide and methane from the coastal Baltic Sea at the end of a summer heat wave. Frontiers in Marine Science 6, 493. doi: 10.3389/fmars.2019.00493. summer heat wave in 2018 led to the highest recorded water temperatures since 1926 – up to 21°C – in bottom coastal waters of the Baltic Sea, with implications for the respiration patterns in these shallow coastal systems. We applied cavity ring-down spectrometer measurements to continuously monitor carbon dioxide (CO2) and methane (CH4) surface-water concentrations, covering the coastal archipelagos of Sweden and Finland and the open and deeper parts of the Northern Baltic Proper. This allowed us to (i) follow an upwelling event near the Swedish coast leading to elevated CO2 and moderate CH4 outgassing, and (ii) to estimate CH4 sources and fluxes along the coast by investigating water column inventories and air-sea fluxes during a storm and an associated downwelling event. At the end of the heat wave, before the storm event, we found elevated CO2 (1583 μatm) and CH4 (70 nmol/L) concentrations. During the storm, a massive CO2 sea-air flux of up to 274 mmol m–2 d–1 was observed. While water-column CO2 concentrations were depleted during several hours of the storm, CH4 concentrations remained elevated. Overall, we found a positive relationship between CO2 and CH4 wind-driven sea-air fluxes, however, the highest CH4 fluxes were observed at low winds whereas highest CO2 fluxes were during peak winds, suggesting different sources and processes controlling their fluxes besides wind. We applied a box-model approach to estimate the CH4 supply needed to sustain these elevated CH4 concentrations and the results suggest a large source flux of CH4 to the water column of 2.5 mmol m–2 d–1. These results are qualitatively supported by acoustic observations of vigorous and widespread outgassing from the sediments, with flares that could be traced throughout the water column penetrating the pycnocline and reaching the sea surface. The results suggest that the heat wave triggered CO2 and CH4 fluxes in the coastal zones that are comparable with maximum emission rates found in other hot spots, such as boreal and arctic lakes and wetlands. Further, the results suggest that heat waves are as important for CO2 and CH4 sea-air fluxes as the ice break up in spring.Hurley, S.J., Close, H.G., Elling, F.J., Jasper, C.E., Gospodinova, K., McNichol, A.P., Pearson, A., 2019. CO2-dependent carbon isotope fractionation in Archaea, Part II: The marine water column. Geochimica et Cosmochimica Acta 261, 383-395. carbon isotope ratios of archaeal glycerol dibiphytanyl glycerol tetraether (GDGT) lipids have been proposed as a proxy to infer past changes in the carbon isotope composition (δ13C) of dissolved inorganic carbon (DIC). The premise for paleo-δ13CDIC reconstructions from GDGTs is based on observations of relatively constant δ13CGDGT values in recent depositional environments. Marine Thaumarchaeota, thought to be the dominant source of GDGTs to marine sediments, fix inorganic carbon using the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) pathway, which is specific to HCO3– as the substrate. Bicarbonate-dependent autotrophy has been the basis for predicting that the stable carbon isotopic composition of GDGTs (δ13CGDGT) should vary in parallel with water column δ13CDIC values, because HCO3– is by far the dominant fraction of DIC in modern seawater. However, this relationship has never been systematically tested. Here we examine the carbon isotopic composition of GDGTs from four water column profiles in the Southwest and Equatorial Atlantic Ocean. Values of δ13CGDGT increase with depth in the water column, in contrast to the characteristic decrease in δ13CDIC values. These divergent trends imply a decrease in the observed total biosynthetic isotope effect (εAr) with depth, i.e., the offset between δ13CDIC and δ13CGDGT is not constant. Instead, we find that values of εAr specifically correlate with oceanographic variables associated with extent of organic remineralization, decreasing as CO2 concentration increases. This observed relationship is consistent in both magnitude and direction with the results of an isotope flux-balance model for Thaumarchaeota that suggests εAr should be sensitive to growth rate (μ) and CO2 availability under conditions of atmospheric pCO2?<?4 times the pre-anthropogenic Holocene level. Further tests of the sensitivity of εAr to ? and CO2 in the modern marine environment will be essential to exploring the potential for a new, archaeal lipid-derived pCO2 paleobarometer.Hutchins, P.D., Russell, J.D., Coon, J.J., 2019. Accelerating lipidomic method development through in silico simulation. Analytical Chemistry 91, 9698-9706. selection of mass spectrometry (MS) acquisition parameters is essential for effectively profiling the broad diversity and dynamic range of biomolecules. Typically, acquisition parameters are individually optimized to maximally characterize analytes from each new sample matrix. This time-consuming process often ignores the synergistic relationship between MS method parameters, producing suboptimal results. Here we detail the creation of an algorithm which accurately simulates LC-MS/MS lipidomic data acquisition performance for a benchtop quadrupole-Orbitrap MS system. By coupling this simulation tool with a genetic algorithm for constrained parameter optimization, we demonstrate the efficient identification of LC-MS/MS method parameter sets individually suited for specific sample matrices. Finally, we utilize the in silico simulation to examine how continued developments in MS acquisition speed and sensitivity will further increase the power of MS lipidomics as a vital tool for impactful biochemical analysis.Hutchinson, D.K., Coxall, H.K., O?Regan, M., Nilsson, J., Caballero, R., de Boer, A.M., 2019. Arctic closure as a trigger for Atlantic overturning at the Eocene-Oligocene Transition. Nature Communications 10, 3797. Eocene-Oligocene Transition (EOT), approximately 34?Ma ago, marks a period of major global cooling and inception of the Antarctic ice sheet. Proxies of deep circulation suggest a contemporaneous onset or strengthening of the Atlantic meridional overturning circulation (AMOC). Proxy evidence of gradual salinification of the North Atlantic and tectonically driven isolation of the Arctic suggest that closing the Arctic-Atlantic gateway could have triggered the AMOC at the EOT. We demonstrate this trigger of the AMOC using a new paleoclimate model with late Eocene boundary conditions. The control simulation reproduces Eocene observations of low Arctic salinities. Subsequent closure of the Arctic-Atlantic gateway triggers the AMOC by blocking freshwater inflow from the Arctic. Salt advection feedbacks then lead to cessation of overturning in the North Pacific. These circulation changes imply major warming of the North Atlantic Ocean, and simultaneous cooling of the North Pacific, but no interhemispheric change in temperatures.Ike, I.A., Karanfil, T., Cho, J., Hur, J., 2019. Oxidation byproducts from the degradation of dissolved organic matter by advanced oxidation processes – A critical review. Water Research 164, 114929. oxidation processes (AOPs) have been increasingly used for the treatment of source waters and wastewaters. AOPs characteristically produce oxidation byproducts (OBPs) from the partial degradation of dissolved organic matter (DOM) and/or the transformation of inorganic ions (especially, halides) into highly toxic substances including bromate and halogenated organic OBPs (X-OBPs). However, despite the enormous health and environmental risks posed by X-OBPs, an integral understanding of the complex OBP formation mechanisms during AOPs is lacking, which limits the development of safe and effective AOP-based water treatment schemes. The present critical and comprehensive review was intended to fill in this important knowledge gap. The study shows, contrary to the hitherto prevailing opinion, that the direct incorporation of halide atoms (X?) into DOM makes an insignificant contribution to the formation of organic X-OBPs. The principal halogenating agent is hypohalous acid/hypohalite (HOX/XO?), whose control is, therefore, critical to the reduction of both organic and inorganic X-OBPs. Significant generation of X-OBPs has been observed during sulfate radical AOPs (SR-AOPs), which arises principally from the oxidizing effects of the unactivated oxidant and/or the applied catalytic activator rather than the sulfate radical as is commonly held. A high organic carbon/X? molar ratio (>5), an effective non-catalytic activator such as UV or Fe2+, a low oxidant concentration, and short treatment time are suggested to limit the accumulation of HOX/XO? and, thus, the generation of X-OBPs during SR-AOPs. At present, there are no established techniques to prevent the formation of X-OBPs during UV/chlor(am)ine AOPs because the maintenance of substantial amounts of active halogen is essential to these processes. The findings and conclusions reached in this review would advance the research and application of AOPs.Ikehara, K., 2019. The origin of tRNA deduced from Pseudomonas aeruginosa 5′ anticodon-stem sequence. Origins of Life and Evolution of Biospheres 49, 61-75. riddle of the origin of life is unsolved as yet. One of the best ways to solve the riddle would be to find a vestige of the first life from databases of DNA and/or protein of modern organisms. It would be, especially, important to know the origin of tRNA, because it mediates between genetic information and the amino acid sequence of a protein. Here I attempt to find a vestige of the origin and evolution of tRNA from base sequences of Pseudomonas aeruginosa tRNA gene. It was first perceived that 5′ anticodon (AntiC) stem sequences of P. aeruginosa tRNA for translation of G-start codon (GNN) are intimately and mutually related. Then, mutual relations among all of the forty-two 5’ AntiC stem sequences of P. aeruginosa tRNA were examined. These relationships imply that P. aeruginosa tRNA originated from four anticodon stem-loops (AntiC-SL) translating GNC codons to the corresponding four amino acids, Gly, Ala, Asp and Val (where N is G, C, A, or T). In contrast to the case of AntiC-stem sequence, a mutual relation map could not be drawn with D-, T- and acceptor-stem sequences of P. aeruginosa tRNA. Thus I conclude that the four AntiC-SLs were the first primeval tRNAs.Inglis, G.N., Farnsworth, A., Collinson, M.E., Carmichael, M.J., Naafs, B.D.A., Lunt, D.J., Valdes, P.J., Pancost, R.D., 2019. Terrestrial environmental change across the onset of the PETM and the associated impact on biomarker proxies: A cautionary tale. Global and Planetary Change 181, 102991. Paleocene-Eocene Thermal Maximum (PETM; ~ 56 million years ago) is the most severe carbon cycle perturbation event of the Cenozoic. Although the PETM is associated with warming in both the surface (up to 8?°C) and deep ocean (up to 5?°C), there are relatively few terrestrial temperature estimates from the onset of this interval. The associated response of the hydrological cycle during the PETM is also poorly constrained. Here, we use biomarker proxies (informed by models) to reconstruct temperature and hydrological change within the Cobham Lignite (UK) during the latest Paleocene and early PETM. Previous work at this site indicates warm terrestrial temperatures during the very latest Paleocene (ca. 22–26?°C). However, biomarker temperature proxies imply cooling during the onset of the PETM (ca. 5–11?°C cooling), inconsistent with other local, regional and global evidence. This coincides with an increase in pH (ca. 2 pH units with pH values >7), enhanced waterlogging, a major reduction in fires and the development of areas of open water within a peatland environment. This profound change in hydrology and environment evidently biases biomarker temperature proxies, including the branched GDGT paleothermometer. This serves as a cautionary tale on the danger of attempting to interpret biomarker proxy records without a wider understanding of their environmental context.Jansen, J., Thornton, B.F., Cortes, A., Sn??lv, J., Wik, M., MacIntyre, S., Crill, P.M., 2019. Drivers of diffusive lake CH4 emissions on daily to multi-year time scales. Biogeosciences Discussions 2019, 1-37. and reservoirs are important emitters of climate forcing trace gases. Various environmental drivers of the flux, such as temperature and wind speed, have been identified, but their relative importance remains poorly understood. Here we use an extensive field dataset to disentangle physical and biogeochemical controls on the turbulence-driven diffusive flux of methane (CH4) on daily to multi-year timescales. We compare 8 years of floating chamber fluxes from three small, shallow subarctic lakes (2010–2017, n?=?1306) with fluxes computed using 9 years of surface water concentration measurements (2009–2017, n?=?606) and a small-eddy surface renewal model informed by in situ meteorological observations. Chamber fluxes averaged 6.9?±?0.3?mg?m?2?d?1 and gas transfer velocities (k600) from the chamber-calibrated surface renewal model averaged 4.0?±?0.1?cm?h?1. We find robust (R2?≥?0.93, p?<?0.01) Arrhenius-type temperature functions of the CH4 flux (Ea'?=?0.90?±?0.14?eV) and of the surface CH4 concentration (Ea'?=?0.88?±?0.09?eV). Chamber derived gas transfer velocities tracked the power-law wind speed relation of the model (k?∝?u3/4). While the flux increased with wind speed, during storm events (U10?≥?6.5?m?s?1) emissions were reduced by rapid water column degassing. Spectral analysis revealed that on timescales shorter than a month emissions were driven by wind shear, but on longer timescales variations in water temperature governed the flux, suggesting emissions were strongly coupled to production. Our findings suggest that accurate short- and long term projections of lake CH4 emissions can be based on distinct weather- and climate controlled drivers of the flux.Jansen, J., Thornton, B.F., Jammet, M.M., Wik, M., Cortés, A., Friborg, T., MacIntyre, S., Crill, P.M., 2019. Climate-sensitive controls on large spring emissions of CH4 and CO2 from northern lakes. Journal of Geophysical Research: Biogeosciences 124, 2379-2399.: Northern lakes are important sources of the climate forcing trace gases methane (CH4) and carbon dioxide (CO2). A substantial portion of lakes' annual emissions can take place immediately after ice melt in spring. The drivers of these fluxes are neither well constrained nor fully understood. We present a detailed carbon gas budget for three subarctic lakes, using 6 years of eddy covariance and 9 years of manual flux measurements. We combine measurements of temperature, dissolved oxygen, and CH4 stable isotopologues to quantify functional relationships between carbon gas production and conversion, energy inputs, and the redox regime. Spring emissions were regulated by the availability of oxygen in winter, rather than temperature as during ice‐free conditions. Under‐ice storage increased predictably with ice‐cover duration, and CH4 accumulation rates (25 ± 2 mg CH4‐C·m?2·day?1) exceeded summer emissions (19 ± 1 mg CH4‐C·m?2·day?1). The seasonally ice‐covered lakes emitted 26–59% of the annual CH4 flux and 15–30% of the annual CO2 flux at ice‐off. Reduced spring emissions were associated with winter snowmelt events, which can transport water downstream and oxygenate the water column. Stable isotopes indicate that 64–96% of accumulated CH4 escaped oxidation, implying that a considerable portion of the dissolved gases produced over winter may evade to the atmosphere.Plain Language Summary: Northern lakes are globally significant sources of greenhouse gases methane and carbon dioxide, but the seasonal pattern of emissions from lakes that are ice covered in winter remains poorly resolved. Our multiyear, multilake study reveals the importance of emissions during the ice‐off period, when carbon gas that had accumulated under ice is released. We show that more than half of the annual methane emissions and a third of the yearly carbon dioxide flux can be released at spring ice‐out. Unlike emissions during summer, which tend to be closely correlated with temperature, spring emissions of both gases are in part regulated by the availability of oxygen under ice. The quantity of carbon gas accumulating under ice, and therefore the amount that can be emitted in spring, scales predictably with ice‐cover duration. Parameterizations of winter and spring carbon cycling processes, such as those described in this study, may contribute to more accurate models of annual, ecosystem‐level carbon fluxes and are essential tools to improve freshwater emission inventories and quantify critical Arctic warming feedbacks.Jasperse, L., Levin, M., Rogers, K., Perkins, C., Bosker, T., Griffitt, R.J., Sepúlveda, M.S., De Guise, S., 2019. Parental exposure to Deepwater Horizon oil in different environmental scenarios alters development of sheepshead minnow (Cyprinodon variegatus) offspring. Marine Environmental Research 150, 104762. explosion of the Deepwater Horizon (DWH) oil exploration platform on April 20, 2010 began a catastrophic leak of approximately 640 million liters crude oil into the northern Gulf of Mexico (GOM), affecting more than 2100 km of coastline, including wetlands and estuaries that provide habitat and nursery for many aquatic species. Estuaries of the GOM are dynamic environments, with constant fluctuations in salinity and dissolved oxygen, including large hypoxic zones during summer months. Spawning fish in northern GOM estuaries following the DWH incident were at significant risk of oil exposure, and adverse environmental conditions at the time of exposure, such as hypoxia and low salinity, could have exacerbated developmental effects in the offspring. The present study investigated the effects of F0 parental oil exposure in different environmental scenarios on development of F1 sheepshead minnow (SHM) offspring. Adult SHM were exposed to the high-energy water accommodated fraction (HEWAF) of crude oil in three environmental scenarios: normoxic (NORM), hypoxic (HYP), and hypoxic with low salinity (HYP-LS). Parental HEWAF exposure in the NORM scenario resulted in developmental effects in F1 offspring, including altered heart rate, decreased length at hatch, and impaired prey capture. Co-exposure of F0 SHM to HEWAF and adverse environmental conditions altered HEWAF effects on F1 heart rate, hatch rate, prey capture, and survival. Time to hatch was not significantly impacted by parental HEWAF in any environmental scenario. The present study demonstrates that parental exposure to HEWAF results in developmental changes in F1 embryos, and co-exposure to adverse environmental conditions altered the effects for several developmental endpoints. These data suggest that SHM exposed to oil in estuaries experiencing hypoxia or low salinity may produce offspring with worsened outcomes. These developmental effects, in addition to previously reported reproductive effects in adult fish, could lead to long-term population level impacts for SHM.Jaumann, R., Schmitz, N., Ho, T.M., Schr?der, S.E., Otto, K.A., Stephan, K., Elgner, S., Krohn, K., Preusker, F., Scholten, F., Biele, J., Ulamec, S., Krause, C., Sugita, S., Matz, K.D., Roatsch, T., Parekh, R., Mottola, S., Grott, M., Michel, P., Trauthan, F., Koncz, A., Michaelis, H., Lange, C., Grundmann, J.T., Maibaum, M., Sasaki, K., Wolff, F., Reill, J., Moussi-Soffys, A., Lorda, L., Neumann, W., Vincent, J.B., Wagner, R., Bibring, J.P., Kameda, S., Yano, H., Watanabe, S., Yoshikawa, M., Tsuda, Y., Okada, T., Yoshimitsu, T., Mimasu, Y., Saiki, T., Yabuta, H., Rauer, H., Honda, R., Morota, T., Yokota, Y., Kouyama, T., 2019. Images from the surface of asteroid Ryugu show rocks similar to carbonaceous chondrite meteorites. Science 365, 817-820.: The near-Earth asteroid (162173) Ryugu is a 900-m-diameter dark object expected to contain primordial material from the solar nebula. The Mobile Asteroid Surface Scout (MASCOT) landed on Ryugu’s surface on 3 October 2018. We present images from the MASCOT camera (MASCam) taken during the descent and while on the surface. The surface is covered by decimeter- to meter-sized rocks, with no deposits of fine-grained material. Rocks appear either bright, with smooth faces and sharp edges, or dark, with a cauliflower-like, crumbly surface. Close-up images of a rock of the latter type reveal a dark matrix with small, bright, spectrally different inclusions, implying that it did not experience extensive aqueous alteration. The inclusions appear similar to those in carbonaceous chondrite meteorites.Editor's summary: Landing on the surface of Ryugu. In October 2018, the Hayabusa2 spacecraft dropped the Mobile Asteroid Surface Scout (MASCOT) lander onto the surface of the asteroid (162173) Ryugu. Jaumann et al. analyzed images taken by the MASCOT camera during its descent and when resting on the surface. Colored light-emitting diodes were used to illuminate the lander's surroundings at night and produce color images. Ryugu's surface is dominated by two types of rock, but there is no evidence for fine-grained dust. Millimeter-sized inclusions in the rocks are similar to those present in carbonaceous chondrite meteorites. MASCOT operated for 17 hours on the surface before its nonrechargeable batteries ran out.Javaux, E.J., 2019. Challenges in evidencing the earliest traces of life. Nature 572, 451-460. has been habitable for 4.3?billion years, and the earliest rock record indicates the presence of a microbial biosphere by at least 3.4?billion years ago—and disputably earlier. Possible traces of life can be morphological or chemical but abiotic processes that mimic or alter them, or subsequent contamination, may challenge their interpretation. Advances in micro- and nanoscale analyses, as well as experimental approaches, are improving the characterization of these biosignatures and constraining abiotic processes, when combined with the geological context. Reassessing the evidence of early life is challenging, but essential and timely in the quest to understand the origin and evolution of life, both on Earth and beyond.Analyses of highly resistant microscopic minerals (zircons) preserved in younger host rocks indicate that Earth was already habitable—that is, had liquid water at the surface or in near-surface environments, as well as some crust—by 4.3 billion years ago (Ga)1. Life could have originated at this time but it is only possible for us to test scenarios for the origin of life experimentally, because the transition from molecules to the first cells is unlikely to be preserved. Moreover, the preserved rock record starts only around 4 Ga. These old rocks, which could potentially preserve early traces of life, have been much altered by geological processes, which makes the interpretation of the environmental conditions of their formation and initial composition challenging. Nevertheless, the ancient record provides evidence for the presence of a crust, rock erosion and recycling, and liquid water1,2, which suggests that life could have accessed nutrients, energy sources and habitats early on.The incompleteness of the rock and fossil records is the first challenge that palaeobiologists and geologists face when searching for early traces of life (Fig. 1). Rocks are transformed, eroded and recycled through time, and fossilization processes are complex and rare. Consequently, the overall proportion of rocks and fossils that are preserved from the early Earth is small, and offers only a glimpse of the histories of our planet and the evolution of life. The possible traces of life that have been reported in early-Earth sediments and rocks are morphological or chemical (Fig. 2). Chemical traces include modified molecules that are originally produced only by biological activity (such as complex lipids and pigments), as well as the isotopic composition of carbon, sulfur, nitrogen and iron, which is indicative of the biological cycling of these elements. Morphological traces comprise microfossils and biosedimentary structures such as stromatolites (laminated rocks produced by microbial precipitation and/or trapping of minerals) in carbonate rocks and other microbially induced sedimentary structures in siliciclastic rocks. Traces of biological activity, such as microbial borings, burrows and tracks (ichnofossils), can indirectly indicate the presence of life but their biological origin is difficult to prove, especially in the Archean eon (the time period from 4 to 2.5 Ga). Many similar traces can also be formed and/or altered by abiotic processes or later contamination, which has left controversies surrounding the earliest record of life on Earth3,4,5,6,7,8,9,10,11,12,13,14,15,16,17ChallengesThe geological contextThe first step in recognizing biosignatures is determining the geological context18 and the environmental conditions of preservation. The samples that host the potential traces of life should come from rocks of known provenance, of established age and demonstrated geographical extent. Moreover, the possible traces should occur in a geological context that is plausible for life; these contexts are mostly in sedimentary environments9,19,20,21,22, although some putative microbial borings have been reported in marine volcanic glass23 (but were later reassessed as abiotic24,25). Fossilization is a complex process that involves microbial, physical and chemical degradation that leads to the decay, preservation and alteration of original biological information and properties, and varies according to the environmental conditions of preservation and the geological processes that affect the rocks. Low-temperature biological, chemical and physical processes of compaction and cementation (diagenesis) transform soft sediments into coherent rocks. High pressure and temperature processes owing to increasing burial depth or deformation (metamorphism), hot fluid circulation (hydrothermalism and metasomatism), and folding and fracturing (tectonics) may modify, alter or erase the original composition and fabric of the rocks, and any biosignatures that they may preserve. The occurrence and extent of these processes must be characterized before any attempt at meaningful interpretation.Observations at different scales—from sedimentary basins (tens to hundreds of kilometres) through outcrops (kilometres to metres), bedrocks (metres) and laminations (centimetres to millimetres) to microscopic examinations of rock samples (micrometres to nanometres)—and using diverse geochemical proxies help to constrain the geological context and the particular environmental conditions of preservation. These analyses provide key information on the age, composition and origin of rocks and fossilized carbonaceous material, on fossilization processes in diverse physicochemical conditions, and on possible alterations. These analyses are also crucial for evaluating the plausibility of abiotic processes, and for assessing the biological or abiotic origin of putative biosignatures.Endogenicity and syngenicity of life tracesAny purported ancient microfossils or other traces of life must pass two tests before they can be considered as possible evidence of early life. Rocks can be dated directly, but fossils or other life traces cannot; their relationship to the rock must, therefore, first be established. Microorganisms or organic material can enter existing rocks through borings or fluids in veins and pores9. Careful microscopic examination of thin sections (petrography) cut through the rock sample can exclude fluid migration, and can reveal whether the microstructure or carbonaceous material is indeed endogenous (occurs within the rock) as well as whether it is syngenetic (contemporaneous) with the rock26. Raman spectroscopy provides evidence of whether the microstructure, putative microfossil or other material is carbonaceous in nature, and of the temperature to which it has been subjected during metamorphism10,17,21,27. This temperature should be consistent with the thermal maturity of the associated carbonaceous material co-occurring in the same rock sample, and with the degree of metamorphism of the host rock, which is itself established by the mineralogy, deformation and regional context of this rock. Raman spectroscopy is thus necessary, but not sufficient, to prove biogenicity28. An organic microstructure incorporated in fine-grained sediments (such as mudstone or shale) at the time of sedimentation should be flattened parallel to the bedding during sediment compaction, which provides another criterion for syngenicity21. If these tests of endogenicity and syngenicity are successful, the challenge then lies in demonstrating the biogenicity of the structure.Abiotic processes that mimic lifeAnother difficulty in identifying unambiguous traces of early life is the occurrence of abiotic processes that may mimic life morphologies and chemistries12. At least since W?hler’s artificial synthesis of urea in 1828, scientists have known that ‘organic’ is not a synonym for ‘biogenic’. Organic molecules (those that contain carbon–hydrogen bonds) can form in the laboratory or in nature, both on Earth and beyond Earth in the interstellar medium, meteorites and comets. Nonetheless, confusion remains in the scientific and public literature, which can lead to over-interpretation. Organic or carbonaceous material can occur as molecules that are insoluble (kerogen) or soluble (bitumen) in organic solvents3. Diverse abiotic processes are known to form gaseous and liquid carbonaceous materials—some of which have carbon and nitrogen isotopic compositions that are similar to those of signatures of life—at low and high temperatures, during metamorphism7,29, in hydrothermal6,30 or volcanic31 environments, and in meteorites32,33. Recently, low temperature alteration of the oceanic crust was shown to produce a range of types of condensed carbonaceous particles34. The possibility that this abiotic carbonaceous material could mature through burial, diagenesis and metamorphism into abiotic kerogen-like material—although plausible—remains to be tested experimentally35,36. Nevertheless, abiotic kerogen, which is associated with a large fractionation of carbon isotopes, is found in carbonaceous meteorites (although its formation is not well-understood)37. Kerogen is preserved in many organic-rich Precambrian rocks as particles; it may also form the organic walls of microfossils, in which biopolymers have been transformed by diverse degradation and condensation reactions3. Other abiotic processes can also fractionate stable isotopes of carbon, sulfur, nitrogen and iron; these include UV dissociation (for sulfur), electric discharge in the laboratory or lightning in nature (for nitrogen) and mineral precipitation6,38,39,40. The isotopic compositions can then be altered by geological processes such as metamorphism, metasomatism and hydrothermalism, during or after deposition6,38.Another complication is the fact that structures that resemble microfossils or stromatolites can also form abiotically. Folded layered rocks or mineral precipitates can be confused with biogenic stromatolites4,8,11,19,41,42,43,44,45 and can be produced in laboratory abiotic experiments46 or by numerical modelling47. Both abiotic and biological organic matter can migrate around quartz minerals in chert (silica-rich rock)26,48 or volcanic glasses49 to create abiotic pseudofossils, some of which are similar in morphology to putative silicified spheroidal or filamentous microfossils5,50,51,52,53 (Fig. 1). Microscopic observations can sometimes help to detect fluid migration26 and to discriminate between biotic and abiotic microstructures, when the distribution of organic matter clearly follows the angular morphology of a mineral15. Mixtures of elemental sulfur with carbon, and carbonate, phosphate or silicate minerals can auto-assemble to form an amazing diversity of objects—sometimes very complex—that mimic life morphologies, in the presence or absence of abiotic or biotic organic molecules (Fig. 1i, j). These ‘biomorphs’ may form naturally (under Earth conditions54,55 and in the Martian meteorite ALH8400156) as well as in laboratory experiments57,58,59. In some cases, these biomorphs differ from true microfossils in their size distribution and the chemical conditions that are required for their formation59. Whether they can have coupled isotopic compositions of carbon, nitrogen, sulfur and iron that are consistent with biological populations, as well as an ultrastructure that is comparable to fossil cell walls, remains to be tested. It is possible that these mineral biomorphs—if associated with organics—could be fossilized as three-dimensional pseudofossils in chert49,60 but not as organic compressions21 in fine-grained sediments, as are true organic-walled microfossils (Figs. 1d–f, 2c, f, h) or eukaryotic microfossils that may possess a multilayered wall ultrastructure and/or ornamented surfaces14,61,62 (Fig. 2g, i). Microtunnels can form through the activity of endolithic organisms that bore into rocks such as basalt or carbonates, which produces ichnofossils23,24. However, it is difficult to demonstrate the biogenicity of these tunnels, because they resemble tubes that form abiotically by pyrite migration within rocks63 or by displacement of other minerals or organics during metamorphism24,25. A complementary approach is to artificially fossilize microorganisms by mineralization or by letting them decay naturally in the laboratory, to improve our understanding of the fossilization processes and to better interpret the fossil record. This idea itself is not new64,65 but in the past decade experiments and high-resolution analytical techniques have examined the effects of mineralization, diagenesis and metamorphism on microbial cells32,66,67,68,69,70. Despite the challenge of reproducing natural conditions, these experimental approaches have explored the physicochemical conditions under which morphological and chemical biological information are retained or altered, and under which pseudosignatures can form. They help to discriminate true life signatures from abiotic products that may also be preserved (sometimes even co-occurring within the same rock)14.Evidencing biogenicityWe might then ask how we can be confident that a purported trace of life is indeed biogenic. The answer lies in the combination of evidence available, and the careful characterization of the geological context and fossilization processes that are crucial for interpreting this evidence, combined with a lack of abiotic explanations for the observations. In the earliest rock record, the evidence rarely is fully conclusive (because of poor preservation) but instead ranges—with increasing confidence—from putative to possible to probable biosignatures. Deciphering the biogenicity of an object or carbonaceous material is very difficult, even when using cutting-edge in situ techniques. This emphasizes the difficulties of finding unambiguous traces of ancient life on other planets without being able to bring samples back to Earth71, but also helps to constrain the best targets for preserving possible biosignatures (such as mudstones and shales72) when designing sampling strategies for Mars missions73.Characterizing the structure, and molecular, elemental and isotopic composition, of ancient carbonaceous matter may give some clues to its origin3,10,14,27,52,74,75 and possible contamination by younger molecules3,13,27, but these techniques are not sufficient to determine the biogenicity of this matter even when using advanced analytical techniques. Other necessary co-occurring sources of evidence include the co-variation of other isotopes, the N/C ratio32,75, the presence of microfossils21,76, stromatolites19,77,78,79,80 or microbial mat structures74,81, and the geological context being plausible for life habitat and preservation. Notably, these observations should not be explicable through abiotic processes.For simple life forms, morphology alone is not sufficient for determining biogenicity, but instead needs to be combined with studies of populations with biological size ranges, observations of cellular division, as well as a hollow structure with continuous carbonaceous cell walls. The presence of organic molecules or a metallome that is indicative of biochemistry, or degradation patterns of decaying, flattened and folded cells, and a distribution that shows fossilized behaviour (orientation and distribution within the rock, caused by mobility and interaction with the environment) may also support a biological origin14,19,20,77,82. The strongest confidence in biogenicity can be reached for Proterozoic eukaryotes that show morphological complexity (Fig. 2g, i). A high confidence for biogenicity can also be achieved for prokaryotes (Fig. 2c–e, h) and (as-yet-unidentified) hollow, organic-walled microfossils with simple morphologies (Fig. 1d–j), when these are preserved as carbonaceous compressions in fine-grained sediments21. The challenge increases in lithologies such as chert. Impregnation by silica-rich fluids (silicification) may lead to exquisite three-dimensional preservation of microfossils in rocks of the Proterozoic eon (and younger rock record) (Fig. 2d, e), such as in the iconic 1.9-Ga Gunflint stromatolitic chert76,83 in Canada (Fig. 2d). The interpretation of microstructures preserved in older cherts of the Archaean eon poses more problems, owing to the simpler morphologies of early putative microfossils. Chert forms by the precipitation of silica gel and crystallization of quartz minerals, or by the silicification of pre-existing rocks by hydrothermal fluids. Under such conditions, abiotic or biological organic molecules may come to coat15,26,84 mineral grains (Fig. 1g) or volcanic particles (tephra)49,55,85 (Fig. 1h), and may have isotopic and kerogenous chemistries that are similar to those of life. Detailed microscopic analyses may help to discriminate between pseudofossils and true microfossils within these assemblages: pseudofossils may show discontinuous organic walls rather than continuous kerogenous cell walls; walls that are granular, or thicker than biological cell walls; and a size frequency distribution with a large standard deviation55,59, unlike the size frequency distributions of prokaryotic populations. However, a large size distribution may also reflect degradational gradients59 or plurimodality, such as the presence of several strains, the life stages of a single strain or various colony sizes.Challenges in identificationOnce the biogenicity of morphological or chemical signatures (as well as their endogenicity and the syngenicity) is established, determining the palaeobiology and identity of these traces of life requires an additional range of observations.A key question is how these signatures can be interpreted after processes have altered or erased part of the original biological information. Most geochemical and morphological traces are compared to, and interpreted in terms of, modern metabolisms or microorganisms. However, these metabolisms and organisms have evolved. It is also possible that the early signatures might have been produced by alternative biochemical pathways in organisms that existed before the three extant domains of life (Bacteria, Archaea and Eukaryota) diverged—that is, before the last universal common ancestor of the three domains of life—or in extinct organisms that paralleled the evolution of these domains (Fig. 3). Some signatures might also be the result of lateral gene transfer between contemporaneous and unrelated organisms within and outside the three domains: in summary, we should consider the limits of actualism in interpreting early putative traces of life.We must also bear in mind that the diversity of life is far from constrained within the three domains86,87,88. Moreover, current understandings of modern microbial life and its taxonomically informative characters or metabolic signatures, in which chemical and morphological convergences are known to exist, even between domains, are still incomplete. In other words, what are the limits of our knowledge in microbiology?Palaeontologists have to rely on information other than the genome and internal cellular organization to identify the biological affinities of early microfossils. In some cases, the morphology, mode of division, presence of ornamentation, ultrastructure and chemistry of carbonaceous cell walls—when combined with the distribution pattern within the hosting rocks and the characteristics of the preservational environment—may help in deciphering the identity of microfossils14,15,61,62,76,82,89. However, most early cellular fossils remain unidentified because they lack taxonomically informative characters, and therefore we cannot relate them to an extant clade (Fig. 3). Moreover, these fossils may record traces of extinct lineages that have no modern counterpart21,52. Several techniques that are applicable to nano- to microscale organic or mineral samples can be used to characterize the chemistry of these organisms3,10, and even have the potential to reveal biomolecules that are specific to extant clades as well as isotopic and metal compositions that are indicative of metabolism. Even if the fossils themselves remain unidentified, their morphological or chemical attributes may provide evidence for biological innovations and the evolution of biochemical pathways that is useful for reconstructing the major steps in the evolution of life14,15.The earliest record of lifeEven if Earth has probably had habitable conditions for 4.3 billion years, strong evidence must support claims for the presence of early traces of life and abiotic explanations for observations must be considered12,20. The oldest record of organic matter with a carbon isotope composition that is consistent with life processes has been reported in 4.1-Ga zircons90, in 3.95-Ga metamorphic rocks from Canada91, and in the 3.8–3.7-Ga Akilia belt92 and Isua belt92,93,3700-Ma sea-floor sedimentary rocks from West Greenland. Science 283, 674–676 (1999)." id="ref-link-section-d33982e1146_2" href="#ref-CR94" data-test="citation-ref" data-track-label="link" data-track-action="reference anchor" data-track="click"94,95 in Greenland. As explained above, the presence of carbonaceous material and the carbon isotopic composition do not constitute sufficient criteria for establishing biogenicity, and the geological context or antiquity of this organic matter has often been debated3,7,96,97, 3.7 Ga Isua (Greenland) supracrustal sequence. Geology 24, 43–46 (1996)." id="ref-link-section-d33982e1160_2" href="#ref-CR98" data-test="citation-ref" data-track-label="link" data-track-action="reference anchor" data-track="click"98,99. Based on carbon and iron isotopes, iron metabolism has previously been inferred in the 3.8-Ga Banded Iron Formation from Isua100,101, but these isotopes can also be altered or fractionated abiotically39,102. Unfortunately, microfossils or microbial mats (which would strengthen claims of biogenicity) are unlikely to be found in these highly metamorphosed rocks, even in less-disputed deep-sea graphitic metasediments3700-Ma sea-floor sedimentary rocks from West Greenland. Science 283, 674–676 (1999)." id="ref-link-section-d33982e1181" aria-label="Reference 94" href="/articles/s41586-019-1436-4#ref-CR94" data-test="citation-ref" data-track-label="link" data-track-action="reference anchor" data-track="click"94,95. Early claims of microfossils in 3.7-Ga Isua metamorphic rocks103 have subsequently been reassessed as fluid inclusions104 or contamination by younger microorganisms boring into and fossilized in the rock9. Convex-up structures from Isua that have more recently been interpreted as the oldest stromatolites105 are more likely to represent deformation structures4,42, because they show convex-down next to convex-up morphologies and occur in tightly folded rocks with a questionable original lithology. Mineral tubes of iron oxide from 3.7-Ga rocks from Canada—originally interpreted as putative iron-oxidizing bacteria preserved in precipitates related to seafloor hydrothermal vents106—have been reassessed as volcanic glass55, and have diameters larger than those of modern iron-oxidizing bacteria. Traces in 3.47-Ga pillow lavas that have been interpreted as endolithic burrows23 can be formed abiotically as titanite tubes of metamorphic origin24, or as ambient inclusions trails that are associated with the displacement of mineral and/or organic inclusions25.Better-preserved (that is, less-metamorphosed) rocks occur in younger Archean cratons, such as the 3.5–3.0-Ga Pilbara craton of Western Australia and the Barberton region of South Africa and Swaziland. The 3.48-Ga Dresser Formation (Australia) was an active volcanic environment, with intense hydrothermal fluid circulation and frequent eruptions107. These rocks preserve putative stromatolites44,108, microfossils8,20,109 and sulfur110,111,112,113 and carbon36,114 isotopic compositions, but most of these have been questioned3,8,43,45,49,99 on the grounds of possible abiotic origins, hydrothermal alteration, a lack of supporting geochemical evidence, the solid rather than hollow nature of their putative filaments, or poor preservation. Among these putative forms of evidence, the biological origin of the sulfur isotopic composition strongly relies on the disputed origin of the minerals in which it is measured, which is important for discarding abiotic high-temperature fractionation as an explanation8,115, despite the use of quadruple sulfur isotopes8,40. Different texture-specific carbon-isotope compositions in carbonaceous material present in disseminated clots and in fine laminae preserved in chert36 have been interpreted as biological, on the basis of this systematic trend and the absence of evidence for hydrocarbon migration. However, this carbonaceous material is not directly associated with microfossils or unambiguous microbial mats and stromatolites, which would help to strengthen claims for its biogenicity. Heterogeneous sulfur-isotope compositions of pyrite112 associated with putative pyritized organic mat layers have been interpreted as microbial, although a thermochemical origin could not be completely discounted. Recently, laminated convex-up precipitates (which have been interpreted as stromatolites with possible gas bubbles and putative microbial fabrics) have been reported in terrestrial hot-spring deposits (geyserites)116, but they are not associated with microfossils and/or carbonaceous material with an isotopic composition that would support a biological origin. Geochemical data are also needed for some of the possible stromatolites that preserve microtextures45. In summary, the Dresser Formation includes a variety of putative or possible morphological and geochemical biosignatures, and is potentially one of the earliest microbial ecosystems that is preserved on Earth. Further study might help to discard abiotic hypotheses, which would push back or reach the limits of confidence in information that can be retrieved from very old rocks.Filamentous microstructures associated with carbonaceous matter enriched in light carbon isotopes in the 3.45-Ga Apex chert Formation (Australia) were initially interpreted as microfossils50. These microstructures were subsequently reconsidered as abiotic pseudofossils, because their morphology was inconsistent with biology and was more compatible with fluid migration around minerals or mineral artefacts48,117,118 and because of a re-evaluation of their geological context as hydrothermal rather than marine shallow water84. The controversy regarding the origin of carbonaceous material and possible traces of life in various locations and chert types of the Apex Formation continues, despite several events of hydrothermal overprinting of the whole succession and the use of high-resolution techniques and recent field sampling by multiple laboratories27,51,59,119,120. Recently, possible microbial mat structures that consist of wavy organic layers that trap grain sediments have been reported in this iconic locality120.Putative microfossils and diverse stromatolites5,121,122 have been reported in the 3.5–3.25-Ga Onverwacht and Fig Tree Groups (Barberton, South Africa). The more convincing of these are conical stromatolites that preserve microbial microtextures in the 2.98-Ga Pongola Supergroup (South Africa) (see discussion and references in refs 5,11). Filamentous, coccoidal and lenticular putative microfossils have been described from the 3.434–3.416-Ga Kromberg Formation (South Africa)8,53,123,124 but have been reconsidered as abiotic, owing to evidence of fluid migration or similarities with volcanic particles8,26,55,85. More-recent analyses of kerogenous lenticular forms from the Kromberg Formation have revealed carbon-isotope compositions that are consistent with biology124, but ultrastructural studies would help to support claims of biogenicity. Geological context, petrography and kerogen geochemistry support a microbial origin for microbial mat structures and ripped-up fragments from the 3.33-Ga Josefdal chert74 and the 3.416-Ga Buck Reef chert125, respectively. Probable silicified microbial mat structures reported in the 3.47-Ga Hooggenoeg Formation85 need in situ geochemical analyses to confirm their biogenicity.One of the strongest cases that has so far been documented for early traces of life is the stromatolites of the 3.426–3.35-Ga Strelley Pool Formation (Australia)19,41,108,126,127,128. Their biogenicity was proposed and then questioned43,129, but the improved characterization of their geological context (which is plausible for life, being a marine shallow-water hypersaline evaporitic carbonate platform19,130) and detailed multiscale studies have provided a combination of evidence that supports their biological origin—albeit perhaps less strongly for stromatolites without preserved organic matter131. These stromatolites occur as seven types of three-dimensional convex-up structures that display a mostly wavy, but sometimes more complex, branching or conical morphology. The most compelling evidence for biogenicity are these branching and conical stromatolites with laminae of variable thicknesses (non-isopachous) that are laterally linked by flat laminated carbonates; so far, it has not been possible to explain these features as the result of abiotic processes8,11. These morphologies vary along a carbonate platform that is several kilometres long, as a function of hydrodynamic conditions and water depth. This pattern repeats itself on different platforms as well as vertically in response to sea-level change, which is suggestive of microbial reef ecology19. Some of the domal stromatolites preserve organic laminae19 that have yielded carbon- and sulfur-isotope signatures and nitrogen and sulfur elements preserved in carbonaceous particles, indicating a chemistry that is consistent with multiple microbial metabolisms131,132,133. Organic material is not preserved in all types of stromatolite but, when it is, the non-random distribution of this material in the domes or convex-up laminae suggests a concentration of organic biopolymers on stromatolite slopes that could serve as a template for the passive precipitation and trapping of minerals. Such criteria, when combined with the morphological complexity of the stromatolites, have previously been used as evidence for the biogenicity of 2.77-Ga stromatolites134. The carbonate laminae show lateral variations in their thickness, microscopic textures that differ between and in the cones, and cannot be traced laterally over hundreds of metres of outcrop, contrary to abiotic mineral precipitates19,47. If stromatolites can be used as a proxy for autotrophic metabolism such as anoxygenic or oxygenic photosynthesis (although their upward growth might be linked to competition for nutrients rather than, or in addition to, light11), then the stromatolites of 3.426–3.35-Ga Strelley Pool Formation provide a minimum age for the evolution of the domain Bacteria, within which this metabolism originated. This implies an earlier date for the last (most recent) common ancestor of Bacteria, an even older last universal common ancestor—and thus an earlier origin of life (Fig. 4). Bedded cherts in the Strelley Pool Formation, as well as the younger 3.0-Ga Farrel quartzite chert (Australia)22,52,135, preserve possible microfossil assemblages that include simple aggregates of spheroids and organic films that are possibly abiotic, and abundant large, flanged lenticular carbonaceous microstructures that are more difficult to explain by abiotic processes49. Abiotic lenticular volcanic structures can be solitary or form chains with their long axes aligned49,54, and can presumably be wrapped or filled in by organics49, which perhaps explains some of the hollow lenses with organic lining that are observed in situ in chert of the Strelley Pool Formation52. However, some of the chains of lenses in the Strelley Pool Formation are entirely kerogenous, keep their integrity and stay attached after extraction using acid demineralization, which represent observations that are more difficult to explain abiotically49,52,55,59. When extracted from the chert, transmission electron microscopy analyses show an alveolar structure52, unlike a single hollow cell or an empty colonial envelope. Associated N/C ratios, elemental maps135 and texture-specific carbon136,137 and nitrogen138 isotopic heterogeneities in the microstructure assemblages of the Strelley Pool Formation and Farrel quartzite may provide further support for a biological origin of the kerogen, but not necessarily of the microstructures. These heterogeneous isotopic features of the microstructure assemblages may also reflect several generations of organic matter or multispecies biofilms from distinct precursors with different isotopic compositions49. It is also possible that some of the flanged kerogenous lenses (with an alveolar ultrastructure) could have been bacterial colonies that were growing in Archaean silica-rich (gel-like) water. Notably, laboratory experiments and theoretical physics have shown how the morphology and size of bacterial colonies growing within a three-dimensional gel matrix change from diffuse and circular to compact and lenticular at higher concentrations of agar concentration, owing to mechanical forces139. These experiments have also documented how a monolayered circular two-dimensional colony changes into a three-dimensional colony with a multilayered, thicker central part and a monolayered outer ring (or flange)140. Further ultrastructural analyses of extracted lenses, and laboratory experiments testing these hypotheses—such as encapsulation or filling of vesicular volcanic sediments by abiotic organics or biofilms49 or bacterial colony growth in silica gel, and artificial fossilization of these—might help to discriminate between possibly co-occurring abiotic and biological microstructures.Beside shallow-water carbonate and volcanic settings, siliciclastic environments can also be colonized by microbial mats, stabilizing intertidal sand or colonizing rock cavities or surfaces, and preserved in situ by silicification or ripped-up and rolled-up by waves or currents. A combination of criteria has been proposed to discriminate organic-rich microbial mat laminations from abiotic accumulation of organics by pressure-solution fronts or fluid migration16,74,81,85,141. These mat layers should occur as sets of fine, crinkly, organic laminae of variable thickness (non-isopachous), which drape detrital grains that are oriented parallel to the laminae and are ‘floating’ without grain-to-grain contact. They should be preserved in a geological context that is plausible for life, have an isotopic composition that is consistent with biology, co-occur with ripped- and rolled-up fragments eroded from the mat (indicating the flexibility of a soft, but coherent, sediment layer that is bound by microbial organic matter) and have a particular pattern of orientation. Cases of such microbial mats are reported in the rock record from 3.47 Ga, in the Barberton area (South Africa) and the Pilbara (Australia)16,81,85,125,141 (although some need confirmation of biogenicity with in situ geochemical analyses). While some of these mat builders have been interpreted as cyanobacteria (on the basis of comparisons with modern analogues), there is no firm evidence so far that supports oxygenic photosynthesis over other autotrophic and heterotrophic metabolisms82. Collectively, these traces—when combined with multiple other biosignatures—indicate that benthic microbial mats colonized marine shallow water, volcanic islands and fluviatile sediments on sub-aerially exposed continental crust early on.In the 3.22-Ga Moodies Group (Barberton Greenstone Belt, South Africa), populations of large organic-walled, spheroidal microfossils are preserved as carbonaceous compressions that are flattened parallel to bedding in tidal shales and siltstones21; these features supports their syngenicity, which is also indicated by Raman spectroscopy. These microfosssils show a continuous and recalcitrant kerogenous cell wall with a carbon isotopic chemistry and degradational features (folding and wrinkling) that are consistent with biology, are hollow and survive acid extraction from the host rock. To our current knowledge, no abiotic processes can reproduce similar structures in such a context, which strengthens the hypothesis of their biogenicity15,21,142. Future investigations might lead to the discovery of other occurrences and further clues to their identity. The Moodies Group also preserves other traces of life, such as extensive microbial mats in shallow-marine tidal deposits141 and terrestrial deposits81, in which they drape fluvial conglomerates and gravelly sandstones and are associated with kerogen with carbon, nitrogen and sulfur isotopic compositions that are consistent with microbial metabolisms143,144. The identity of the Moodies microfossils—whether prokaryotic, eukaryotic or even another extinct form of life—is unknown. Nevertheless, these microfossils indicate the evolution of large benthic or planktonic cells or colonial envelopes, which synthesized recalcitrant organic biopolymers and lived in marine shallow water21 not far from microbial mats. The age of the domain Eukaryota is unconstrained and stem eukaryotes could presumably be as old as the Archaean eon, but this hypothesis is difficult to test in the absence of diagnostic fossil molecules or microfossils with a morphological complexity that is unknown in prokaryotes. To date, the oldest unambiguous traces of eukaryotes are hollow microfossils with ornamented organic walls that are preserved in 1.65-Ga shales from Australia62 (Fig. 4) and China145.The Archaea have a unique metabolism, methanogenesis, that can be evidenced by strongly negative fractionations of carbon isotopes in kerogen, which are reported worldwide between 2.8 and 2.6 Ga6,79,93, including in the stromatolites of the lacustrine 2.77–2.72-Ga Fortescue Group78,79, perhaps in the 3.42–3.35-Ga Strelley Pool Formation (for which other metabolisms are possible)132 and (debatably) in 3.48-Ga hydrothermally derived methane-bearing fluid inclusions99,114. Indirectly, the oldest fossil traces of eukaryotes at 1.65 Ga62,145 provide a minimum age for the domain Archaea (although not necessarily for methanogenic Archaea) (Fig. 4), because eukaryotes are thought to originate from an archaeal ancestor88.Despite important challenges, the oldest unambiguous traces of life preserved on Earth thus firmly support the presence of a microbial biosphere in terrestrial habitats since at least 3.2 Ga and in marine settings since at least 3.42 Ga, and perhaps earlier (Fig. 4). Convincing data provide constraints on the minimum ages of the three domains of life (Bacteria, more than 3.42 Ga; Archaea, more than 2.77 Ga; and Eukaryota, more than 1.65 Ga), which suggests an origin for these domains earlier than these respective dates. These data also document the early evolution of specific metabolisms and other biological innovations, as well as unidentified forms of cellular life and microbial mats.PerspectivesAmong the challenges discussed here, three in particular limit our understanding of traces of early life and require additional fundamental research: (1) the abiotic processes that mimic biological morphologies and chemistries; (2) our incomplete knowledge of fundamental microbiology, such as the morphology, molecular composition, isotopic composition, metallome, ultrastructure of preservable cellular components, and the diversity, metabolisms and phylogeny of microbial life; and (3) the effects of fossilization processes (that is, taphonomy—how morphological and chemical traces get preserved and altered). The diversity and resolution of techniques available for characterizing possible biosignatures are now impressive, but are only meaningful if interpreted in their micro- and macroscale geological contexts and in combination with other approaches. As research and analytic development progresses, newly discovered and previously known geological sites—including those presented here, as well as many others—can be investigated or reinvestigated, and their possible signatures of life can be assessed with a greater confidence, to the limits of their preservation. The characterization of reliable biosignatures for microbial life is crucial for understanding the early evolution of the biosphere of the Earth. We can then address questions regarding the conditions for the appearance and development of life on other planetary bodies (habitability), and the probability for an extraterrestrial biosphere to develop complex metabolisms, such as anoxygenic or oxygenic photosynthesis, or morphologies, such as complex multicellularity. This research is critical for the advancement of life-detection strategies, instruments and missions that are applicable to other planets of the solar system and to the atmospheres of rocky exoplanets, as space agencies have recently come to appreciate.Jha, N.K., Ali, M., Iglauer, S., Lebedev, M., Roshan, H., Barifcani, A., Sangwai, J.S., Sarmadivaleh, M., 2019. Wettability alteration of quartz surface by low-salinity surfactant nanofluids at high-pressure and high-temperature conditions. Energy & Fuels 33, 7062-7068. low-salinity aqueous formulations have shown promising results for rock wettability modification and interfacial tension reduction. Additives, such as surfactant and nanoparticles, can be used for such formulations. The interaction of these novel formulations with different fluid phases and the rock surface is, however, yet to be understood in detail. Thus, an experimental study was conducted in this study to investigate the interfacial tension and wettability of carbon dioxide and anionic surfactant (SDBS, 1.435 mM) at high pressure and temperature. The results show that the anionic surfactant (SDBS, 1.435 mM) augmented the effect of zirconia (ZrO2) nanoparticles (100–2000 mg/L concentration) at low-salinity conditions and proved to be an effective wettability and interfacial tension modifier when used at appropriate divalent cation/sulfate ion ratios. Low-salinity surfactant nanofluids may thus be applied for wettability alteration and interfacial tension reduction for recovering residual oil, carbon dioxide-enhanced oil recovery, as well as carbon dioxide geosequestration. We also demonstrate in this study that the ratio of divalent cations to sulfate ions (0 ≤ M2+/SO42–≤ 4.427) has a significant role in interfacial tension reduction and wettability modification. We further show using contact angle wettability measurements that initial weak water–wet quartz surfaces can turn to more water–wet when zirconia nanoparticles used in the low-salinity formulation are in the range of 100–1000 mg/L. Interestingly, further incremental nanoparticle concentration decreases the water wettability but further reduces the carbon dioxide/brine interfacial tension.Ji, J.-H., Liu, Y.-F., Zhou, L., Mbadinga, S.M., Pan, P., Chen, J., Liu, J.-F., Yang, S.-Z., Sand, W., Gu, J.-D., Mu, B.-Z., 2019. Methanogenic degradation of long n-alkanes requires fumarate-dependent activation. Applied and Environmental Microbiology 85, e00985-19.: Methanogenic degradation of n-alkanes is prevalent in n-alkane-impacted anoxic oil reservoirs and oil-polluted sites. However, little is known about the initial activation mechanism of the substrate, especially n-alkanes with a chain length above C16. Here, a methanogenic C16 to C20 n-alkane-degrading enrichment culture was established from production water of a low-temperature oil reservoir. At the end of the incubation (364?days), C16 to C20 (1-methylalkyl)succinates were detected in the n-alkane-amended enrichment culture, suggesting that fumarate addition had occurred in the degradation process. This evidence is supported further by the positive amplification of the assA gene encoding the alpha subunit of alkylsuccinate synthase. A phylogenetic analysis shows these assA amplicons to be affiliated with Smithella and Desulfatibacillum clades. Together with the high abundance of these clades in the bacterial community, these two species are postulated to be the key players in the degradation of C16 to C20 n-alkanes in the present study. Our results provide evidence that long n-alkanes are activated via a fumarate addition mechanism under methanogenic conditions.Importance: Methanogenic hydrocarbon degradation is the major process for oil degradation in subsurface oil reservoirs and is blamed for the formation of heavy oil and oil sands. Addition of n-alkanes to fumarate yielding alkyl-substituted succinates is a well-characterized anaerobic activation mechanism for hydrocarbons and is the most common activation mechanism in the anaerobic biodegradation of n-alkanes with chain lengths less than C16. However, the activation mechanism involved in the methanogenic biodegradation of n-alkanes longer than C16 is still uncertain. In this study, we analyzed a methanogenic enrichment culture amended with a mixture of C16 to C20 n-alkanes. These n-alkanes can be activated via fumarate addition by mixed cultures containing Smithella and Desulfatibacillum species under methanogenic conditions. These observations provide a fundamental understanding of long-n-alkane metabolism under methanogenic conditions and have important applications for the remediation of oil-contaminated sites and for energy recovery from oil reservoirs.Jia, T.Z., Chandru, K., Hongo, Y., Afrin, R., Usui, T., Myojo, K., Cleaves, H.J., 2019. Membraneless polyester microdroplets as primordial compartments at the origins of life. Proceedings of the National Academy of Sciences 116, 15830-15835.: The prebiotic milieu was likely heterogeneous, consisting of a large number of chemicals and their associated reactions, including those not only of biological compounds, but also nonbiological compounds. Although origins of life research has focused primarily on biological molecules, the nonbiological molecules which were also present may have assisted evolving chemical systems in unforeseen ways. Thus, we synthesized and assembled membraneless polyester microdroplets from drying of pools of simple α-hydroxy acid monomers and showed that they can act as plausible prebiotic compartments. By having the capacity to undergo combinatorial rearrangement, these microdroplets could have developed versatile abilities to host early genetic and metabolic systems critical for the origins of life.Abstract: Compartmentalization was likely essential for primitive chemical systems during the emergence of life, both for preventing leakage of important components, i.e., genetic materials, and for enhancing chemical reactions. Although life as we know it uses lipid bilayer-based compartments, the diversity of prebiotic chemistry may have enabled primitive living systems to start from other types of boundary systems. Here, we demonstrate membraneless compartmentalization based on prebiotically available organic compounds, α-hydroxy acids (αHAs), which are generally coproduced along with α-amino acids in prebiotic settings. Facile polymerization of αHAs provides a model pathway for the assembly of combinatorially diverse primitive compartments on early Earth. We characterized membraneless microdroplets generated from homo- and heteropolyesters synthesized from drying solutions of αHAs endowed with various side chains. These compartments can preferentially and differentially segregate and compartmentalize fluorescent dyes and fluorescently tagged RNA, providing readily available compartments that could have facilitated chemical evolution by protecting, exchanging, and encapsulating primitive components. Protein function within and RNA function in the presence of certain droplets is also preserved, suggesting the potential relevance of such droplets to various origins of life models. As a lipid amphiphile can also assemble around certain droplets, this further shows the droplets’ potential compatibility with and scaffolding ability for nascent biomolecular systems that could have coexisted in complex chemical systems. These model compartments could have been more accessible in a “messy” prebiotic environment, enabling the localization of a variety of protometabolic and replication processes that could be subjected to further chemical evolution before the advent of the Last Universal Common Ancestor.Jiang, Z., Lu, Y., Xu, J., Li, M., Shan, G., Li, Q., 2019. Exploring the characteristics of dissolved organic matter and succession of bacterial community during composting. Bioresource Technology 292, 121942. objective of this study was to explore the relationships among physico-chemical parameters, dissolved organic matters (DOM), and bacterial community during composting to better understand composting performances. The results showed total Kjeldahl nitrogen (TKN) (57%), temperature (39%), and pH (3%) were main factors driving the succession of bacterial communities. Firmicutes was a crucial phylum degrading organic matters for DOM formation, whereas the aromaticity and humification of DOM were closely related to Luteimonas (R2?=?0.971, p?<?0.05) and Sphingobacteriaceae (R2?=?0.931, p?<?0.05). Additionally, total phosphorus (TP), total potassium (TK), and TKN increased by 34.84%, 43.66%, and 65.91%, respectively, while organic matter decreased by 61.79%. The final compost had a C/N of 6.91 (<15) and a germination index of 97.81% (>80%), indicating that compost reached maturity and could be safely applied for soil amendment.Jiao, B., Ding, W., Gu, Y., Xiao, Z., Shi, S., Zhao, G., Liu, T., 2019. The reservoir characteristics of marine shale and its effect on the adsorption of methane in Northern Guizhou. Petroleum Science and Technology 37, 2199-2206. reservoir characteristics of the Lower Paleozoic marine shale in Fenggang block of northern Guizhou are evaluated from three aspects: gas-bearing characteristics, petrological characteristics and reservoir space by a series of experimental data. The effect of total organic carbon content, kerogen type and clay mineral content on shale adsorption capacity is discussed. The results show that the reservoir characteristics of the Wufeng-Longmaxi Formation shale in the study area are conducive to the enrichment of shale gas. In the case of quantitative clay minerals, the chlorite content has a significant adverse effect on the methane adsorption of the samples. The shale gas methane adsorption has an excellent increasing trend with the increase of total organic carbon content. The type II1 organic matter is more conducive to the adsorption of methane than the type I organic matter.Jin, C., Li, C., Algeo, T.J., Wu, S., Cheng, M., Zhang, Z., Shi, W., 2020. Controls on organic matter accumulation on the early-Cambrian western Yangtze Platform, South China. Marine and Petroleum Geology 111, 75-87. origin of widespread organic-rich shales on the early Cambrian Yangtze Platform of Nanhua Basin (South China) has been attributed to high primary productivity. To test this hypothesis, we generated multiple paleoproductivity (OCAR and PAR), paleoredox (Corg/P ratios), upwelling/restriction (CoEF?×?MnEF, Co (ppm)?×?Mn (%), Mo/TOC, and Cd/Mo ratios), and terrigenous flux proxies (Al and unreactive Fe (FeU)) for the lower Cambrian Niutitang Formation in the outer-shelf Jinsha section, which records a typical transition from the organic-rich black shales to overlying organic-lean mudstones or siltstones. These new data were integrated with published paleoredox proxies (iron speciation and redox-sensitive trace metals) for the same section. Our results suggest that the organic-rich (TOC?=?4.6?±?1.8%) lower member (LM; 0–37?m) of the Niutitang Formation records ferruginous conditions, high productivity levels, and low siliciclastic fluxes, and that the organic-poor (TOC?=?0.1?±?0.1%) upper member (UM; 37–329?m) was characterized by dominantly oxic conditions, declining productivity levels, and high siliciclastic fluxes. Our results suggest a redox shift from ferruginous to oxic conditions and enhanced terrigenous fluxes in response to falling sea level from the LM to the UM. Secular variations in primary productivity and redox conditions are strongly correlated, which is consistent with a positive feedback: high primary productivity led to increasing water-column anoxia, which enhanced organic P recycling, stimulating further productivity. Variations in primary productivity may reflect variable upwelling intensity in a semi-restricted shelf setting linked to sea-level changes. Taken together, these findings suggest that a combination of primary productivity, redox conditions, and terrigenous fluxes driven by sea-level changes played a key role in organic matter accumulation on the early-Cambrian western Yangtze Platform.Joglar, V., Prieto, A., Barber-Lluch, E., Hernández-Ruiz, M., Fernández, E., Teira, E., 2019. Spatial and temporal variability in the response of phytoplankton and bacterioplankton to B-vitamin amendments in an upwelling system. Biogeosciences Discussions 2019, 1-43. evaluated the temporal (inter-day and inter-season) and spatial variability in microbial plankton responses to vitamins B12 and B1 supply in coastal and oceanic waters. Inter-day variability in microbial plankton responses to B-vitamins was not of great concern, suggesting that B-vitamins availability was controlled by factors operating at larger temporal scales, such as those driving microbial community seasonal succession. Most positive responses were produced by treatments containing either B12 alone or B12 combined with B1 in oceanic waters, which was consistent with the significantly lower average vitamin B12 ambient concentrations compared to that in the coastal station. Growth stimulation by B1 addition was more frequent on bacteria, which is coherent with their widespread dependence on exogenous sources for this growth factor. Negative responses to B-vitamins were generalized in coastal waters in summer, and were associated to a high contribution of Flavobacteriales to the prokaryote community. This observation suggests that the external supply of B12 and/or B1 may promote negative interactions between microbial components when B-vitamins auxotrophs are abundant. The microbial response patterns to B12 and/or B1 amendments were significantly correlated with changes in the prokaryotic community composition, highlighting the pivotal role of prokaryotes in B-vitamins cycling in marine ecosystems.Jolie, E., 2019. Detecting gas-rich hydrothermal vents in Ngozi Crater Lake using integrated exploration tools. Scientific Reports 9, 12164. hydrothermal vents in crater lakes might pose an acute danger to people living nearby due to the risk of limnic eruptions as a result of gas accumulation in the water column. This phenomenon has been reported from several incidents, e.g., the catastrophic Lake Nyos limnic eruption. CO2 accumulation has been determined from a variety of lakes worldwide, which does not always evolve in the same way as in Lake Nyos and consequently requires a site-specific hazard assessment. This paper discusses the current state of Lake Ngozi in Tanzania and presents an efficient approach how major gas-rich hydrothermal feed zones can be identified based on a multi-disciplinary concept. The concept combines bathymetry, thermal mapping of the lake floor and gas emission studies on the water surface. The approach is fully transferable to other volcanic lakes, and results will help to identify high-risk areas and develop suitable monitoring and risk mitigation measures. Due to the absence of a chemical and thermal stratification of Lake Ngozi the risk of limnic eruptions is rather unlikely at present, but an adapted monitoring concept is strongly advised as sudden CO2 input into the lake could occur as a result of changes in the magmatic system.Jones, E.A., Simon, D., Karancsi, T., Balog, J., Pringle, S.D., Takats, Z., 2019. Matrix assisted rapid evaporative ionization mass spectrometry. Analytical Chemistry 91, 9784-9791. evaporative ionization mass spectrometry (REIMS) is a highly versatile technique allowing the sampling of a range of biological solid or liquid samples with no sample preparation. The cost of such a direct approach is that certain sample types provide only moderate amounts of chemical information. Here, we introduce a matrix assisted version of the technique (MA-REIMS), where an aerosol of a pure solvent, such as isopropanol, is mixed with the sample aerosol generated by rapid evaporation of the sample, and it is shown to enhance the signal intensity obtained from a REIMS sampling event by over 2 orders of magnitude. Such an increase greatly expands the scope of the technique, while providing additional benefits such as reducing the fouling of the REIMS source and allowing for a simple method of constant introduction of a calibration correction compound for accurate mass measurements. A range of experiments are presented in order to investigate the processes that occur within this modified approach, and applications where such enhancements are critical, such as intrasurgical tissue identification, are discussed.Jones, M.W., de Arag?o, L.E.O.C., Dittmar, T., de Rezende, C.E., Almeida, M.G., Johnson, B.T., Marques, J.S.J., Niggemann, J., Rangel, T.P., Quine, T.A., 2019. Environmental controls on the riverine export of dissolved black carbon. Global Biogeochemical Cycles 33, 849-874. year, tropical rivers export a dissolved organic carbon (DOC) flux to the global oceans that is equivalent to ~4% of the global land sink for atmospheric CO2. Among the most refractory fractions of terrigenous DOC is dissolved black carbon (DBC), which constitutes ~10% of the total DOC flux and derives from the charcoal and soot (aerosol) produced during biomass burning and fossil fuel combustion. Black carbon (BC) has disproportionate storage potential in oceanic pools and so its export has implications for the fate and residence time of terrigenous organic carbon (OC). In contrast to bulk DOC, there is limited knowledge of the environmental factors that control riverine fluxes of DBC. We thus completed a comprehensive assessment of the factors controlling DBC export in tropical rivers with catchments distributed across environmental gradients of hydrology, topography, climate, and soil properties. Generalized linear models explained 70 and 64% of the observed variance in DOC and DBC concentrations, respectively. DOC and DBC concentrations displayed coupled responses to the dominant factors controlling their riverine export (soil moisture, catchment slope, and catchment stocks of OC or BC, respectively) but varied divergently across gradients of temperature and soil properties. DBC concentrations also varied strongly with aerosol BC deposition rate, indicating further potential for deviation of DBC fluxes from those of DOC due to secondary inputs of DBC from this unmatched source. Overall, this study identifies the specific drivers of BC dynamics in river catchments and fundamentally enhances our understanding of refractory DOC export to the global oceans.Juárez Tomás, M.S., Carrasco, M.G., Lobo, C.B., Alessandrello, M.J., Sánchez, L., Ferrero, M.A., 2019. PAH removal by simultaneous and sequential inoculation of Pseudomonas monteilii P26 and Gordonia sp. H19 in the presence of biostimulants. International Biodeterioration & Biodegradation 144, 104752. and bioaugmentation have been proposed as sustainable alternatives to physicochemical treatments for the environmental decontamination of polycyclic aromatic hydrocarbons (PAH). PAH-removing Pseudomonas monteilii P26 and Gordonia sp. H19, alone or combined with organic and inorganic biostimulants, were previously proposed as candidates to be included in biotechnological products to be used in eco-friendly decontamination processes. This work aims to study the effect of biostimulants on the growth, cell hydrophobicity and emulsifying activity of P. monteilii P26 and Gordonia sp. H19, and to evaluate the influence of selected biostimulants and bacterial inoculation procedure on PAH bioremoval. A complete factorial experimental design was applied to determine the effect of KNO3, K2HPO4, corn steep liquor (CSL) and a PAH mixture on the growth, cell hydrophobicity and bioemulsifying activity of bacterial cultures. The kinetics of PAH bioremoval was evaluated in simultaneous and sequential cultures of P. monteilii P26 and Gordonia sp. H19 in the presence of selected biostimulants. CSL was the only nutrient that exerted positive effects on all responses evaluated, although these effects were not significant in all cases. In mixed cultures, maximum bioremoval of phenanthrene and pyrene was evidenced when the bacterial strains were simultaneously inoculated, independently of the presence or absence of CSL. These results support the biotechnological characterization of two PAH-removing autochthonous Patagonian strains.Junot, C., Fenaille, F., 2019. Chapter 11 - Metabolomics using Fourier transform mass spectrometry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 325-356. metabolome is the set of small molecular mass compounds found in biological media, and metabolomics, which refers to as the analysis of metabolome in a given biological condition, deals with the large scale detection and quantification of metabolites in biological media. The metabolome is characterized by a large number of molecules exhibiting a high diversity of chemical structures and abundances, requiring complementary analytical platforms for extensive coverage. Among them, atmospheric pressure ionization Fourier transform mass spectrometry (FT/MS) instruments are now very popular because they provide accurate mass measurements with ppm and even sub-ppm errors, high and ultra-high resolving power, and also the possibility to perform MSn experiments for annotation and identification of metabolites.This chapter deals with the improvements provided by the different kinds of FT/MS instruments for metabolomics, together with their ability to cover the various analytical needs for metabolomics, from global metabolite profiling to structural characterization of compounds. The specificities of FT/MS in terms of data pre-processing and the input of accurate mass measurements for biological interpretation are also addressed.Kaal, J., Serrano, O., Martínez Cortizas, A., Baldock, J.A., Lavery, P.S., 2019. Millennial-scale changes in the molecular composition of Posidonia australis seagrass deposits: Implications for Blue Carbon sequestration. Organic Geochemistry 137, 103898. ecosystems are recognised for their role in climate change mitigation, due to their capacity to form organic-rich sediments. The chemical recalcitrance of seagrass organs is one characteristic driving carbon storage, but the molecular background of this feature is poorly understood. We assessed molecular composition changes of Posidonia australis sheaths (SH) and roots plus rhizomes (RR) along a sediment core, encompassing 3200?cal. yr BP, by means of nuclear magnetic resonance spectroscopy (13C NMR), conventional analytical pyrolysis (Py-GC–MS) and thermally assisted hydrolysis and methylation (THM-GC–MS). Significant trends with depth (age) in the composition of both SH and RR remains of P. australis were observed from all methods. In general terms, polysaccharides become depleted (degraded) and lignin enriched (selectively preserved) as age increases, and the minor constituents cutin, suberin and condensed tannin are also preferentially depleted during ageing in both fractions. Molecular changes with ageing were smaller in SH, especially regarding polysaccharides, indicative of a superior stability compared to RR. The molecular changes observed are most pronounced within the first 75?cm of the record, which reflects the recalcitrance of P. australis detritus once it is buried below that depth (corresponding to approximately 700?cal. yr BP). The capacity of P. australis to act as a long-term carbon sink seems to be mainly related to the resistance of buried lignocellulose materials to decomposition. The results on diagenetic effects on the molecular fingerprint of seagrass detritus contribute to our understanding of carbon sequestration in Blue Carbon ecosystems. Furthermore, data comparison of the methods applied using principal component analysis (PCA) allowed us to identify consistencies, discrepancies and complementarities.Kadoya, S., Catling, D.C., 2019. Constraints on hydrogen levels in the Archean atmosphere based on detrital magnetite. Geochimica et Cosmochimica Acta 262, 207-219. partial pressure of atmospheric hydrogen (pH2) on the early Earth is important because it has been proposed that high pH2 warmed the planet or allowed prebiotic chemistry in the early atmosphere. However, such hypotheses lack observational constraints on pH2. Here, we use the existence of detrital magnetites in (～3.0Ga) Archean riverbeds to constrain pH2. Under the condition of high pH2, magnetite should disappear via reductive dissolution. We investigated the timescale for a magnetite particle in a river to dissolve, which depends on pH2 and pCO2. Using published estimates of Archean pCO2 and assuming the presence of Fe(III)-reducing microbes, the survival timescale is ～ 1?kyr when pH2 is ～10-2bar, and decreases as pH2 increases. Considering that the residence time of a particle in a short river (<1000km) is ～1kyr, the existence of detrital magnetite particles in Archean riverbeds likely indicates that pH2 was below ～10-2bar. Such a level would preclude H2 as a greenhouse gas or a strongly reducing Archean atmosphere. It is also consistent with limits imposed on H2 by consumption by methanogens because conversion to CH4 is thermodynamically favored.Kaimaki, D.M., Haire, B.T., Ryan, H.P., Jiménez-Serratos, G., Alloway, R.M., Little, M., Morrison, J., Salama, I.E., Tillotson, M.J., Smith, B.E., Moorhouse, S.J., Totton, T.S., Hodges, M., Yeates, S.G., Quayle, P., Clarke, S.M., Müller, E.A., Durkan, C., 2019. Multiscale approach linking self-aggregation and surface interactions of synthesized foulants to fouling mitigation strategies. Energy & Fuels 33, 7216-7224. of oil-exposed surfaces remains a crucial issue as a result of the continued importance of oil as the world’s primary energy source. The key perpetrators in crude oil fouling have been identified as asphaltenes, a poorly described mixture of diverse polyfunctional molecules that form part of the heaviest fractions of oil. Asphaltenes are responsible for a decrease in oil production and energy efficiency and an increase in the risk of environmental hazards. Hence, understanding and managing systems that are prone to fouling is of great value but constitutes a challenge as a result of their complexity. In an effort to reduce that complexity, a study of a synthesized foulant of archipelago structure is presented. A critical perspective on previously described solubility and aggregation mechanisms (e.g., critical nanoaggrerate concentration and critical clustering concentration) is offered because the characterized system favors a continuous distribution of n-mers instead. A battery of experimental and modeling techniques have been employed to link the bulk and interfacial behavior of a representative foulant monomer to effective fouling mitigation strategies. This systematic approach defines a new multiscale methodology in the investigation of fouling systems.Kalvoda, J., Kumpan, T., Qie, W., Fr?da, J., Bábek, O., 2019. Mercury spikes at the Devonian-Carboniferous boundary in the eastern part of the Rhenohercynian Zone (central Europe) and in the South China Block. Palaeogeography, Palaeoclimatology, Palaeoecology 531. (Hg) chemostratigraphy is an efficient tool for tracing distal volcanism, as suggested in many recent studies. In our research, we focused on Hg and other trace element contents in two Devonian-Carboniferous boundary sections from two different and spatially distant areas. The Lesní lom section (Czech Republic) was located in the south-eastern part of the Laurussia plate and the Duli (Guangxi, China) section in the South China Plate. In both studied sections, the highest Hg, Hg/Fexs or Hg/Al values occurred at the Devonian-Carboniferous boundary. In Lesní lom, organic matter remineralization was connected with origin of pyrite which sequestered a part of the Hg content. The decoupling of Hg and TOC within the Duli section strata and the significant correlation with Al and Fe may suggest that Hg is hosted primarily by clay particles, derived from the landmass into the marine realm. Mercury was also incorporated into pyrites but the poor correlation between Hg and TS (total sulfur) indicates a possible loss of S during oxygenation events. In the Lesní lom section, and partly in the Duli section, Fe and Mn redox cycling may have played an important role in sediment Hg content. Both sections were influenced by widespread hydrothermal and volcanic activity, indicated by positive Eu anomalies, MSI, Fe/Ti, Zr/Al2O3 and Ti/Al2O3 values. It remains to be clarified whether, besides the interplay of local magmatic activity and redox oscillations, there may have been some additional influence of the multi-phase Viluy Large Igneous Province, although its younger phase (364.4?±?1.7?Ma) slightly precedes the Hg anomalies obtained.Kamjunke, N., Hertkorn, N., Harir, M., Schmitt-Kopplin, P., Griebler, C., Brauns, M., von Tümpling, W., Weitere, M., Herzsprung, P., 2019. Molecular change of dissolved organic matter and patterns of bacterial activity in a stream along a land-use gradient. Water Research 164, 114919. networks are globally relevant for the processing of dissolved organic matter (DOM). To investigate the change in molecular DOM diversity along the river course, high-field FTICR mass spectrometry and NMR spectroscopy of riverine DOM as well as bacterial abundance and activity were measured in a third order stream along a land-use gradient from pristine, agricultural to urban landscapes. DOM composition showed a clear evolution along the river course with an initial decrease of average oxidation and unsaturation followed by an increased relative abundance of CHNO and CHOS compounds introduced by agriculture and waste water, respectively. DOM composition was dominated by rather unsaturated CHO compounds (H/C?≤?1) in headwaters and by more aliphatic molecules at downstream sites. Oxygenated functional groups shifted from aromatic ethers and hydroxyl groups to aliphatic carboxylic acids and aliphatic hydroxyl groups. This massive dislocation of oxygen significantly increased the diversity of atomic environments in branched aliphatic groups from headwater to downstream DOM. Mass spectra of DOM enabled the detection of compositional relationships to bacterial abundance and activity which was positively related to more aliphatic components (H/C?>?1) and negatively related to unsaturated components. FTICR mass and NMR spectra corroborated the initial decline in DOM molecular diversity predicted by the River Continuum Concept (RCC) but demonstrated an anthropogenic increase in the molecular diversity of DOM further downstream. While the high DOM molecular diversity in first order headwater streams was the result of small scale ecosystem plurality, agriculture and waste water treatment introduced many components in the lower reaches. These anthropogenic influences together with massive bacterial oxidation of DOM contributed to a growth of molecular diversity of downstream DOM whose composition and structure differed entirely from those found in pristine headwaters.Kanawati, B., Schmitt-Kopplin, P., 2019. Fundamentals and Applications of Fourier Transform Mass Spectrometry. 978-0-12-814013-0, 786 pp. and Applications of Fourier Transform Mass Spectrometry is the first book to delve into the underlying principles on the topic and their linkage to industrial applications. Drs. Schmitt-Kopplin and Kanawati have brought together a team of leading experts in their respective fields to present this technique from many different perspectives, describing, at length, the pros and cons of FT-ICR and Orbitrap. Numerous examples help researchers decide which instruments to use for their particular scientific problem and which data analysis methods should be applied to get the most out of their data.Covers FT-ICR-MS and Orbitrap’s fundamentals, enhancing researcher knowledgeIncludes details on ion sources, data processing, chemical analysis and imagingProvides examples across the wide spectrum of applications, including omics, environmental, chemical, pharmaceutical and food analysisSection A: Historical chaptersWanczek, K.P., Kanawati, B., 2019. Chapter 1 - Historical developments in Fourier transform ion cyclotron resonance mass spectrometry pp. 3-33.Section B: Fundamental/technology chaptersMakarov, A., Grinfeld, D., Ayzikov, K., 2019. Chapter 2 - Fundamentals of Orbitrap analyzer, 37-61.Easterling, M.L., Agar, J.N., 2019. Chapter 3 - Fundamentals, strengths, and future directions for Fourier transform ion cyclotron resonance mass spectrometry, pp. 63-88.Nikolaev, E.N., Kostyukevich, Y.I., Vladimirov, G., 2019. Chapter 4 - Fundamentals and simulations in FT-ICR-MS, pp. 89-111.Tsybin, Y.O., Nagornov, K.O., Kozhinov, A.N., 2019. Chapter 5 - Advanced fundamentals in Fourier transform mass spectrometry, pp. 113-132.Kanawati, B., Wanczek, K.P., Schmitt-Kopplin, P., 2019. Chapter 6 - Data processing and automation in Fourier transform mass spectrometry, pp. 133-185.Floris, F., O'Connor, P.B., 2019. Chapter 7 - Fundamentals of two dimensional Fourier transform mass spectrometry, pp. 187-232.Fernandez-Lima, F., 2019. Chapter 8 - Trapped ion mobility spectrometry coupled to FT-ICR MS: Fundamentals and applications, pp. 233-251.Kreutzer, L., Aichler, M., Walch, A.K., 2019. Chapter 9 - In situ metabolomics in cancer tissue by high-resolution mass spectrometry imaging, pp. 253-279.Aubriet, F., Carré, V., 2019. Chapter 10 - Fourier transform ion cyclotron resonance mass spectrometry and laser: A versatile tool, pp. 281-322.Section C: Applications chaptersJunot, C., Fenaille, F., 2019. Chapter 11 - Metabolomics using Fourier transform mass spectrometry, pp. 325-356.Moritz, F., Hemmler, D., Kanawati, B., Schnitzler, J.-P., Schmitt-Kopplin, P., 2019. Chapter 12 - Mass differences in metabolome analyses of untargeted direct infusion ultra-high resolution MS data, pp. 357-405.Gonsior, M., 2019. Chapter 13 - FT-ICR MS and Orbitrap mass spectrometry approaches in environmental chemistry, pp. 407-423.Kovalev, S.V., Lebedev, A.T., 2019. Chapter 14 - Identification of biologically active peptides by means of Fourier transform mass spectrometry, pp. 425-468.Filho, J.F.A., Lacerda, V., Rom?o, W., 2019. Chapter 15 - Fourier transform mass spectrometry applied to forensic chemistry, pp. 469-508.Pereira, I., de Aguiar, D.V.A., Vasconselos, G., Vaz, B.G., 2019. Chapter 16 - Fourier transform mass spectrometry applied to petroleomics, pp. 509-528.Vinh, J., 2019. Chapter 17 - Proteomics and proteoforms: Bottom-up or top-down, how to use high-resolution mass spectrometry to reach the Grail, pp. 529-567.Wanczek, K.P., Kanawati, B., 2019. Chapter 18 - Gas phase ion-molecule reactions of inorganic compounds in FT-ICR-MS, pp. 569-591.Dillinger, S., Niedner-Schatteburg, G., 2019. Chapter 19 - Cryo trapping by FT-MS for kinetics and spectroscopy, pp. 593-621.Duan, J., Amster, I.J., 2019. Chapter 20 - Application of FTMS to the analysis of glycosaminoglycans, pp. 623-649.Rychlik, M., Kanawati, B., Roullier-Gall, C., Hemmler, D., Liu, Y., Alexandre, H., Gougeon, R.D., Gmelch, L., Gotthardt, M., Schmitt-Kopplin, P., 2019. Chapter 21 - Foodomics assessed by Fourier transform mass spectrometry, pp. 651-677.Hertzog, J., Carré, V., Aubriet, F., 2019. Chapter 22 - Contribution of Fourier transform mass spectrometry to bio-oil study, pp. 679-733.Index pp. 735-754.Kanawati, B., Wanczek, K.P., Schmitt-Kopplin, P., 2019. Chapter 6 - Data processing and automation in Fourier transform mass spectrometry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 133-185. resolution mass spectrometers produce large amount of MS and MS/MS spectra, whose interpretations may not be easy even for experts in this field. Noise among other interfering problems (such as chemical background, side lobes, side bands, multiple harmonics) gather in those spectra and make them complex. Moreover, all physical characteristics (resolution, peak shape, signal to noise ratio and signal intensity) of mass spectra originate and are actually derived from their corresponding frequency spectra, which are generally obtained by applying Fourier transform to time domain detected transients. In this chapter, several data processing techniques will be discussed for obtaining magnitude and absorption modes frequency spectra and a review of most important mass calibration equations will be discussed in great detail. De-noising, peak alignment, sum formula calculations and batch processing of FTMS spectra will also be discussed in this chapter. Moreover, automation of FT-ICR mass spectrometers is reviewed here and the author illustrates in this chapter a hand-on technical experience for achieving a successful full automation of the 12T FT-ICR mass spectrometer in Helmholtz Zentrum München metabolomics research laboratory, which could greatly enhance the productivity, by efficiently running in unattended mode on 24h basis. We selected over 135 related references in signal processing and automation in an attempt to provide a comprehensive guidance to mass spectrometry scientists.Kang, W.-Y., Thompson, P.T., El-Amouri, S.S., Fan, T.W.M., Lane, A.N., Higashi, R.M., 2019. Improved segmented-scan spectral stitching for stable isotope resolved metabolomics (SIRM) by ultra-high-resolution Fourier transform mass spectrometry. Analytica Chimica Acta 1080, 104-115. have implemented a linear ion trap (LIT)-based SIM-stitching method for ultra-high-resolution Fourier transform mass spectrometry (FTMS) that increases the S/N over a wide m/z range compared to non-segmented wide full-scan (WFS) spectra. Here we described an improved segmented spectral scan stitching method that was based on quadrupole mass filter (QMF)-SIM, which overcame previous limitations of ion signal loss in LIT. This allowed for accurate representation of isotopologue distributions, both at natural abundance and in stable isotope-resolved metabolomics (SIRM)-based experiments. We also introduced a new spectral binning method that provided more precise and resolution-independent bins for irreversibly noise-suppressed FTMS spectra. We demonstrated a substantial improvement in S/N and sensitivity (typically?>?10-fold) for 13C labeled lipid extracts of human macrophages grown as three-dimensional (3D) cell culture, with detection of an increased number of 13C isotopologue ions. The method also enabled analysis of extracts from very limited biological samples.Kasting, J.F., 2019. The Goldilocks planet? How silicate weathering maintains Earth “just right”. Elements 15, 235-240.'s climate is buffered over long timescales by a negative feedback between atmospheric CO2 level and surface temperature. The rate of silicate weathering slows as the climate cools, causing CO2 to increase and warming the surface through the greenhouse effect. This buffering system has kept liquid water stable at Earth's surface, except perhaps during certain ‘Snowball Earth’ episodes at the beginning and end of the Proterozoic. A similar stabilizing feedback is predicted to occur on rocky planets orbiting other stars if they share analogous properties with Earth, most importantly an adequate (but not overly large) abundance of water and a mechanism for recycling carbonate rocks into CO2. Periodic oscillations between globally glaciated and ice-free climates may occur on planets with weak stellar insolation and/or slow volcanic outgassing rates. Most silicate weathering is thought to occur on the continents today, but seafloor weathering (and reverse weathering) may have been equally important earlier in Earth's history.Kazarina, A., Gerhards, G., Petersone-Gordina, E., Kimsis, J., Pole, I., Zole, E., Leonova, V., Ranka, R., 2019. Analysis of the bacterial communities in ancient human bones and burial soil samples: Tracing the impact of environmental bacteria. Journal of Archaeological Science 109, 104989. our attempts to reveal the hidden fragments of the history of the natural world, ancient DNA (aDNA) is the precious missing key that allows us to discover hidden truths about ourselves and the world around us. Not only does aDNA encrypt genetic data from a particular individual, it also carries information about the microbial communities that were present in the individual. However, the process of such data mining has many intrinsic challenges. One of the main challenges in aDNA research is the contamination of archaeological material with environmental bacteria from the surrounding soil and postmortem microbial sources.The goal of this study was to identify the microbial communities in human archaeological bone samples dated 15th - 17th century AD and to compare the microbiome patterns with the corresponding soil samples of the burial environment. Samples were analysed by 16S rRNA-based profiling of bacterial communities using Ion Torrent technology. The results showed that the most represented phyla in the bone samples were Firmicutes followed by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Nitrospirae, Planctomycetes, Gemmatimonadetes and Bacteroidetes.All identified microbial taxa of the bone samples coincided with the corresponding soil samples, indicating significant infiltration and contamination of archaeological remains with microbial species of the burial environment. However, differences in microbial community composition between the bone and soil samples were observed at both the phylum and genus levels, as indicated by statistically significant beta-diversity analysis results. A deeper investigation of the Firmicutes phylum showed significant differences between the bone and soil samples by alpha- and beta-diversity analyses. Several genera belonging to Firmicutes were significantly more abundant in the soil samples than in the bone samples and vice versa.In conclusion, the analysis of the microbiome profiles of archaeological bone and corresponding soil samples revealed significant diversity in microbial compositions. It appeared that some bacteria may infiltrate the bone matter through the process of tissue decomposition and remain trapped inside for a longer period of time. Archaeological human bone samples might provide significant data on the investigation of ancient human microbiomes; however, environmental bacteria from the surrounding soil must be considered an important contamination factor.Kazlauskas, D., Varsani, A., Koonin, E.V., Krupovic, M., 2019. Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial?and archaeal plasmids. Nature Communications 10, 3425. (ss) DNA viruses are a major component of the earth virome. In particular, the circular, Rep-encoding ssDNA (CRESS-DNA) viruses show high diversity and abundance in various habitats. By combining sequence similarity network and phylogenetic analyses of the replication proteins (Rep) belonging to the HUH endonuclease superfamily, we show that the replication machinery of the CRESS-DNA viruses evolved, on three independent occasions, from the Reps of bacterial rolling circle-replicating plasmids. The CRESS-DNA viruses emerged via recombination between such plasmids and cDNA copies of capsid genes of eukaryotic positive-sense RNA viruses. Similarly, the rep genes of prokaryotic DNA viruses appear to have evolved from HUH endonuclease genes of various bacterial and archaeal plasmids. Our findings also suggest that eukaryotic polyomaviruses and papillomaviruses with dsDNA genomes have evolved via parvoviruses from CRESS-DNA viruses. Collectively, our results shed light on the complex evolutionary history of a major class of viruses revealing its polyphyletic origins.Kerimov, V.Y., Kuznetsov, N.B., Osipov, A.V., 2019. Geodynamic conditions of oil-and-gas accumulations in the Ural–Novaya Zemlya Belt. Doklady Earth Sciences 487, 741-744. paper provides a brief tectonic and geological overview of the Ural– Novaya Zemlya Forebelt of Oil-and-Gas Accumulation and describes the conditions under which the hydrocarbon deposits were formed in the structures of high- and low-angle reverse faults (upthrust-and-thrust) on the eastern side of the belt. It is shown that the early stages of belt formation are associated with Paleozoic subduction and obduction processes that occurred in the transition zone between the Paleo-European continent and the Ural paleo-ocean located eastward (in modern coordinates) of the continent. The intensive cover-folded dislocations of the western vergency are fixed into the eastern side of the Ural–Novaya Zemlya Forebelt of Oil-and-Gas Accumulation. We associate these dislocations with the continental collision that occurred during the closure of the Ural paleo-ocean in the Late Paleozoic, and in the northern-most segments of the belt, probably in the Early Mesozoic. The structural paragenesis of the eastern side of the Ural–Novaya Zemlya Forebelt of Oil-and Gas-Accumulation includes upthrust–thrusts and thrusts, as well as structural units of different sizes, which were formed under the conditions of latitudinal compression.Khan, M.Z., Feng, Q., Zhang, K., Guo, W., 2019. Biogenic silica and organic carbon fluxes provide evidence of enhanced marine productivity in the Upper Ordovician-Lower Silurian of South China. Palaeogeography, Palaeoclimatology, Palaeoecology 534, 109278. silica is a powerful palaeoproductivity proxy in palaeomarine environments and is significant within shale gas reservoirs, demonstrating the association of marine hydrocarbon source rocks with the abundance of micro-siliceous fossils, yet detailed studies that investigate this strong alliance in the Ordovician-Silurian transition are still lacking. The bulk of TOC in marine sediments is commonly assumed to have been derived predominantly from marine phytoplankton, with modern ocean surveys indicating good correspondence between silica content and primary productivity. This study discovers a strong positive correlation between biogenic silica (Bio-Si) and TOC in the Upper Ordovician-Lower Silurian Wufeng and Longmaxi formations of South China in the Jiaoye 41-5 (R?=?+0.68, p(α)?<?0.01, n?=?69) and Jiaoye 51-2 (R?=?+0.68, p(α)?<?0.01, n?=?48) cores, implying that enhanced marine productivity has a strong effect on organic carbon enrichment. Geochemical and palaeontological analyses revealed that silica within these shales generally had a biogenic origin in Jiaoye 41-5 and Jiaoye 51-2, subsequently modified by silica dissolution and re-crystallization of radiolarians and sponge spicules. Palaeoproductivity proxies, including biogenic silica, barium, phosphorous, copper and nickel, were applied, together with the occurrence of pyritized or “ghost” radiolarians, to confirm high palaeoproductivity in the O-S transition. Synchronous OCAR and Bio-SiAR profiles imply that silica originating from siliceous organisms (Bio-Si) served as a likely vector for organic carbon enrichment in the Palaeozoic Wufeng-Longmaxi marine siliceous source rock, providing two possibilities: (i) the abundance of radiolarians was linked to algal proliferation, and consequently, high productivity resulted in a large organic carbon flux and/or (ii) radiolarians contributed to TOC (supported by studies revealing that modern radiolarians exhibit lipid contents of up to 47%).Kim, D., Jung, J.-H., Ha, S.Y., An, J.G., Shankar, R., Kwon, J.-H., Yim, U.H., Kim, S., 2019. Molecular level determination of water accommodated fraction with embryonic developmental toxicity generated by photooxidation of spilled oil. Chemosphere 237, 124346. this study, developmental toxicity was increased as the oil was further degraded under natural sunlight. Detailed chemical composition of the degraded oils was examined by use of gas chromatography (GC) and (?) electrospray ionization ultrahigh resolution mass spectrometry (UHR-MS). Baseline toxicities were estimated based on chemical activities of polycyclic aromatic hydrocarbons, and it was obvious that the predicted chemical activities can not explain increased toxicity alone. However, the ultrahigh resolution mass spectral abundance of polar compounds including O3 and O4 class compounds was significantly increased as the photodegradation proceeded. Further examination of double bond equivalence values of the compounds showed that polar compounds with both non-aromatic and aromatic polar structures were increased. Statistical analysis indicates that the increased toxicity can be well explained by the increased polar compounds. Therefore, the oxygenated compounds identified in this study can play an important role in toxicity of degraded oils.Kim, G., Lee, H., Chen, Z., Athichanagorn, S., Shin, H., 2019. Effect of reservoir characteristics on the productivity and production forecasting of the Montney shale gas in Canada. Journal of Petroleum Science and Engineering 182, 106276. gas is a typical unconventional gas trapped in a tight shale formation, which is considered as a source as well as reservoir rock. Therefore, the productivity of shale gas is closely related to the reservoir parameters making it very important to understand the characteristics of shale reservoirs. In this study, the production data of Montney shale was analyzed and the impact of the reservoir characteristics on the productivity was quantified. The reservoir characteristics can be divided into the reservoir quality (RQ) and completion quality (CQ) parameters. The productivity of shale gas, which is defined as the production decline variables, such as the peak monthly rate (PMR), the initial decline rate, and the decline exponent, was compared with the RQ and CQ.Among the CQ parameters, the brittleness index (BI) was found to affect the overall decline trend in production and had a qualitative correlation with the initial decline rate and decline exponent. Moreover, among the RQ, the total organic carbon (TOC) is closely related to the PMR and the amount of organic carbon (S1) already generated as hydrocarbon is strongly correlated with the initial decline rate and the decline exponent, especially in the transient linear flow regime. Therefore, it is possible to quantify the effects of the organic carbon contents on the productivity of shale gas and estimate the production in the transient linear flow regime.Kim, J.-G., Kim, S.-J., Cvirkaite-Krupovic, V., Yu, W.-J., Gwak, J.-H., López-Pérez, M., Rodriguez-Valera, F., Krupovic, M., Cho, J.-C., Rhee, S.-K., 2019. Spindle-shaped viruses infect marine ammonia-oxidizing thaumarchaea. Proceedings of the National Academy of Sciences 116, 15645-15650.: Ammonia-oxidizing archaea (AOA) are major players in global nitrogen cycling. The physicochemical and metabolic factors affecting the composition of AOA communities and their efficiency of resource utilization have been studied extensively. However, viral predation on AOA remains unexplored due to lack of isolated virus–host systems. Here we report on the isolation and characterization of three Nitrosopumilus spindle-shaped viruses (NSVs) that infect AOA hosts. NSVs represent a potentially important group of marine viruses with a chronic infection cycle, providing important insights into the diversity and evolution of the archaeal virosphere. The wide spread of NSVs in AOA-containing marine environments suggests that NSV predation might regulate the diversity and dynamics of AOA communities, thereby affecting the carbon and nitrogen cycling.Abstract: Ammonia-oxidizing archaea (AOA) from the phylum Thaumarchaeota are ubiquitous in marine ecosystems and play a prominent role in carbon and nitrogen cycling. Previous studies have suggested that, like all microbes, thaumarchaea are infected by viruses and that viral predation has a profound impact on thaumarchaeal functioning and mortality, thereby regulating global biogeochemical cycles. However, not a single virus capable of infecting thaumarchaea has been reported thus far. Here we describe the isolation and characterization of three Nitrosopumilus spindle-shaped viruses (NSVs) that infect AOA and are distinct from other known marine viruses. Although NSVs have a narrow host range, they efficiently infect autochthonous Nitrosopumilus strains and display high rates of adsorption to their host cells. The NSVs have linear double-stranded DNA genomes of ～28 kb that do not display appreciable sequence similarity to genomes of other known archaeal or bacterial viruses and could be considered as representatives of a new virus family, the “Thaspiviridae.” Upon infection, NSV replication leads to inhibition of AOA growth, accompanied by severe reduction in the rate of ammonia oxidation and nitrite reduction. Nevertheless, unlike in the case of lytic bacteriophages, NSV propagation is not associated with detectable degradation of the host chromosome or a decrease in cell counts. The broad distribution of NSVs in AOA-dominated marine environments suggests that NSV predation might regulate the diversity and dynamics of AOA communities. Collectively, our results shed light on the diversity, evolution, and potential impact of the virosphere associated with ecologically important mesophilic archaea.Kitjanukit, S., Sasaki, K., Okibe, N., 2019. Production of highly catalytic, archaeal Pd(0) bionanoparticles using Sulfolobus tokodaii. Extremophiles 23, 549-556. thermo-acidophilic archaeon, Sulfolobus tokodaii, was utilized for the production of Pd(0) bionanoparticles from acidic Pd(II) solution. Use of active cells was essential to form well-dispersed Pd(0) nanoparticles located on the cell surface. The particle size could be manipulated by modifying the concentration of formate (as electron donor; e-donor) and by addition of enzymatic inhibitor (Cu2+) in the range of 14–63 nm mean size. Since robust Pd(II) reduction progressed in pre-grown S. tokodaii cells even in the presence of up to 500 mM Cl?, it was possible to conversely utilize the effect of Cl? to produce even finer and denser particles in the range of 8.7–15 nm mean size. This effect likely resulted from the increasing stability of anionic Pd(II)–chloride complex at elevated Cl? concentrations, eventually allowing involvement of greater number of initial Pd(0) crystal nucleation sites (enzymatic sites). The catalytic activity [evaluated based on Cr(VI) reduction reaction] of Pd(0) bionanoparticles of varying particle size formed under different conditions were compared. The finest Pd(0) bionanoparticles obtained at 50 mM Cl? (mean 8.7 nm; median 5.6 nm) exhibited the greatest specific Cr(VI) reduction rate, with four times higher catalytic activity compared to commercial Pd/C. The potential applicability of S. tokodaii cells in the recovery of highly catalytic Pd(0) nanoparticles from actual acidic chloride leachate was, thus, suggested.Kocheva, L.S., Karmanov, A.P., Lutoev, V.P., Shumilov, I.K., Glukhov, Y.V., Pokryshkin, S.A., 2019. Structural and chemical features of organic matter in carbonized wood of the Devonian and Jurassic periods. Doklady Earth Sciences 486, 634-637. results of studies of the chemical structure of organic matter in Devonian and Jurassic carbonized wood using IR, ESR, and GC–MS techniques along with elemental analysis are presented. It is shown that the examined samples consist of metamorphism products of natural lignin, which confirms the hypothesis of the key role of lignin in coal formation.Konecky, B., Dee, S.G., Noone, D.C., 2019. WaxPSM: A forward model of leaf wax hydrogen isotope ratios to bridge proxy and model estimates of past climate. Journal of Geophysical Research: Biogeosciences 124, 2107-2125. D/H ratio of epicuticular plant waxes (δDwax) preserved in sedimentary archives is a powerful tool for paleoclimate reconstruction, but comparisons to other proxy records or to climate model simulations requires a proxy system model (PSM) that accounts for transformations between δDprecip and δDwax. Here we present a new, publicly available PSM for plant waxes, WaxPSM. WaxPSM predicts δDwax from observational data or any isotope‐enabled modern, paleo, or future climate model experiment. δD values of the C29 n‐alkane are calculated based on precipitation or soil water δD and observed apparent fractionation values, adjusted for plant‐type differences. Using WaxPSM, we assess three key uncertainties in δDwax records: the degree to which variations in δD may reflect changes in vegetation rather than climate, structural uncertainties that arise from limited water isotopic observations, and the impacts of land cover change on climate reconstructions during the Last Glacial Maximum and the Preindustrial period. Parametric and structural uncertainties can cause δDwax variations up to 50‰, but in most cases, the differences are ～10–30‰. The drier subtropics are additionally impacted by the incorrect structural assumption that plants' source water, δDsoil, is isotopically similar to the climate variable of interest, δDprecip. We recommend a coordinated, systematic effort to elevate observational constraints on δDprecip, δDsoil, and the δD of multiple compound classes, which would dramatically reduce parametric and structural uncertainties and allow further complexity to be built into the model.Kong, J.D., Wang, H., Siddique, T., Foght, J., Semple, K., Burkus, Z., Lewis, M.A., 2019. Second-generation stoichiometric mathematical model to predict methane emissions from oil sands tailings. Science of The Total Environment 694, 133645. metabolism of fugitive hydrocarbons produces greenhouse gas (GHG) emissions from oil sands tailings ponds (OSTP) and end pit lakes (EPL) that retain fluid tailings from surface mining of oil sands ores. Predicting GHG production, particularly methane (CH4), would help oil sands operators mitigate tailings emissions and may assist regulators evaluating the trajectory of reclamation scenarios. Using empirical datasets from laboratory incubation of OSTP sediments with pertinent hydrocarbons, we developed a stoichiometric model for CH4 generation by indigenous microbes. This model improved on previous first-approximation models by considering long-term biodegradation kinetics for 18 relevant hydrocarbons from three different oil sands operations, lag times, nutrient limitations, and microbial growth and death rates. Laboratory measurements were used to estimate model parameter values and to validate the new model. Goodness of fit analysis showed that the stoichiometric model predicted CH4 production well; normalized mean square error analysis revealed that it surpassed previous models. Comparison of model predictions with field measurements of CH4 emissions further validated the new model. Importantly, the model also identified in-situ parameters that are currently lacking but are needed to enable future robust modeling of CH4 production from OSTP and EPL in-situ.Kontakiotis, G., Besiou, E., Antonarakou, A., Zarkogiannis, S.D., Kostis, A., Mortyn, P.G., Moissette, P., Cornée, J.J., Schulbert, C., Drinia, H., Anastasakis, G., Karakitsios, V., 2019. Decoding sea surface and paleoclimate conditions in the eastern Mediterranean over the Tortonian-Messinian Transition. Palaeogeography, Palaeoclimatology, Palaeoecology 534, 109312. sedimentological, micropaleontological and geochemical data from the Upper Miocene pre-evaporitic sedimentary sequence of the Faneromeni section (Crete Island, eastern Mediterranean) revealed a stepwise restriction of the Mediterranean Sea preceding the Messinian Salinity Crisis (MSC), which was modulated by a sedimentary cyclicity responding to orbital parameters. This cyclicity is manifested by lithological alternations from laminated to indurated homogeneous marls and clayey limestones, and covers the Tortonian-Messinian Transition (TMT; 7.6–6.7?Ma). This time window covers the successive closure of the marine Mediterranean-Atlantic gateways, which culminated in the onset of the MSC. In the present study, we present the first evidence for changes in the upper water column reflected by sea surface temperature (SST) and salinity (SSS) variations that correlate with pronounced paleoclimatic fluctuations. Planktonic foraminiferal isotopes, in combination with paired mixed layer Sr/Ca-derived SST data, reveal that the very warm late Tortonian interval has been followed by a strong long-term cooling (~10?°C) and desalination (~10‰) trend during the earliest Messinian, attributed to the paroxysmal phase of the so-called “siphon” event. In particular, the climate shift that occurred at the end of a global carbon isotope (δ13C) decrease suggests that changes in the carbon cycle were instrumental in driving late Miocene climate dynamics (cooling and aridity) in the progressively isolated eastern Mediterranean Sea. The observed salinity variability during this time interval also provides further insights about seasonal freshwater inputs and gives new support to the much-debated hydrologic regime (linear salinity increase vs step-function evolution with strong salinity fluctuations) preceding the deposition of evaporites. The novel methodology of foraminiferal Sr/Ca paleothermometry and results of this study could have numerous potential applications to other regions and relevant extreme geological events. Therefore, in the near future we expect this approach to add important new information to our understanding of Neogene climates.Kord, S., Soleymanzadeh, A., Miri, R., 2019. A generalized scaling equation to predict asphaltene precipitation during precipitant dilution, natural depletion, water injection and gas injection. Journal of Petroleum Science and Engineering 182, 106320. precipitation and subsequent deposition on the rock surface during natural depletion and Enhanced Oil Recovery (EOR) methods are two challenging flow assurance issues, causing a sudden decline in oil production. Different precipitation mechanisms and absence of an appropriate generalized characterization parameter have questioned the predictive potential of numerous available thermodynamic models. To overcome the complexity of using available thermodynamic models, different scaling equations were developed to represent a simple yet accurate estimation of the amount of asphaltene precipitation. Nonetheless, most of the proposed correlations are not generalized and are best suited to a specific scenario such as addition of a precipitant or gas injection.In this study, several asphaltene precipitation experiments were conducted on different real oil samples to investigate the amount of precipitated asphaltene due to the compositional changes cause by injection of Methane and Water and also due to pressure variations representing natural depletion mechanism. Besides performing the experiments, the collected literature data for precipitant dilution and gas injection were used to propose a new generalized scaling equation by developing the idea suggested by Kord and Ayatollahi to model all types of asphaltene precipitation phenomena. The results indicated that the new generalized scaling equation can successfully model all types of asphaltene precipitation scenarios. The amount of precipitation can be estimated at different thermodynamic conditions for four precipitation phenomena. The results illustrated that the new generalized scaling equation can successfully model all factors triggering asphaltene precipitation at various stages of production, demonstrating its potential for use as an efficient tool to identify, assess and mitigate risk of asphaltene deposition.Kotu, S.P., Mannan, M.S., Jayaraman, A., 2019. Emerging molecular techniques for studying microbial community composition and function in microbiologically influenced corrosion. International Biodeterioration & Biodegradation 144, 104722. influenced corrosion (MIC) accounts for approximately 20–50% of total corrosion costs in the United States. Microorganisms causing MIC in various field locations such as oil pipelines and cooling water systems have been historically studied using either culture- or DNA hybridization- or polymerase chain reaction (PCR)-based methods to estimate levels of the microorganisms (e.g., sulfate reducing bacteria) present in the community and obtain an accurate microbial fingerprint of the community. While these approaches provide information on the community composition at each MIC-impacted field location, the composition of microbial communities is distinct at different MIC impacted field locations and equipment. Moreover, all the microorganisms identified at a specific MIC impacted location need not contribute to the observed corrosion at that location. Since metabolism gives a direct readout of microbial activity, an emerging hypothesis is that correlating the metabolic footprint of the community to the microbial community composition can provide information on the key microbial species involved in MIC. This review discusses advances in molecular methods for investigating microbial community composition and metabolic footprint that are needed, along with information on electrochemical mechanisms, to develop a comprehensive understanding of MIC mechanisms.Kovalev, S.V., Lebedev, A.T., 2019. Chapter 14 - Identification of biologically active peptides by means of Fourier transform mass spectrometry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 425-468. the most various advantageous properties peptides are ubiquitous participants in nearly all biological processes. Elucidation of their structure is important in terms of physiology, for synthesis of their analogs, and for biomarkers discovery. New “omics” techniques and especially peptidomics, based on mass spectrometry (MS), have been applied to peptide structure elucidation. Fourier transform mass spectrometry (FTMS) offers advantages of high resolution and mass accuracy that are especially helpful in peptide mass fingerprinting and mass mapping. Tandem FTMS (a combination of FTMS with various ion activation and dissociation techniques) provides reliable information about the amino acid sequence. This chapter reviews application of FTMS for characterization and sequencing of bioactive peptides. Aspects of MS imaging, mass mapping, basics of different tandem MS methods, their advantages and drawbacks are discussed. Major peptidomics objects include amphibian skin secretion, venoms of vertebrates and invertebrates, neuropeptides of crustaceans and endogenous peptides in human biological fluids.Kreutzer, L., Aichler, M., Walch, A.K., 2019. Chapter 9 - In situ metabolomics in cancer tissue by high-resolution mass spectrometry imaging, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 253-279. chapter introduces the in situ investigation on metabolomics in cancer tissues by high-resolution mass spectrometry imaging. Metabolomics is a rapidly increasing field, since the detection of biochemical processes can improve the diagnostic, therapeutic treatment prediction, and prognosis in diseases such as cancer. By analyzing metabolic alterations in cancer tissues, insights into the pathway regulations and the resulting clinical outcome can be obtained and associated. In recent years, especially high-resolution matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) was an emerging technique in the analysis of metabolite molecular data and their spatial distribution in tissues. The main intentions in the combination of metabolomics with MALDI MSI are the discovery of molecular biomarkers and metabolic pathways altered in tumors, as well as therapy response prediction and method development. Therefore, increasing numbers of studies were published recently, investigating the optimization of the MSI methods, overcoming the current difficulties and studying the role of clinical translation.Krot, A.N., 2019. Refractory inclusions in carbonaceous chondrites: Records of early solar system processes. Meteoritics & Planetary Science 54, 1647-1691. consist of three major components: refractory inclusions (Ca,Al‐rich inclusions [CAIs] and amoeboid olivine aggregates), chondrules, and matrix. Here, I summarize recent results on the mineralogy, petrology, oxygen, and aluminum‐magnesium isotope systematics of the chondritic components (mainly CAIs in carbonaceous chondrites) and their significance for understanding processes in the protoplanetary disk (PPD) and on chondrite parent asteroids. CAIs are the oldest solids originated in the solar system: their U‐corrected Pb‐Pb absolute age of 4567.3 ± 0.16 Ma is considered to represent time 0 of its evolution. CAIs formed by evaporation, condensation, and aggregation in a gas of approximately solar composition in a hot (ambient temperature >1300 K) disk region exposed to irradiation by solar energetic particles, probably near the protoSun; subsequently, some CAIs were melted in and outside their formation region during transient heating events of still unknown nature. In unmetamorphosed, type 2–3.0 chondrites, CAIs show large variations in the initial 26Al/27Al ratios, from <5 × 10–6 to ~5.25 × 10–5. These variations and the inferred low initial abundance of 60Fe in the PPD suggest late injection of 26Al by a wind from a nearby Wolf–Rayet star into the protosolar molecular cloud core prior to or during its collapse. Although there are multiple generations of CAIs characterized by distinct mineralogies, textures, and isotopic (O, Mg, Ca, Ti, Mo, etc.) compositions, the 26Al heterogeneity in the CAI‐forming region(s) precludes determining the duration of CAIs formation using 26Al‐26Mg systematics. The existence of multiple generations of CAIs and the observed differences in CAI abundances in carbonaceous and noncarbonaceous chondrites may indicate that CAIs were episodically formed and ejected by a disk wind from near the Sun to the outer solar system and then spiraled inward due to gas drag. In type 2–3.0 chondrites, most CAIs surrounded by Wark–Lovering rims have uniform Δ17O (= δ17O?0.52 × δ18O) of ~ ?24‰; however, there is a large range of Δ17O (from ~?40 to ~ ?5‰) among them, suggesting the coexistence of 16O‐rich (low Δ17O) and 16O‐poor (high Δ17O) gaseous reservoirs at the earliest stages of the PPD evolution. The observed variations in Δ17O of CAIs may be explained if three major O‐bearing species in the solar system (CO, H2O, and silicate dust) had different O‐isotope compositions, with H2O and possibly silicate dust being 16O‐depleted relative to both the Genesis solar wind Δ17O of ?28.4 ± 3.6‰ and even more 16O‐enriched CO. Oxygen isotopic compositions of CO and H2O could have resulted from CO self‐shielding in the protosolar molecular cloud (PMC) and the outer PPD. The nature of 16O‐depleted dust at the earliest stages of PPD evolution remains unclear: it could have either been inherited from the PMC or the initially 16O‐rich (solar‐like) MC dust experienced O‐isotope exchange during thermal processing in the PPD. To understand the chemical and isotopic composition of the protosolar MC material and the degree of its thermal processing in PPD, samples of the primordial silicates and ices, which may have survived in the outer solar system, are required. In metamorphosed CO3 and CV3 chondrites, most CAIs exhibit O‐isotope heterogeneity that often appears to be mineralogically controlled: anorthite, melilite, grossite, krotite, perovskite, and Zr‐ and Sc‐rich oxides and silicates are 16O‐depleted relative to corundum, hibonite, spinel, Al,Ti‐diopside, forsterite, and enstatite. In texturally fine‐grained CAIs with grain sizes of ~10–20 μm, this O‐isotope heterogeneity is most likely due to O‐isotope exchange with 16O‐poor (Δ17O ~0‰) aqueous fluids on the CO and CV chondrite parent asteroids. In CO3.1 and CV3.1 chondrites, this process did not affect Al‐Mg isotope systematics of CAIs. In some coarse‐grained igneous CV CAIs, O‐isotope heterogeneity of anorthite, melilite, and igneously zoned Al,Ti‐diopside appears to be consistent with their crystallization from melts of isotopically evolving O‐isotope compositions. These CAIs could have recorded O‐isotope exchange during incomplete melting in nebular gaseous reservoir(s) with different O‐isotope compositions and during aqueous fluid–rock interaction on the CV asteroid.Kuippers, G., Boothman, C., Bagshaw, H., Beard, R., Bryan, N.D., Lloyd, J.R., 2019. Microbial reduction of Fe(III) coupled to the biodegradation of isosaccharinic acid (ISA). Applied Geochemistry 109, 104399. acid (ISA) forms through alkaline hydrolysis of cellulose in intermediate level nuclear waste and is a strong complexant of metals with the potential to mobilize priority radionuclides in an underground geological disposal facility (GDF). In this study, microbial ISA degradation was studied under anaerobic conditions with Fe(III) oxyhydroxide as the terminal electron acceptor at pH 7 to 10, representative of conditions in the geosphere surrounding a geological disposal facility. A multidisciplinary approach was used to study the fate and limits of ISA biodegradation, including mineralogical analyses (XRD, ESEM and TEM), alongside geochemical profiling of ISA and its biodegradation products, and microbial community analysis by 16S rRNA gene sequencing. Under the conditions imposed, ISA degradation was constrained to a pH limit of ≤9 and was degraded via Fe(III) reduction and fermentation. Biominerals, resulting from ISA degradation, were analyzed. These revealed two Fe(II) minerals, siderite [FeCO3] and vivianite [(Fe3PO4)2·8H2O], not normally associated with the microbial reduction of ferrihydrite in laboratory cultures, possibly as a result of chelation of ISA with Fe(III) that made the electron acceptor more soluble. After the enrichment at pH 7, a complex microbial consortium, including Clostridia and close relatives to known Fe(III)-reducing bacteria Geobacter sp. and Rhodoferax ferrireducens, was associated with these activities. The results are discussed in the context of geological disposal safety case development, including the potential impact on priority radionuclides including U(VI), Np(V), and Tc(VII), which are highly susceptible to reductive immobilization when in contact with Fe(II)-bearing biominerals.Kumar, H., Mishra, M.K., Mishra, S., 2019. Sorption capacity of Indian coal and its variation with rank parameters. Journal of Petroleum Exploration and Production Technology 9, 2175-2184. study of gas sorption characteristics is important for practical assessment of coal bed methane (CBM) production and CO2 sequestration in coal seam. Adsorption isotherm is one of the critical parameters for the establishment of production as well as injection well. Adsorption isotherm provides information about the reservoir conditions and critical desorption pressure as well as volume of gas that can be sequestered in deep coal seam. Alteration in sorption isotherm reflects the increase or decrease of the gas production as well as CO2 sequestration. Therefore, in this paper, experimental investigation was carried out to determine the CO2/CH4 sorption capacity of five different coal samples taken from different locations of Jharia coalfield (Moonidih area) of Gondwana basin. Gas sorption capacity was determined at 27 °C temperature and up to 7.5 MPa pressure. CO2 adsorption was observed to be higher than that of the CH4. The sorption ratio of CO2/CH4 varied from 1.6:1 to 1.2:1 for all coal samples. Furthermore, the experimental results were correlated using established Langmuir, Freundlich, Temkin and D–R isotherm models. Experimentally obtained values satisfactorily fitted to the Langmuir and Freundlich model with comparable accuracy. The excess adsorption capacity of coal was also compared with different rank parameters to understand the variation of sorption capacity with rank of coal.Kundu, K., Marozava, S., Ehrl, B., Merl-Pham, J., Griebler, C., Elsner, M., 2019. Defining lower limits of biodegradation: atrazine degradation regulated by mass transfer and maintenance demand in Arthrobacter aurescens TC1. The ISME Journal 13, 2236-2251. adaptive strategies by which microorganisms function and survive in low-energy natural environments remains a grand goal of microbiology, and may help address a prime challenge of the 21st century: degradation of man-made chemicals at low concentrations (“micropollutants”). Here we explore physiological adaptation and maintenance energy requirements of a herbicide (atrazine)-degrading microorganism (Arthrobacter aurescens TC1) while concomitantly observing mass transfer limitations directly by compound-specific isotope fractionation analysis. Chemostat-based growth triggered the onset of mass transfer limitation at residual concentrations of 30?μg?L?1 of atrazine with a bacterial population doubling time (td) of 14 days, whereas exacerbated energy limitation was induced by retentostat-based near-zero growth (td?=?265 days) at 12?±?3?μg?L?1 residual concentration. Retentostat cultivation resulted in (i) complete mass transfer limitation evidenced by the disappearance of isotope fractionation (ε13C?=??0.45‰?±?0.36‰) and (ii) a twofold decrease in maintenance energy requirement compared with chemostat cultivation. Proteomics revealed that retentostat and chemostat cultivation under mass transfer limitation share low protein turnover and expression of stress-related proteins. Mass transfer limitation effectuated slow-down of metabolism in retentostats and a transition from growth phase to maintenance phase indicating a limit of ≈10?μg?L?1 for long-term atrazine degradation. Further studies on other ecosystem-relevant microorganisms will substantiate the general applicability of our finding that mass transfer limitation serves as a trigger for physiological adaptation, which subsequently defines a lower limit of biodegradation.Kusch, S., Winterfeld, M., Mollenhauer, G., H?fle, S.T., Schirrmeister, L., Schwamborn, G., Rethemeyer, J., 2019. Glycerol dialkyl glycerol tetraethers (GDGTs) in high latitude Siberian permafrost: Diversity, environmental controls, and implications for proxy applications. Organic Geochemistry 136, 103888. and bacterial glycerol dialkyl glycerol tetraethers (GDGTs) are globally abundant in soils under various climatic conditions, but little is known about their sources, relative distribution, and environmental controls on their diversity in high latitude permafrost deposits. Thus, constraints on GDGT-based proxies, such as methylation of branched GDGTs (MBT) or cyclization of branched GDGTs (CBT) used to infer mean annual temperature or soil pH, are also sparse. We investigated the GDGT diversity in typical North Siberian permafrost deposits including the active layer of polygonal tundra soils (seasonally frozen ground), fluvial terrace/floodplain sediments, Holocene and Pleistocene thermokarst sediments, and late Pleistocene Ice Complex (Yedoma). Our data show that isoprenoid GDGTs are produced by both methanotrophic and methanogenic Euryarchaeota, as well as Thaumarchaeota, but their abundance does not seem to be controlled by the investigated physicochemical parameters including %TOC, %TN, and soil pH. Branched GDGTs (brGDGTs) show similar distributional changes to those observed in other high latitude soil samples, i.e., a dominance of pentamethylated and hexamethylated brGDGTs, likely reflecting the adaptation to low temperatures and a positive correlation of the degree of cyclization with soil pH. Specifically, brGDGT-IIIa correlates positively with %TOC and %TN and negatively with soil pH, while brGDGT-Ib and brGDGT-IIb correlate negatively with %TOC and %TN and positively with pH. Moreover, we observe a negative correlation between 5-methyl and 6-methyl brGDGTs without cyclopentane moieties (except brGDGT-IIIa), but this anticorrelation does not seem to be related to the investigated physicochemical parameters. The observed brGDGT distribution yields a permafrost-specific soil pH calibration, pH'PF=1.8451&#xD7;CBT'PF+8.5396"pH'PF=1.8451×CBT'PF+8.5396 (r2?=?0.60, RMSE?=?0.074; n?=?109).The different investigated deposit types show some distinct GDGT distributional changes and appear to be distinguishable based on the relative abundance of crenarchaeol, GDGT-0/(crenarchaeol?+?GDGT-0) ratios, and CBT’PF values, although we also observe strong heterogeneity for each deposit type. In particular, Yedoma and the active layer of polygonal tundra soils represent distinct endmembers, which differ from each other, as well as from fluvial terrace/floodplain sediments and thermokarst sediments, while the latter two deposit types have similar GDGT fingerprints that are not easily distinguishable. Yet, the observed GDGT distributional differences have implications for GDGT proxies analyzed in aquatic suspended matter and sediments. Quantitative estimates of permafrost erosion, as well as soil pH inferred using BIT indices or CBT’PF, respectively, may be biased by changing relative contributions of different deposit types (carrying their respective GDGT signals) to the exported permafrost OC, particularly from Yedoma and the active layer of polygonal tundra soils.Lambert, J., 2019. Scientists glimpse oddball microbe that could help explain rise of complex life. Nature 572, 294.‘Lokiarchaea’, previously known only from DNA, is isolated and grown in culture. Biologists have for the first time captured and grown an elusive type of microbe that is similar to those that might have given rise to all complex life on Earth.In a preprint posted to the bioRxiv repository1, scientists in Japan report that they have isolated and grown microbes from an ancient lineage of archaea — single-celled microbes that look, superficially, like bacteria but are quite distinct — that was previously known only from genomic sequences.It took the researchers 12 years to cultivate pure laboratory cultures of these microbes from deep-sea mud. The effort gives scientists their first look at the kind of organisms that could have made the jump from simple, bacteria-like cells to eukaryotes — the group of organisms whose cells have nuclei and other structures, and which includes plants, fungi, and humans and other animals.“This is a monumental paper that reflects a tremendous amount of work and perseverance,” says Thijs Ettema, an evolutionary microbiologist at Wageningen University in the Netherlands. “It’s a major step forward in understanding this important lineage.”Muddy origins: The mysterious group, called Lokiarchaea, rose to prominence from microbial muck dredged up not far from Loki’s Castle, a sea-floor hydrothermal vent field off the coast of Greenland. In 2015, Ettema and his colleagues sequenced genetic fragments from the mishmash of microbes in the sediment and assembled them into fuller genomes of individual species2, a method called metagenomics. One genome stood out. It was clearly a member of the archaea. But dotted throughout this genome were eukaryotic-like genes, suggesting to Ettema that this oddball could help to bridge the evolutionary gap between simpler microbes and eukaryotes. The researchers called it Lokiarchaea, after Loki, the trickster of Norse mythology.Soon, other labs found additional Loki-like archaea, and together these formed the Asgard archaea, named after a mythological region inhabited by Norse gods. Although the organisms’ precise place in the tree of life remains contentious, many analyses pair Asgards and eukaryotes together, which could mean that some distant Asgard-like ancestor gave rise to all eukaryotes — everything from panda bears to portabello mushrooms.Two become one: Proponents of this view think that, some 2 billion years ago, an Asgard-like archaeon gobbled up a bacterium. Instead of providing a meal, the ingestion sparked a mutually beneficial relationship, a phenomenon known as endosymbiosis. Eventually, according to this hypothesis, the bacterium evolved into mitochondria, the ‘powerhouse’ organelles of the cell that helped to fuel eukaryotes’ rise. A similar merger could have led to the first nucleated cells.Not all researchers agree that Asgards made this jump. Some have argued that the eukaryotic-like genes that make Asgards special are just contamination from other sediment microbes. And without an actual organism to study in the lab, it was hard to know what the eukaryotic-like genes actually do, or begin to understand how endosymbiosis might have progressed. “We’ve learnt a lot from the genome, but without a lab culture, we can only learn so much,” says Ettema.Because Asgards hail from extreme environments and have very slow growth rates, no one has previously succeeded in growing them in the lab. “The whole field has been waiting for this moment for a long time,” says Simonetta Gribaldo, an evolutionary microbiologist at the Pasteur Institute in Paris. Twelve years of workYears before anyone knew Asgard archaea even existed, Hiroyuki Imachi, a microbiologist at the Japan Agency for Marine-Earth Science and Technology in Yokosuka and his collaborators began the painstaking work that would eventually bring Asgards to the lab. To cultivate microbes from deep-sea sediments, Imachi and his colleagues built a bioreactor that mimicked the conditions of a deep-sea methane vent. Over the course of 5 years, the researchers waited for the slow-growing microbes in the reactor to multiply.They then took samples from the reactor and placed these, along with nutrients, in glass tubes, which sat for another year before showing any signs of life. Genetic analysis revealed a barely perceptible population of Lokiarchaea. The researchers patiently coaxed the Lokiarchaea — which took 2–3 weeks to undergo cell division — into higher abundance and purified the samples. “It’s one of the slowest-dividing organisms I know of,” says Ettema.Finally, after 12 years of work, the researchers produced a stable lab culture containing only this new Lokiarchaeon and a different methane-producing archaeon. Together, the two microbes formed a symbiotic relationship (similar colonies of bacteria and archaea have been observed before). The scientists named the cultured Lokiarchaeon Prometheoarchaeum syntrophicum. The authors declined requests for interviews from Nature's news team while their paper was under review at a journal.“It’s a tremendous effort,” says Gribaldo. “And it’s a really nice story because they started out before the Asgard frenzy even started. Halfway through their experiment they must’ve realized they had gold in their hands.”‘An organism from outer space’: Under the microscope, that gold took the form of round cells less than one micrometre wide. Like other archaea and bacteria, they have relatively simple interiors, but their external surface can produce wisp-like protrusions that extend from their bodies. “I don’t think anyone predicted that it would look like this,” says Ettema. “It’s sort of an organism from outer space.”The researchers report that the cultured Lokiarchaeon produces energy by breaking down amino acids and that it can exchange molecules used to carry energy with symbiotic partners. Ettema says the Asgard genomes hinted at these capabilities, but without a lab culture they weren’t confirmed.Finally, because the researchers could extract and sequence DNA from a pure sample, rather than sediment containing a multitude of organisms, their findings would confirm that Lokiarchaea do, in fact, contain numerous eukaryote-like genes. “It puts to rest any concerns about contamination,” says Gribaldo.Ettema says this research opens the door to the next stage of Asgard research, although he stresses that many more Asgards will need to be cultured for researchers to work out whether, and how, Asgard-like archaea gave rise to eukaryotes.“We can’t just go back in time and observe what happened,” says Ettema. The Asgards we see today are not the same as the microbe that gave rise to eukaryotes. But he says that culturing more Asgards and studying what their eukaryotic-like genes actually do will give a fuller picture of the evolutionary tree, and help researchers to better infer how simple, single-celled organisms made the first giant leap towards complexity.References1. Imachi, H. et al. Preprint at (2019).2. Spang, A. et al. Nature 521, 173–179 (2015).Larter, S., Silva, R.C., Marcano, N., Snowdon, L.R., Villarreal-Barajas, J.E., Sonei, R., Paredes Gutiérrez, L.C., Huang, H., Stopford, A., Oldenburg, T.B.P., Zhao, J., Weerawardhena, P., Nightingale, M., Mayer, B., Pedersen, J.H., di Primio, R., 2019. The dating of petroleum fluid residence time in subsurface reservoirs. Part 1: A radiolysis-based geochemical toolbox. Geochimica et Cosmochimica Acta 261, 305-326. radiometric dating of geological events was a crucial achievement leading to the establishment of the geological time scale. The dating of the timing of petroleum charge into, and the determination of petroleum residence times in a geological trap would also be significant, as it would remove ubiquitous speculation concerning the history of reservoir charging in any basin setting. A thorough review of prior strategies to estimate the residence time of petroleum fluids in subsurface reservoirs revealed that few if any methods currently used provide useful estimates of the residence age of fluids. This paper is focused on the age dating of petroleum residence time in reservoirs based on the compositional alterations of reservoired fluids caused by natural radiation. This preliminary paper sets out the geochemical landscape and constraints on radiation-based age dating proxies. We report results on the propagation of radiation through reservoir rocks, which indicate that gamma radiolysis is a primary route to crude oil alteration. Gamma ray radiolysis experiments on crude oils at both natural and elevated radiation doses have been completed and the changing crude oil composition observed using LC, GC-MS and NMR. Reservoir fluids are naturally immersed in radioactive subsurface media that cause systematic alteration to crude oil composition with time, but the chemical changes are small in most natural settings. The degree of radiolysis of individual petroleum compounds was found to depend on chemical class, molecular size, initial compound concentration and the nature of the oil matrix, indicating that a proxy system for dating of petroleum charge times and oil residence times in petroleum traps will likely depend on case-specific calibrations. We define the apparent gamma ray radiolysis susceptibility (kGy?1) of different compounds. Large alkanes, such as high molecular weight normal alkanes (>C22) or hopanes, have high radiolysis susceptibility and show the most rapid decrease in component concentration with increasing radiation dose. In contrast, condensed aromatic hydrocarbons and diamondoid hydrocarbons are more resistant to decomposition through radiolysis. While assessing the decrease in concentration of a compound through radiolysis is a practical objective, it is more difficult to assess the production of new, unique radiolysis products given the great diversity and low concentrations of individual compounds produced. However, monitoring the production of specific functional groups during radiolysis of crude oils, using NMR spectroscopy, was found to be a feasible proxy analytical target. Analysis of newly generated carbon-carbon double bonds in bulk crude oils may represent an optimal approach for development as a radiolysis proxy. We propose a route to assessing in-reservoir crude oil radiation dose.Lastauskien?, E., Novickij, V., Zinkevi?ien?, A., Girkontait?, I., Pa?kevi?ius, A., ?vedien?, J., Markovskaja, S., Novickij, J., 2019. Application of pulsed electric fields for the elimination of highly drug-resistant Candida grown under modelled microgravity conditions. International Journal of Astrobiology 18, 405-411. lusitaniae and C. guilliermondii are perfect model organisms for the study of Candida genera behaviour in various conditions. Both of them are rare pathogens capable to cause candidiasis in the patients with weakened immune system and can undergo morphology switches related to the increased antifungal drug resistance. Candida genera yeasts are able to inhabit diverse range of ecological niches including space ships and space stations. During the long-term expeditions, astronauts are affected by various factors that can change the state immune system. In such conditions, the commensal usually non-pathogenic microorganisms can spread through the body of the host and cause infections. Weakened immune system and limited use of drugs in spaceships promote the search of the alternative methods for the biocontrol of microorganisms. Several studies demonstrate that microorganisms are altering their gene expression, physiology, morphology, pathogenicity and evolving resistance to the antifungals under microgravity conditions. Our research indicated that switch to the pseudohyphae morphology leads up 30-fold increased resistance to amphotericin B in C. lusitaniae and C. guilliermondii. Cultivation of yeasts in rotary cell culture system (RCCS) is related to the altered cell growth and resistance to the antifungal treatment. Our results showed that growth in the RCCS led to the extreme increase in cell resistance to amphotericin B as compared with the standard growth conditions. In our research, we applied electroporation for the biocontrol of two Candida species. C. lusitaniae and C. guilliermondii cells grown in RCCS exhibited significantly increased survivability after pulsed electric field (PEF) treatment in comparison with cells grown under routine conditions. We have shown that PEF bursts of 2.5–25 kV cm?1 of 100 ?s × 8 duration display a dose-dependent permeabilization of both studied Candida species. Our research indicated that budding cells and pseudohyphae morphology cells, with increased resistance to amphotericin B, can be effectively inactivated after applying PEF higher than 15 kV cm?1.Lattaud, J., Erdem, Z., Weiss, G.M., Rush, D., Balzano, S., Chivall, D., van der Meer, M.T.J., Hopmans, E.C., Sinninghe Damsté, J.S., Schouten, S., 2019. Hydrogen isotopic ratios of long-chain diols reflect salinity. Organic Geochemistry 137, 103904. diols (LCDs) are ubiquitous lipids produced by freshwater and marine algae. A combination of semi-preparative high performance liquid chromatography and gas chromatography isotope ratio monitoring mass spectrometry, allowed the measurement of δ2H of individual LCDs from cultures, which indicated a correlation with the hydrogen isotope composition of the growth water and a species-specific effect. Results from environmental samples along a salinity gradient indicated the potential of δ2H ratios of LCDs to trace the hydrogen isotopic composition of water and sea surface salinity.Lazzari, E., Arena, K., Caram?o, E.B., Herrero, M., 2019. Quantitative analysis of aqueous phases of bio-oils resulting from pyrolysis of different biomasses by two-dimensional comprehensive liquid chromatography. Journal of Chromatography A 1602, 359-367. by-products are perfect candidates to be further processed under the concept of circular economy, in order to produce their valorization. Although significant amounts of food-related wastes that are discarded are produced worldwide, these might still be rich in valuable compounds. A strategy to further valorize agrifood-related by-products is based on pyrolysis processes. The result of this process is a liquid product termed bio-oil which is composed of an organic phase and an aqueous phase. This bio-oil is rich on a variety of components and its analysis implies several challenges. In this work, quantitative on-line comprehensive two-dimensional liquid chromatography (LC?×?LC) is proposed for the first time to characterize several aqueous phases of different bio-oils. Rice husk, peanut shell, spent coffee grounds, peach core and Eucalyptus sawdust biomasses were analyzed. The developed quantitative LC?×?LC method presented very good linearity, precision, reproducibility, recovery and LODs and LOQs as low as 0.05?μg mL?1 and 0.16?μg mL?1, respectively. As much as 28 components were simultaneously separated and quantified in those samples. Our results found that the composition of these bio-oils was different but strongly related to the agrifood by-product submitted to pyrolysis. The developed methodology is foreseen as a valuable tool for the quantitative study of other bio-oils, considering the great complexity and high dimensionality of these samples.Lee, C., Hong, S., Noh, J., Lee, J., Yoon, S.J., Kim, T., Kim, H., Kwon, B.-O., Lee, H., Ha, S.Y., Ryu, J., Kim, J.-J., Kwon, K.K., Yim, U.H., Khim, J.S., 2019. Comparative evaluation of bioremediation techniques on oil contaminated sediments in long-term recovery of benthic community health. Environmental Pollution 252, 137-145. various bioremediation techniques have been widely used at oil spill sites, the in situ efficiency of such techniques on recovering the benthic communities in intertidal areas has not been quantified. Here, the performance of several bioremediation tools such as emulsifiers, multi-enzyme liquid (MEL), microbes, and rice-straw was evaluated by a 90-days semi-field experiment, particularly targeting recovery of benthic community. Temporal efficiency in the removal of sedimentary total petroleum hydrocarbons (TPH), reduction of residual toxicity, and recovery of bacterial diversity, microalgal growth, and benthic production was comprehensively determined. Concentrations of TPH and amphipod mortality for all treatments rapidly decreased within the first 10 days. In addition, the density of bacteria and microphytobenthos generally increased over time for all treatments, indicating recovery in the benthic community health. However, the recovery of some nitrifying bacteria, such as the class Nitrospinia (which are sensitive to oil components) remained incomplete (13–56%) during 90 days. Combination of microbe treatments showed rapid and effective for recovering the benthic community, but after 90 days, all treatments showed high recovery efficiency. Of consideration, the “no action” treatment showed a similar level of recovery to those of microbe and MEL treatments, indicating that the natural recovery process could prevail in certain situations.Lee, H., Feng, X., Mastalerz, M., Feakins, S.J., 2019. Characterizing lignin: Combining lignin phenol, methoxy quantification, and dual stable carbon and hydrogen isotopic techniques. Organic Geochemistry 136, 103894. is a major structural plant biochemical and biogeochemical compound present in peat and lignite. Its monomeric (phenolic) and polymeric structures include varying amounts of ether-bonded methyl groups (i.e., methoxy or OCH3). These methoxy groups are generally underused targets for both structural characterization and isotopic analyses. We analyzed the quantity and C and H isotopic composition of methoxy groups within a range of substrates including lignin phenols, lignin, wood, peat, lignite, and sub-bituminous and bituminous coal. We used the Zeisel method to cleave the ether bonds with hydroiodic acid to yield iodomethane which can be analyzed by gas chromatography (GC). Finding inconsistent transfer and isotope effects associated with room temperature headspace injections, we instead used isooctane as a solvent for the iodomethane analyte (the liquid method). Using the liquid method, we obtained a linear response by GC-flame ionization detection (GC-FID) for iodomethane and a linear calibration and 85?±?6% recovery of methyl from methoxy groups from solid standards of phenolic compounds of known stoichiometry. We introduced quantification via lignin phenolic compounds to calibrate both analytical and experimental yield. Methyl yields provided structural information and confirmed that lignin oxidation products (LOPs) from copper oxide oxidation underestimate the number of methoxy-bearing phenols (yield?<?0.3 of expected based on stoichiometry); in combination the two approaches provide structural information and quantification. We found that concentrations of methyl from methoxy groups in geologic sediments (lignite, sub-bituminous and bituminous coal) initially increase with diagenesis as lignin to cellulose ratio increases, and then decline to low concentrations during coalification, offering new possibilities for characterizing the transformation of peat and lignite. We assessed an array of plant biochemicals and established that natural and synthetic methoxy groups span a broad range of dual stable carbon and hydrogen isotopic compositions indicating scope for biogeochemical and forensic applications.Lee, J., Jung, D., Park, K., 2019. Hydrophobic deep eutectic solvents for the extraction of organic and inorganic analytes from aqueous environments. TrAC Trends in Analytical Chemistry 118, 853-868. solvents termed deep eutectic solvents (DESs) are attracting increasing attention as eco-friendly solvents in analytical chemistry. Recently, a new subclass of DESs called hydrophobic DESs (hDESs) has been reported. hDESs are generally immiscible with water and have high extraction efficiency for nonpolar analytes; thus, they have been suggested as potential extraction media to replace toxic organic solvents or expensive hydrophobic ionic liquids. Since the first introduction of hDESs in 2015, a growing number of studies on the application of hDESs in sample preparation methods have been reported. The present review provides an overview on the preparation and physicochemical properties of hDESs, followed by applications of hDESs in the extraction of organic and inorganic analytes from aqueous environments. In this review, up-to-date studies of conventional (liquid–liquid extraction) and miniaturized (liquid-phase microextraction) scale processes will be discussed with a focus on work up to January 2019.Lee, J.H., Lee, K.S., 2019. Investigation of asphaltene-derived formation damage and nano-confinement on the performance of CO2 huff-n-puff in shale oil reservoirs. Journal of Petroleum Science and Engineering 182, 106304. this study, the behavior of asphaltene formation and nano-confinement during the CO2 huff-n-puff process in liquid-rich shale reservoirs is investigated. Asphaltene precipitation and deposition in the pore volume of shale formation from mixing between oil and CO2 could cause formation damage, which reduces the permeability and/or changes the rock surface condition toward more oil-wet. In addition, the nano-confinement effect changes the phase behavior of the fluid affecting the asphaltene formation in tight shale formations. With the development of a reservoir simulation model that incorporates both asphaltene formation and the nano-confinement effect, this study quantifies the effects of asphaltene deposition and nano-confinement on shale oil production of CO2 huff-n-puff.While ignoring the permeability reduction and wettability alteration due to asphaltene deposition, the nano-confinement effect increases the shale oil production by up to 42% during the CO2 huff-n-puff process. However, the nano-confinement effect increases the asphaltene precipitation and deposition in nano-scaled tight formation. On incorporating the formation damage due to asphaltene deposition, more deposited asphaltene due to nano-confinement effect decreases the oil production by 4%. This study clarifies that the effects of asphaltene formation and nano-confinement should be taken into consideration for an accurate prediction of hydrocarbon production during CO2 huff-n-puff in tight shale formation.Lerche, I., 2019. A review of economic risking methods commonly used in hydrocarbon exploration. Journal of Petroleum Exploration and Production Technology 9, 1579-1591. different risking methods for hydrocarbon exploration projects are discussed. The so-called Cozzolino procedure is shown to have the major drawback that it predicts less and less involvement should be taken in a project the greater the potential gains. The Kelly procedure circumvents this weakness but has itself the weakness that it can only allow involvement in a project when the expected value is positive despite the fact that the expected value has a standard deviation that allows for a positive domain around a negative expected value. The corporate confidence risk assessment allows for involvement in a project even when the expected value is negative, but has the weakness that there are some ad hoc factors involved that, nevertheless, permit a practical approach to obtain allowing a corporation to assess the confidence the corporation has in an exploration assessment. Numerical illustrations are provided to show how the Kelly procedure and the corporate confidence procedure operate for both single and multiple projects. Only some simple examples are given for the Cozzolino method for which an exhaustive investigation has been given elsewhere in other publications, demonstrating the major flaws. The search for a more robust risking method is ongoing.Leu, M., Bucher, H., Goudemand, N., 2019. Clade-dependent size response of conodonts to environmental changes during the late Smithian extinction. Earth-Science Reviews 195, 52-67. contrast to the benthos whose taxonomic recovery was lagging way behind that of the nekton, highly diverse Smithian conodont and ammonoid faunas were profoundly decimated during the late Smithian, ca. 2 Myr after the Permian-Triassic boundary mass extinction. As body size reduction is a common evolutionary response to heavy environmental stress, we investigate how the size of the P1 elements of different conodont clades responded during the late Smithian crisis based on three sections from the northern Indian Margin. A major and world-wide positive carbon excursion is also a consistent signature of the late Smithian time interval. Where adequate ammonoid biochronological control is lacking (i.e., Kashmir), a new carbonate carbon isotope record provides an independent age proxy for correlations with southern Tibet and the Salt Range. Assuming a positive correlation between the size of P1 elements and body size, we confirm that segminate conodonts underwent a size decrease during the late Smithian. However, segminiplanate conodonts consistently displayed a substantial size increase during the same time interval, thus highlighting clade specific, diverging answers and precluding any simplistic generalization of size responses to the same stress event. Additionally, a moderate but consistent size increase during the early Spathian is documented for both clades, thus obscuring any simple general relation between temperature stress and size among conodonts. Comparison of size time series with the oxygen isotopic composition of conodonts (a proxy for sea-water temperature) suggests that only the size of segminate P1 elements may correlate positively with temperature. Although at a slower pace, the size of segminiplanate P1 elements continued to increase during the early Spathian, when temperature rose again after the late Smithian cooling event. Therefore, temperature alone cannot explain the size variations of segminiplanate conodonts. The late Smithian was also a time of increasing burial of organic matter on continental shelves, but lateral variations of this factor also obscure any relation with the documented size changes. Last but not least, the stratigraphically more comprehensive study in Nammal reveals a segminiplanate gap during the middle Smithian thermal high. The biogeographical expansion of this clade towards the low latitudes during the Griesbachian, the early Smithian, the late Smithian and the early Spathian apparently occurred during the coolest intervals of the Early Triassic, in agreement with their supposed cooler habitat.Li, C., Zhu, H., Yang, F., Liu, H., Wang, F., Sun, G., Yao, B., 2019. Effect of asphaltene polarity on wax precipitation and deposition characteristics of waxy oils. Energy & Fuels 33, 7225-7233. are natural pour point depressants, and the effect of asphaltene polarity on the low-temperature rheology of waxy oils has been well studied. In this paper, the influence of asphaltene polarity on the wax precipitation and deposition characteristics of synthetic waxy oils was investigated through a differential scanning calorimeter (DSC), a rheometer, a polarizing microscope, and a Couette wax deposition experimental device. It was found that the asphaltenes with lower polarity have higher H/C ratio and can disperse into smaller associating particles in the synthetic waxy oils, which is beneficial for the cocrystallization interaction between asphaltenes and wax molecules, and also provide more nucleating sites for wax molecules. With the decrease of asphaltene polarity, the wax crystals of synthetic waxy oils are gradually changed from long needle-like to small needle-like or nearly spherical, which is not conducive to the overlap and insertion of wax crystals, thus greatly improving the rheological properties of synthetic waxy oils. The addition of asphaltenes with lower polarity can significantly reduce the wax deposition rate but increase the aging rate; that is, a thinner and harder wax deposit tends to form with the decrease of asphaltene polarity. Meanwhile, the formed wax deposits become heterogeneous along the radial direction after the asphaltenes addition; the wax contents of the wax deposits increase gradually from the bottom layer to the surface layer. On the one hand, with the decrease of asphaltene polarity, the low-temperature structural strength of synthetic waxy oils is continuously decreased. Therefore, the initial wax deposit layers require higher solid wax contents to resist shearing of pipe flow. On the other hand, the lower viscosity and smaller aspect ratio of wax crystals are also beneficial for the diffusion of wax molecules in the bulk oil and wax deposit, which increases the aging rate of wax deposits. Therefore, with the decrease of asphaltene polarity, the difference of wax content between the surface and bottom wax deposits in the formed heterogeneous wax deposit structure becomes larger and larger.Li, G., Pang, K., Chen, L., Zhou, G., Han, C., Yang, L., Wang, W., Yang, F., Yin, L., 2019. Organic-walled microfossils from the Tonian Tongjiazhuang Formation of the Tumen Group in western Shandong, North China Craton and their biostratigraphic significance. Gondwana Research 76, 260-289. successions in western Shandong of North China Craton contain fine-grained siliciclastic rocks which offer a unique opportunity to explore the Neoproterozoic biosphere. In this study, we have revealed a well-preserved and diversified microfossil assemblage from the Tongjiazhuang Formation, Tumen Group in western Shandong, North China Craton, which is characterized by abundant smooth-walled sphaeromorphic acritarchs and cyanobacterium-like filamentous forms and relatively low abundance of more complex acritarchs. A total of 40 microfossil taxa belonging to 20 morphological genera have been identified, most of which are described for the first time from the Tongjiazhuang Formation of the Tumen Group in western Shandong, including Simia sp., Trachyhystrichosphaera aimika, T. botula, Germinosphaera bispinosa, Unnamed sp. A, Jacutianema solubila, and Pololeptus rugosus. The Tongjiazhuang assemblage revealed in this study is much more diverse than previously reported and well comparable to the Tonian Liulaobei and Gouhou assemblages in the Xuhuai region. Particularly, the occurrence of T. aimika, T. botula, G. bispinosa, J. solubila, and P. rugosus indicates a late Mesoproterozoic to Tonian age for the Tongjiazhuang Formation. In addition, the occurrences of macroscopic carbonaceous compressions, including Chuaria-Tawuia assemblage from the Tongjiazhuang Formation and Tawuia and Sinosabellidites from the Shiwangzhuang Formation, are consistent with geochronological data, suggesting a Tonian age for the Tongjiazhuang, Fulaishan, and Shiwangzhuang formations of the middle and upper Tumen Group, while the Heishanguan and Erqingshan formations of the lower Tumen Group are likely late Mesoproterozoic to Tonian in age. Thus, available biostratigraphic data, lithostratigraphic correlation, and geochronological data suggest that the whole Tumen Group is late Mesoproterozoic to Tonian in age, rather than Cryogenian or Ediacaran. This study significantly improves our knowledge about the diversity of the Tonian biosphere and implies a ~200–300 million years unconformity (the ‘Great Unconformity’) between the late Mesoprotoerozoic to Tonian Tumen Group and the early Cambrian Liguan Formation in western Shandong.Li, J., Mau, R.L., Dijkstra, P., Koch, B.J., Schwartz, E., Liu, X.-J.A., Morrissey, E.M., Blazewicz, S.J., Pett-Ridge, J., Stone, B.W., Hayer, M., Hungate, B.A., 2019. Predictive genomic traits for bacterial growth in culture versus actual growth in soil. The ISME Journal 13, 2162-2172. between microbial genes and performance are often evaluated in the laboratory in pure cultures, with little validation in nature. Here, we show that genomic traits related to laboratory measurements of maximum growth potential failed to predict the growth rates of bacteria in unamended soil, but successfully predicted growth responses to resource pulses: growth increased with 16S rRNA gene copy number and declined with genome size after substrate addition to soils, responses that were repeated in four different ecosystems. Genome size best predicted growth rate in response to addition of glucose alone; adding ammonium with glucose weakened the relationship, and the relationship was absent in nutrient-replete pure cultures, consistent with the idea that reduced genome size is a mechanism of nutrient conservation. Our findings demonstrate that genomic traits of soil bacteria can map to their ecological performance in nature, but the mapping is poor under native soil conditions, where genomic traits related to stress tolerance may prove more predictive. These results remind that phenotype depends on environmental context, underscoring the importance of verifying proposed schemes of trait-based strategies through direct measurement of performance in nature, an important and currently missing foundation for translating microbial processes from genes to ecosystems.Li, J., Zhang, P., Lu, S., Chen, C., Xue, H., Wang, S., Li, W., 2019. Scale-dependent nature of porosity and pore size distribution in lacustrine shales: An investigation by BIB-SEM and X-Ray CT methods. Journal of Earth Science 30, 823-833. to heterogeneous pore distributions within shales, petrophysical properties of shales determined by scanning electron microscopy (SEM) and X-ray computed tomography (CT) methods strongly depend on the observed domain size (analysis scale). In this paper, the influence of the analysis scale on areal and bulk porosities and pore size distribution (PSD) for lacustrine shales from the Dongying sag of Bohai Bay Basin, China were investigated using broad ion beam (BIB)-SEM and X-ray CT methods. The BIB-SEM cross-sections with high imaging resolution (10 nm/pixel) and a large field of view (>1 mm2) mainly describe the 2D nanoscale pore system in the two shales (samples F41#-2 and Y556#-1), while CTbased 3D reconstructions with resolutions of 0.42 (F41#-1) and 0.5 μm/pixel (H172#-1) reflect the 3D submicron pore system. The results indicate that the areal (bulk) porosity exhibits a multiple power-law distribution with increasing analysis area (volume), which can be used to extrapolate the porosity of a given area (volume). Based on SEM and CT investigations, the sizes of the minimum representative elementary areas (REAs) and volumes (REVs) were determined respectively, which are closely associated with the heterogeneousness of the pore system. Minimum REAs are proposed to be 2.93×104 (F41#-2) and 0.91×104 μm2 (Y556#-1), and minimum REVs are 0.016 (F41#-1) and 0.027 mm3 (H172#-1). As the analyzed areas (volumes) are larger than the minimum REA (REV), obtained 2D (3D) PSDs are comparable to each other and can be considered to reflect the shale PSD. These results provide insights into the porosity and PSD characterization of shales by SEM and X-ray CT methods.Li, N., Li, C., Fan, J., Algeo, T.J., Yan, D., Zhu, G., Wu, S., Tang, S., Cheng, M., Jin, C., 2019. Sulfate-controlled marine euxinia in the semi-restricted inner Yangtze Sea (South China) during the Ordovician-Silurian transition. Palaeogeography, Palaeoclimatology, Palaeoecology 534, 109281. published interpretations of marine redox conditions during the Ordovician-Silurian transition (OST) may have been linked to spatial redox heterogeneity during this interval. However, details of the pattern of redox heterogeneity and its underlying causes remain unclear. Here, we present a high-resolution geochemical study of a drillcore section (Pengye #1) from Pengshui County (Chongqing municipality, southwestern China) that was located in the semi-restricted inner Yangtze Sea during the OST. We analyzed Fe-speciation, redox-sensitive trace elements, major elements, and pyrite δ34S compositions (δ34Spy) and then compared these data with published results from coeval sections at Datianba and Shuanghe in the same basin. The integrated dataset demonstrates pronounced spatiotemporal heterogeneity of redox conditions—especially the local development of euxinic conditions in the inner Yangtze Sea during the OST. Integrated data further suggest that high primary productivity and ample Fe fluxes in the inner Yangtze Sea may have depleted dissolved sulfate through microbial sulfate reduction (MSR) and subsequent pyrite formation, except in areas with enhanced sulfate supply from continental weathering or open-ocean exchange, which varied as a function of both tectonic (i.e., the regional Kwangsian Orogeny) and eustatic changes (i.e., the global Hirnantian glaciation). Limited sulfate availability thus likely prevented the development of euxinic conditions in some regions of the inner Yangtze Sea, as reflected in spatial variation of δ34Spy. Our study highlights the potential role of sulfate availability on the development of watermass euxinia in semi-restricted marginal-marine basins during the OST.Li, Q., Jew, A.D., Kohli, A., Maher, K., Brown, G.E., Bargar, J.R., 2019. Thicknesses of chemically altered zones in shale matrices resulting from interactions with hydraulic fracturing fluid. Energy & Fuels 33, 6878-6889. fracturing of unconventional shale reservoirs increases the fracture network surface area to access hydrocarbons from the low permeability rock matrix. Porosity and permeability of the matrix, through which hydrocarbons migrate to fractures, are important for determining production efficiency and can be altered by chemical interactions between shale and hydraulic fracturing fluids (HFFs). Here, we present results from an experimental study that characterizes the thickness of the alteration zone in the shale matrix after shale–HFF interactions. Experiments were conducted with whole cores submerged in HFF both with and without added barium and sulfate to promote barite scale formation. After 3 weeks of reaction at 77 bar and 80 °C, the cores were characterized using X-ray microtomography, synchrotron X-ray fluorescence microprobe imaging, and synchrotron X-ray absorption spectroscopy. Our results show that the thickness of the altered zone depends on shale mineralogical composition and varies for different chemical reactions. For reactions between the low-carbonate Marcellus shale and HFF, pyrite (FeS2) oxidation manifests as both a thick zone of sulfur oxidation (>0.5 cm) and a thinner zone of iron oxidation (100–150 μm). Carbonate dissolution extended 100–200 μm into the matrix, with the resulting observable secondary porosity localized at the shale–fluid interface where mineral grains were removed by either dissolution or mechanical erosion. In solutions oversaturated with respect to barite, barite precipitates were observed in the reaction fluid and at the shal–HFF interface. In contrast, the carbonate dissolution zone in the high-carbonate Eagle Ford was only 30–40 μm thick, within which a uniform texture of increased porosity was observed. Pyrite oxidation in the Eagle Ford was evident from an iron oxidation zone (150–200 μm thick), while sulfur oxidation was minor and hard to observe. Barite precipitation extended 1–2 mm into the matrix when the initial HFF was oversaturated with respect to barite, filling shale microcracks down to the submicrometer length scale. Our findings provide a scientific basis to predict the extent of chemical alteration in shale reservoirs during hydraulic fracturing and its impacts on hydrocarbon production.Li, Y., Chen, S., Wang, Y., Su, K., He, Q., Qiu, W., Xiao, Z., 2020. Relationships between hydrocarbon evolution and the geochemistry of solid bitumen in the Guanwushan Formation, NW Sichuan Basin. Marine and Petroleum Geology 111, 116-134., the Devonian Guanwushan Formation in the northwestern Sichuan Basin gained industrial attention when solid bitumen was discovered in reservoirs and outcrops. This discovery initiated the exploration and development of the Devonian natural gas. Devonian in the northwestern Sichuan Basin is a new stratum for the exploration and development of Paleozoic marine natural gas in Sichuan Basin. However, the unclear recognition on the genesis, the sources and the hydrocarbon evolution history of solid bitumen and natural gas seriously restricted further exploration and development. Based on the solid bitumen reflectance, carbon isotopes, saturated hydrocarbon chromatography, and solvent extract bitumen biomarkers combined with the component and carbon isotopes of natural gas, comprehensive analyses have been performed on the origin of the solid bitumen and the accumulation and evolution of the natural gases. The results showed that the outcrop solid bitumen is derived from biodegraded oil from the Lower Cambrian source rocks, and is characterised by low bitumen reflectance, low saturated/aromatic hydrocarbon ratios, seriously damaged normal-alkanes, and severe migration of the gas chromatographic baseline. The reservoir bitumen formed through thermal cracking of oil from Lower Cambrian and Lower Permian source rocks, and is characterised by high bitumen reflectance, high saturated/aromatic hydrocarbons, and complete normal-alkanes. The differences of tectonic evolution take control of the two different-genesis bitumen. The Longmen Mountain strata in the northwestern Sichuan Basin were uplifted sharply after the Jurassic and the early generated crude oil was biodegraded during uplifting and formed the outcrop bitumen. However, strata in Well Shuangtan-3 (ST3) continued to subside and the paleo reservoir thermal-cracked during deep burial into dry gas and heavy components gathered to form reservoir bitumen. Revealing the Devonian hydrocarbon evolution in Sichuan Basin is of highly significance and is meaningful to guide further researches on the gas-source correlation of natural from paleo-strata. It is of great significance to reveal the Devonian hydrocarbon evolution in Sichuan Basin and to guide further researches on the gas-source correlation of natural gas from paleo-strata.Li, Z., Jiang, Z., Liang, Z., Yu, H., Yang, Y., 2019. Pore-structure characterisation of tectonically deformed shales: a case study of Wufeng-Longmaxi Formation in western Hunan Province, southern China. Australian Journal of Earth Sciences 66, 1075-1084. impacts of tectonic deformation on pore structure of the Wufeng-Longmaxi shales in southern China were studied on tectonically deformed shales. Core description, thin-section observation, total organic carbon, X-ray diffraction, low-pressure gas (N2 and CO2) adsorption, mercury intrusion capillary pressure and field emission-scanning electron microscopy experiments were performed. The undeformed shale (UDS), brittle deformed shale (BDS) and ductile deformed shale (DDS) can be sorted based on the variability of original texture, fabric and structure properties of the shale samples. In addition, shale samples with different deformation mechanisms have various pore-structure characteristics. Organic matter pores and interparticle pores in clay minerals are the dominant pore types in the selected shale samples. The BDS sample has a greater proportion of macropores (or micro-fractures), indicating brittle tectonic deformation has a significant effect on the development of macropores in shales. In contrast, the DDS sample has more micropores than the UDS and BDS samples, suggesting ductile tectonic deformation may damage larger pores owing to the compression by complex tectonic stress.Li, Z., Liu, D., Cai, Y., Wang, Y., Teng, J., 2019. Adsorption pore structure and its fractal characteristics of coals by N2 adsorption/desorption and FESEM image analyses. Fuel 257, 116031. adsorption pore structure and its fractal characteristics of coals (0.69–2.79% Ro,m) were investigated by N2 adsorption/desorption and field emission scanning electron microscopy. First, organic matter (OM) pores and interparticle pores (InterP) with various shapes are distinguished in different rank coals. The OM pores present irregular shapes in low-/middle-rank bituminous coals, and circular, oval and slit shapes in high-rank bituminous coal and anthracite with width from 50?nm to 2?μm. In contrast, the InterP pores show polygonal/elongated shapes and exist between mineral grains or mineral and OM with width >100?nm. Second, the coals with H1 type hysteresis loop of N2 adsorption/desorption isotherms are favorable for gas adsorption due to large pore surface area, whereas coals with H2 and H3 types are conducive to gas desorption and diffusion because of open pores with good connectivity. Moreover, the fractal dimension of pore shape was obtained from FESEM images and ranges from 1.068 and 1.30, indicating the adsorption pore shape is relatively regular. The surface and volume fractal dimensions of micropores and mesopores were calculated from the N2 adsorption data on the basis of surface fractal model and FHH model, respectively. The fractal dimension of micropore and mesopore surface respectively ranges from 2.18 to 2.69 and 1.78 to 2.41, whereas that of micropore and mesopore volume respectively ranges from 2.18 to 2.67 and 2.29 to 2.79. The pore structure and coal composition during different coalification stages have specific effects on the fractal characteristics of pore shape, surface and volume.Liang, R., Davidova, I., Hirano, S.-i., Duncan, K.E., Suflita, J.M., 2019. Community succession in an anaerobic long-chain paraffin-degrading consortium and impact on chemical and electrical microbially influenced iron corrosion. FEMS Microbiology Ecology 95. compositional changes and the corrosion of carbon steel in the presence of different electron donor and acceptor combinations were examined with a methanogenic consortium enriched for its ability to mineralize paraffins. Despite cultivation in the absence of sulfate, metagenomic analysis revealed the persistence of several sulfate-reducing bacterial taxa. Upon sulfate amendment, the consortium was able to couple C28H58 biodegradation with sulfate reduction. Comparative analysis suggested that Desulforhabdus and/or Desulfovibrio likely supplanted methanogens as syntrophic partners needed for C28H58 mineralization. Further enrichment in the absence of a paraffin revealed that the consortium could also utilize carbon steel as a source of electrons. The severity of both general and localized corrosion increased in the presence of sulfate, regardless of the electron donor utilized. With carbon steel as an electron donor, Desulfobulbus dominated in the consortium and electrons from iron accounted for ～92% of that required for sulfate reduction. An isolated Desulfovibrio spp. was able to extract electrons from iron and accelerate corrosion. Thus, hydrogenotrophic partner microorganisms required for syntrophic paraffin metabolism can be readily substituted depending on the availability of an external electron acceptor and a single paraffin-degrading consortium harbored microbes capable of both chemical and electrical microbially influenced iron corrosion.Liang, Y., Wang, L., Wang, Z., Zhao, J., Yang, Q., Wang, M., Yang, K., Zhang, L., Jiao, N., Zhang, Y., 2019. Metagenomic analysis of the diversity of DNA viruses in the surface and deep sea of the South China Sea. Frontiers in Microbiology 10, 1951. doi: 10.3389/fmicb.2019.01951. metagenomic analysis of the viral community from five surface and five deep sea water (>2000 m below the surface, mbs) samples collected from the central basin of the South China Sea and adjacent Northwest Pacific Ocean during July–August 2017 was conducted herein. We builded up a South China Sea DNA virome (SCSV) dataset of 29,967 viral Operational Taxonomic Units (vOTUs), which is comparable to the viral populations from the original Tara Ocean and Malaspina expeditions. The most abundant and widespread viral populations were from the uncultivated viruses annotated from the viral metagenomics. Only 74 and 37 vOTUs have similarity with the reported genomes from the cultivated viruses and the single-virus genomics, respectively. The community structures of deep sea viromes in the SCSV were generally different from the surface viromes. The carbon flux and nutrients (PO4 and NOx) were related to the surface and deep sea viromes in the SCSV, respectively. In the SCSV, the annotated vOTUs could be affiliated to the cultivated viruses mainly including Pelagibacter (SAR11) phage HTVC010P, Prochlorococcus phages (P-GSP1, P-SSM4, and P-TIM68), Cyanophages (MED4-184 and MED4-117) and Mycobacterium phages (Sparky and Squirty). It indicated that phage infection to the SAR11 cluster may occur ubiquitously and has significant impacts on bathypelagic SAR11 communities in the deep sea. Meanwhile, as Prochlorococcus is prominently distributed in the euphotic ocean, the existence of their potential phages in the deep sea suggested the sedimentation mechanism might contribute to the formation of the deep sea viromes. Intriguingly, the presence of Mycobacterium phages only in the deep sea viromes, suggests inhabitance of endemic viral populations in the deep sea viromes in the SCSV. This study provided an insight of the viral community in the South China Sea and for the first time uncovered the deep sea viral diversity in the central basin of the South China Sea.Lin, W.-R., Tan, S.-I., Hsiang, C.-C., Sung, P.-K., Ng, I.S., 2019. Challenges and opportunity of recent genome editing and multi-omics in cyanobacteria and microalgae for biorefinery. Bioresource Technology 291, 121932. and cyanobacteria are easy to culture, with higher growth rates and photosynthetic efficiencies compared to terrestrial plants, and thus generating higher productivity. The concept of microalgal biorefinery is to assimilate carbon dioxide and convert it to chemical energy/value-added products, such as vitamins, carotenoids, fatty acids, proteins and nucleic acids, to be applied in bioenergy, health foods, aquaculture feed, pharmaceutical and medical fields. Therefore, microalgae are annotated as the third generation feedstock in bioenergy and biorefinery. In past decades, many studies thrived to improve the carbon sequestration efficiency as well as enhance value-added compounds from different algae, especially via genetic engineering, synthetic biology, metabolic design and regulation. From the traditional Agrobacterium-mediated transformation DNA to novel CRISPR (clustered regularly interspaced short palindromic repeats) technology applied in microalgae and cyanobacteria, this review has highlighted the genome editing technology for biorefinery that is a highly environmental friendly trend to sustainable and renewable development.Liu, C.-y., Huang, L., Zhao, H.-g., Wang, J.-q., Zhang, L., Deng, Y., Zhao, J.-f., Zhang, D.-d., Fan, C.-y., 2019. Small-scale petroliferous basins in China: Characteristics and hydrocarbon occurrence. American Association of Petroleum Geologists Bulletin 103, 2139-2175. large number of small-scale lacustrine sedimentary basins are widely distributed across China. Studies of such basins have been limited. These basins have complex characteristics and thus exhibit significant differences in terms of their hydrocarbon potential. At present, among the known 348 small-scale basins with areas less than 20,000 km2 (<7700 mi2), 13 commercial petroliferous lacustrine basins have been identified. Of these, some are referred to as “small but enriched” because they have hydrocarbon abundances per unit area that are far higher than large- to medium-sized petroliferous basins. Small-scale petroliferous basins can be divided into the following two types based on their characteristics and causes for their small size: remnant and proto–small-scale basins. Remnant basins are sedimentary basins retained from predecessor large basins that were far larger than 20,000 km2 (7700 mi2) and have undergone later modification because of tectonic deformation and erosion; it is conspicuous that later modifications caused their small size. Examples of remnant basins include the Jiuxi, Jiudong, Yanqi, and Santanghu Basins. Proto–small-scale basins are small basins during their entire evolutionary history, and either they did not experience later modifications or the old basin was a small-scale basin before modification and it was their dynamics that caused their small size. According to differences in their formation dynamics responsible for their small size, the proto–small-scale basin can be divided into two subtypes: thermal basins and strike-slip basins. The thermal basin formation and evolution are reflective of a deep thermal origin; that is, there is direct or indirect evidence for existing asthenospheric upwelling that led to basin formation, and examples of thermal basins include the Nanxiang and Jinggu Basins. Strike-slip basin formation was closely related to activity on large strike-slip fault systems, and examples of strike-slip basins include the Yitong, Baise, Sanshui, Baoshan, Luliang, Qujing, and Lunpola Basins.For these small-scale lacustrine basins, the most important fact contributing to the formation of hydrocarbons and reservoirs is that these basins allowed for the deposition, preservation, and maturation of high-quality hydrocarbon source rocks. Furthermore, three common key factors that significantly affected the hydrocarbon occurrence within small-scale sedimentary basins are as follows: (1) a later modification process that benefits the preservation and maturation of the high-quality source rocks (i.e., the uplift and erosion without the destruction of main source rocks followed by basin subsidence), (2) a high geothermal background characterized by high geothermal gradient and hydrothermal activity, and (3) an elevated deep-lake sedimentation rate (>200 m/m.y. [>656 ft/m.y.]) during deposition of the source rocks within underfilled and balanced-filled lakes.Liu, D., Li, Z., Jiang, Z., Zhang, C., Zhang, Z., Wang, J., Yang, D., Song, Y., Luo, Q., 2019. Impact of laminae on pore structures of lacustrine shales in the southern Songliao Basin, NE China. Journal of Asian Earth Sciences 182, 103935. the influences of laminae on shale pore structures is vital to understand the enrichment mechanism of lacustrine shale gas. This study investigates lacustrine shales from the lower Cretaceous Shahezi Formation in the Changling Sag, southern Songliao Basin, NE China, using mineralogical and geochemical analyses, CO2 & N2 adsorption, and high-pressure mercury intrusion porosimetry (MIP), to compare pore structure characteristics between laminated and massive shales, and elucidate their main controlling factors. Our results show that, laminae in lacustrine shales from the Shahezi Formation include those clay-rich, organic-rich, and silty ones, and minor carbonate-rich ones. Micropores in both laminated and massive shales show tri-modal distributions with main peaks at 0.47–0.54?nm, 0.57–0.63?nm, and 0.80–0.85?nm, respectively; however, the laminated shales exhibit great variations in micropore volumes among different samples. Mesopores within the laminated shales are smaller than those in the massive shales, and their pore volumes (PV) are about 1/3 less than those of the massive shales. This is due to that the laminated shales are rich in slit-like pores whereas the massive shales have more plate-like and ink-bottle pores. Thermal maturity (Ro) and total organic carbon (TOC) contents are the essential factors controlling the development of micropores and mesopores in the laminated shales, however they show weak effects on macropore development in this formation; this may be related to that shales from the Shahezi Formation generally have low TOC contents and type III kerogen. Clay minerals and quartz both have weak relevance to pore development in this formation.Liu, D., Yu, N., Papineau, D., Fan, Q., Wang, H., Qiu, X., She, Z., Luo, G., 2019. The catalytic role of planktonic aerobic heterotrophic bacteria in protodolomite formation: Results from Lake Jibuhulangtu Nuur, Inner Mongolia, China. Geochimica et Cosmochimica Acta 263, 31-49. nucleation and subsequent crystallization are kinetically-controlled processes. Modern dolomite-forming environments provide clues to the trigger factors that facilitate dolomite formation under Earth surface conditions. It has been documented that certain types of benthic microorganisms promoted the precipitation of protodolomite from sediment pore waters. As protodolomite is thought to be a possible precursor of sedimentary ordered dolomite, microbial mediation has thus been suggested as one interpretation of the occurrence of dolomite in modern sediments. To date, however, it is still unclear whether planktonic microorganisms could directly initiate protodolomite crystallization in the upper water column of present dolomite depositing environments. In this study, we report on the occurrence of authigenic protodolomite in the upmost sediments of a high-sulfate, Chinese inland saline lake (Lake Jibuhulangtu Nuur). This lake was therefore considered to be a natural laboratory to test the catalytic effect of planktonic aerobic heterotrophic bacteria on protodolomite formation. Laboratory mineralization experiments were conducted in a liquid medium that mimicked the ion concentrations and pH condition of lake surface water. The incubation experiments showed that aragonite formed in the abiotic systems, while protodolomite predominantly occurred in the bioreactors using either an enrichment culture or pure isolates of aerobic heterotrophic and halophilic bacteria from lake water. The resulting microbially-induced protodolomite crystals displayed spherical morphology and had MgCO3 composition ranging from 42.7?mol% to 47.1?mol%. These protodolomite spherulites were formed by aggregation of randomly-distributed nano-crystals. Compared to synthetic abiotic protodolomite, microbially-induced protodolomite contained considerable amounts of organic matter, which might occur as intracrystalline inclusion or was located between nano-crystals of protodolomite spherulite. Our results support the emerging view that dissolved sulfate is not an inhibitor for the formation of low-temperature (proto-)dolomite. The presence of organic matter intimately associated with dolomite crystals may serve as a hallmark indicative of a biotically induced origin for some types of dolomite.Liu, H., Liu, W., 2019. Hydrogen isotope fractionation variations of n-alkanes and fatty acids in algae and submerged plants from Tibetan Plateau lakes: Implications for palaeoclimatic reconstruction. Science of The Total Environment 695, 133925. hydrogen isotope compositions (δD) of n-alkanes and fatty acids (FAs) are widely applied in palaeoclimatic reconstructions, and the determinations of their hydrogen isotope fractionation factor values (ε) are vital for quantitatively reconstructing past precipitation variations. Currently, studies on n-alkane and FA ε values focus on terrestrial plants, which, however, show large uncertainties because of the influence of evapotranspiration. Therefore, in this study, we analysed the ε values of algae and submerged plants immersed in lakes, which are not affected by evapotranspiration, to understand the hydrogen isotope fractionation of plant lipid synthesis. By investigating the δD values of lipids (n-alkanes and FAs) in algae and submerged plants and the δD values of co-existing water (including lake bottom water, surface sediment water, and leaf water of algae and submerged plants) from five Tibetan Plateau lakes, we find that the n-alkane ε values of algae and submerged plants show narrow changes, ranging from ?176 to ?159‰ and ?167 to ?142‰, respectively. The FA ε values of algae and submerged plants also show small variations, ranging from ?160 to ?121‰ (except Chara) and ?161 to ?138‰, respectively. Therefore, the average biosynthetic hydrogen isotope fractionation of these plants is ?162‰ for n-alkanes and ?145‰ for FAs, and the small ε differences between FAs and n-alkanes can be related to the different magnitudes of FA utilization in n-alkane synthesis. Finally, we find that the biosynthetic hydrogen isotope fractionation factors of aquatic plants are close to those of terrestrial grasses but slightly more negative than those of terrestrial woody plants. Thus, our results are helpful for understanding the hydrogen isotope fractionation variations in terrestrial plant lipids, which is beneficial for palaeohydrological reconstructions.Liu, H., Sun, W.-d., Zartman, R., Tang, M., 2019. Continuous plate subduction marked by the rise of alkali magmatism 2.1 billion years ago. Nature Communications 10, 3408. the Earth’s evolutionary history, the style of plate subduction has evolved through time due to the secular cooling of the mantle. While continuous subduction is a typical feature of modern plate tectonics, a stagnant-lid tectonic regime with localized episodic subduction likely characterized the early Earth. The timing of the transition between these two subduction styles bears important insights into Earth’s cooling history. Here we apply a statistical analysis to a large geochemical dataset of mafic rocks spanning the last 3.5 Ga, which shows an increasing magnitude of alkali basaltic magmatism beginning at ca. 2.1 Ga. We propose that the rapid rise of continental alkali basalts correlates with an abruptly decreasing degree of mantle melting resulting from the enhanced cooling of the mantle at ca. 2.1 Ga. This might be a consequence of the initiation of continuous subduction, which recycled increasing volumes of cold oceanic crust into the mantle.Liu, J.-S., Algeo, T.J., Jaminski, J., Kuhn, T., Joachimski, M.M., 2019. Evaluation of high-frequency paleoenvironmental variation using an optimized cyclostratigraphic framework: Example for C-S-Fe analysis of Devonian-Mississippian black shales (Central Appalachian Basin, U.S.A.). Chemical Geology 525, 303-320. successions are rarely sampled at sufficiently dense spacing to permit evaluation of paleoenvironmental variation at the shortest fundamental frequency operative in the depositional system of interest, often because that frequency remains undetermined. Here, we provide an example of a sampling strategy optimized for recovery of high-frequency paleoenvironmental signals, based on (1) full-core analysis using a continuous survey tool such as X-radiography, followed by (2) fine sampling of selected small-scale cycles that record significant short-term paleoenvironmental variation. We show that this strategy results in recovery of high-frequency paleoenvironmental signals that are completely missed by low-density sampling protocols, permitting key insights into depositional and early diagenetic processes that may otherwise by overlooked.The present case study is based on C-S-Fe systematics of the Cleveland and Sunbury shales, which belong to the Upper Devonian-lowermost Carboniferous black shale succession of the Central Appalachian Basin in eastern North America. In these units, the fundamental scale of paleoenvironmental variation is recorded by pervasive decimeter-scale (~5- to 20-cm-thick) compositional cycles that are readily visible in outcrop, in which high-organic layers weather out as resistant ledges. We identified these cycles in drillcores using X-radiography, which proved to be an effective proxy for compositional variation owing to control of bulk density primarily by total organic carbon (TOC) content. We then sampled selected dm-scale cycles (n?=?21) at a centimeter spacing, generating short, high-resolution, multiproxy chemostratigraphic records including TOC, sulfur and Fe concentrations, Fepy/FeHR (a redox proxy), δ34Spyrite, and organic maceral content. This analysis yielded the novel insight that all proxies related to authigenic iron sulfides (e.g., Stotal and Spyrite, Fetotal and Fepyrite, Fepy/FeHR, and δ34Spyrite) covary negatively with TOC within the dm-scale cycles.We interpret the unusual pattern of negative TOC-pyrite covariation in the Cleveland and Sunbury shales to have resulted from differential distributions of labile organic matter (OM), which drove H2S production via microbial sulfate reduction (MSR), and reactive Fe, which controlled pyrite formation. Labile OM was concentrated in high-TOC layers whereas reactive Fe was concentrated in low-TOC layers (possibly as Fe-oxyhydroxide coatings on silt grains), as a consequence of which part of the H2S generated in the high-TOC layers diffused upward into the low-TOC layers before becoming fixed as pyrite. This process is evidenced by several contrasts between high-TOC and low-TOC layers: (1) higher Spyrite concentrations and Fepy/FeHR values in the latter, (2) concentration of pyrite in the lower part of low-TOC layers, immediately above high-TOC layers, and (3) higher δ34Spyrite values in the latter, reflecting late diagenetic formation of the H2S that diffused upward into the low-TOC layers. To our knowledge, this process has not been documented previously in ancient marine shales, probably owing to insufficiently high-resolution analysis in earlier studies.Liu, J., Hartmann, S.C., Keppler, F., Lai, D.Y.F., 2019. Simultaneous abiotic production of greenhouse gases (CO2, CH4, and N2O) in subtropical soils. Journal of Geophysical Research: Biogeosciences 124, 1977-1987.: Soils exert considerable influence on the global biogeochemical cycles, but their role in the abiotic production of volatile compounds remains poorly understood. In this study, we demonstrated evidence for the abiotic production of three major greenhouse gases (GHGs), namely carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O), simultaneously in six different subtropical surface soils under thermal treatment at 30 to 90 °C, wetting, and the addition of hydrogen peroxide. This study identified soils as a novel source of N2O through abiotic processes such as thermal treatment and the oxidation of reactive oxygen species. Our results showed that the abiotic production rate of all three GHGs increased exponentially with temperature, while that of CO2 and CH4 increased linearly with hydrogen peroxide concentrations. Wetting of soil samples could further enhance the rate of abiotic CO2 and N2O production in soils. These findings highlight the potential contribution of abiotic processes in the production of GHGs in subtropical soils and help constrain the uncertainties of the global GHG budgets.Plain Language Summary: While the production of greenhouse gases (GHGs) in soils by microbial activities has been widely documented and investigated, the role of nonmicrobial processes in soil GHG production is still poorly understood. In this study, we found that sterilized soil samples, in the absence of microbial activities, could produce three major GHGs, including carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O), simultaneously under heating, wetting, and the addition of hydrogen peroxide (a powerful oxidizing agent). Also, this study discovered a new source of atmospheric N2O arising from the abiotic production in soils under a high temperature and the presence of hydrogen peroxide. The abiotic production rates of all three GHGs increased exponentially with temperature, implying that global warming could enhance nonmicrobial GHG production rates and induce a positive climate feedback.Liu, J., Sheng, J.J., Huang, W., 2019. Experimental investigation of microscopic mechanisms of surfactant-enhanced spontaneous imbibition in shale cores. Energy & Fuels 33, 7188-7199. surfactants in fracturing fluids is a practical method for enhancing spontaneous imbibition of shale oil reservoirs. However, both positive and negative observations are found in the field practice. The mechanisms of different types of surfactants for enhancing spontaneous imbibition still need further investigation. In this work, we applied the nuclear magnetic resonance technique to measure the fluid distributions in shale pores during the spontaneous imbibition process. We found that surfactants mainly recover oil in the macropores but have less impact on the production of oil in the micropores. Combining with scanning electron microscopy, high-pressure mercury intrusion, and X-ray diffraction experiments, the pore structure and mineral composition of shales are carefully analyzed. We observed that the surfaces of large pores are mostly quartz and feldspars, while the surfaces of small pores are organic matter and clay. The wettability of a shale rock is a key factor affecting spontaneous imbibition; moreover, various minerals that make up the shale have different wettability. Therefore, we performed the contact angle experiments for the pure mineral chips (quartz, feldspar, calcite, dolomite, clay minerals, etc.) to measure the wettabilities at the initial condition after aging and after being altered by surfactants. The experimental results indicate that surfaces of macropores can be easily altered to be water-wet by surfactants. However, it is not for the micropores, especially for organic matter pores and intracrystalline pores within pyrite framboids. It appears that the anionic surfactant performs better in terms of spontaneous imbibition recovery due to the high efficiency on wettability alteration of clay surfaces.Liu, J., Xie, L., Elsworth, D., Gan, Q., 2019. CO2/CH4 competitive adsorption in shale: Implications for enhancement in gas production and reduction in carbon emissions. Environmental Science & Technology 53, 9328-9336. interaction determines the prospects for complementary enhanced gas recovery (EGR) associated with CO2 sequestration in shale. We characterize the competitive adsorption of CO2 and CH4 in shale using low-field NMR. Competitive sorption of CO2 relative to CH4 is defined as the CO2/CH4 competitive adsorption ratio (CO2/CH4 CAR for short) when CO2 and CH4 have the same original partial pressure in shale. Results indicate the CO2/CH4 CAR decreases with the logarithm of increasing pressure. Observed CO2/CH4 CARs are on the order of 4.28–5.81 (YDN-1) to 3.43–5.57 (YDN-2), describing the remarkable competitive advantage of CO2 sorption relative to CH4 for shale. Results also indicate that increasing the CO2/CH4 pressure ratio (1) increases the adsorption capacity of shales to CO2 and decreases that to CH4 logarithmically with pressure, and (2) boosts CO2–CH4 displacement and generates greater EGR efficiency in shale, where the EGR efficiency can be inferred by the CO2/CH4 pressure ratio using a Langmuir-like function. Furthermore, the maximum sequestration capacity of adsorbed CO2 during CO2–CH4 competition is on the order of ～3.87 cm3/g (YDN-1) to ～5.13 cm3/g (YDN-2). These promising results for EGR and CO2 storage reveal the considerable potential for carbon capture and geological sequestration in shale.Liu, R., Li, J., Xiao, Z., Li, J., Zhang, H., Lu, Y., Zhang, B., Ma, W., Li, D., Liu, M., 2019. Geochemical characteristics and their gas and oil source correlation implication in the Tugeerming area of the Kuqa Depression, Tarim Basin, China. Journal of Natural Gas Geoscience 4, 161-168. Tugeerming area is located in the eastern part of the Kuqa Depression, Tarim Basin. In recent years, prolific oil and gas flow in the Jurassic Yangxia Formation of Well Tudong 2 indicates broad prospects of exploration in the said area. This paper carries out the oil-gas and source correlation in the Tugeerming area. The findings acquired as briefed as follows. The biomarker characteristics of the crude oil of the Yangxia Formation of the Tugeerming Jurassic group showed that the hydrocarbon precursor types were a typical freshwater source of terrestrial organic matters with in the Yangxia Formation. The natural gas of the group is coal-type condensate with associated gas. The maturity of the natural gas is the same as that of the crude oil, where both of them are derived from the same hydrocarbon source rocks. In this paper, the biomarker comparison technique, n-alkane carbon isotope comparison technique, and kerogen carbon isotope-crude carbon isotope comparison technology system were used to study the Jurassic Yangxia Formation oil in the Tugeerming area, as well as the hydrocarbon source rocks of Jurassic and Triassic in the area. The differences between the source rocks are comprehensive. The results show that there is a maternal relationship between the Yangxia Formation crude oil and the source rocks of the Jurassic Yangxia and Kezilenur formations, which provides an important reference for the evaluation of oil and gas resources in this area.Liu, S., Liang, Y., Li, B., Wan, Q., Han, X., 2019. Interaction relationship analysis between heat transfer and hydrate decomposition for optimization exploitation. Fuel 256, 115742. transfer influences hydrate decomposition. Hydrate dissociation produces water. Then, water remained in the hydrate sediment shows impact on heat transfer. Six runs of experiment with different exploitation methods and well arrangements were conducted to study the interaction relationship between heat transfer and hydrate decomposition. For water production, results show that by combination method, the wellbore heating can greatly improve the water produced outside the reactor in production stage (WPII) until the hydrate decomposition ceases. While in depressurization regime, the WPII is more easily influenced by hydrate distribution and the water produced outside the reactor in the free and mix gas stage (WPI). For heat transfer, the overall heat transfer trend is not affected by less WPII. So the decomposition was hardly impacted. On the other hand, the heat transfer promotes heat absorption by hydrates, which improves hydrate decomposition. Subsequently, the hydrate decomposition consumes heat, but it cannot prevent the rise of temperature even in depressurization. So the heat from the surrounding environment is enough for hydrate decomposition. Then, the heat absorption by hydrate decomposition (Qd) and the heat absorption rate (Rd) are quantitatively studied. Specially, the heat absorption ratio (λ) is firstly defined to show the ratio of Qd to the wellbore heating consumption (Ec). It provides a fresh attitude for optimizing exploitation according to the heat transfer. In order to save more heat and improve λ, we need to utilize the heat transfer from the ambient environment and make progress in reducing wellbore heating consumption.Liu, W., Wang, H., Leng, Q., Liu, H., Zhang, H., Xing, M., Cao, Y., Yang, H., 2019. Hydrogen isotopic compositions along a precipitation gradient of Chinese Loess Plateau: Critical roles of precipitation/evaporation and vegetation change as controls for leaf wax δD. Chemical Geology 528, 119278. hydrogen isotopic compositions (δD) of long-chain plant leaf waxes can reflect changes of continental hydrology and thus have been increasingly utilized for paleoclimate reconstruction. One of the unresolved major issues is whether variations of leaf wax δD (δDwax) signals along a precipitation gradient reflect changes of precipitation δD, precipitation amount, and/or evapo-transpiration. This ambiguity limits our interpretation of δDwax in geological records as well as the quantitative reconstruction of paleohydrological variability. Here we systematically investigated δD of soil water and waxes extracted from soil and plant leaves in the Chinese Loess Plateau (CLP) and its surrounding areas along a precipitation gradient with mean annual precipitation (MAP) varying from 140?mm to 676?mm. The results showed that while the variation of modeled precipitation δD has no significant correlation with MAP, soil water δD, soil δDwax, and individual plant δDwax exhibit negative correlations with MAP. In relatively arid areas, the δD values of soil water and plant leaf waxes are significantly more positive due to much lower precipitation relative to evapo-transpiration, suggesting that effective precipitation (P:E ratio) has played a crucial role in the D-enrichment of soil and plant leaf waxes in this region. While parallel decreasing trends in δDwax are found along the increase of precipitation gradient among dominant plants (including Artemisia spp., Aster hispidus, Stipa bungeana, and Cleistogenes squarrosa) in the region with similar slopes, the large δD offsets between plant groups suggest that plant type is an important factor in controlling plant hydrogen isotope fractionations. Our results indicate that δDwax preserved in paleosols can be used to infer past conditions of water availability in arid and semi-arid inland regions, but with a mechanism that is different from the influence of “amount effect” in humid areas. Moreover, vegetation changes should be constrained by independent paleobotanical data before monsoon related paleohydrology in the CLP and its surrounding areas can be quantitatively reconstructed using the plant wax δD proxy.Liu, W., Ye, L., Wang, Z., Yu, S., 2019. Formation mechanism of organic-rich source rocks in Bozhong sub-basin, Bohai Bay basin, China. Arabian Journal of Geosciences 12, 504. the main source rocks, the third member of Shahejie Formation (Es3), the first member of Shahejie Formation (Es1) and the third member of Dongying Formation (Ed3) have abundant oil reserves. However, the formation mechanism is unclear, especially the paleoproductivity. This paper discussed the paleoproductivity and paleoenvironment such as terrigenous organic matter (TOM) input, sedimentation rate, and redox conditions. Previous studies considered that all the source rocks have high paleoproductivity during deposition, but they ignored the time attribute. Based on the definition of total organic carbon (TOC), we deduced a new formula and calculated the paleoproductivity of Ed3, Ed1, and Es3. The results suggested that the paleoproductivity was high during Ed3 and Es3 deposition, and low during Es1 deposition. The TOM input was moderate during Es3 deposition, high during Ed3 deposition, and low during Es1 deposition. The lake was saline during Es1 deposition, and fresh to brackish during Ed3 and Es3 deposition. The salinization of the lake water in the study area formed good redox conditions, in which the accumulation of organic matter at a low sedimentation rate was the main controlling factor for the formation of organic-rich source rocks in Es1. In contrast, the high paleoproductivity at a high sedimentation rate was the main controlling factor in Ed3 and Es3.Liu, X., Jiang, Z., Zhang, K., Song, Y., Jiang, L., Jiang, S., Xuan, Q., Wen, M., Huang, Y., Wang, X., Liu, T., Xie, X., 2019. Mechanism analysis of organic matter enrichment of Upper Ordovician-Lower Silurian shale in the Upper Yangtze area: Taking Jiaoye-1 Well in the Jiaoshiba Block as an example. Geofluids 2019, 5806023. matter is the material basis of shale hydrocarbon generation. The current organic matter content in shale is controlled by the original sedimentary organic matter abundance. Therefore, the study of the enrichment mechanism of sedimentary organic matter in shale has become an important issue to be solved. The Upper Yangtze area is the important exploration and exploitation area of marine shale gas in China. The shale of the Upper Ordovician Wufeng Formation-Lower Silurian Longmaxi Formation in the Yangtze area is the research object. Choosing redox indicator and biological productivity indicator, the study explores the enrichment mechanism of sedimentary organic matter from two aspects, sealing of water and volcanic activity. The results show that excess siliceous mineral in the shale of the Wufeng Formation-Longmaxi Formation in the Upper Yangtze area is bioorigin. Excess siliceous mineral can be used as one of the indicators of biological productivity. On the one hand, layer phenomenon occurred since the strong water sealing during the sedimentary period of Wufeng and the lower section of the Longmaxi Formation, which results in the high content of oxygen in surface water. On the other hand, the active volcanic activity brought volcanic ash which was beneficial to biological reproduction. Both of these factors led to higher biological productivity during this period. At the same time, the strong sealing of water made the lower layer of the water more reductive, and the active volcanic activity caused climate change, enhancing the reduction of the lower layer of the water, which made the rich organic matter deposited from the surface water well preserved. In the sedimentary period of the upper section of the Longmaxi Formation 1st member in the Upper Yangtze area, on the one hand, due to the weakened sealing of water, the oxygen content of the upper water decreased. On the other hand, the volcanic activity weakened until it stopped, and the source of volcanic ash rich in nutrient elements decreased. These two aspects led to lower biological productivity during this period. At the same time, the weaker water sealing could lead to a decrease in the reduction of the lower layer of the water, and the gradual cessation of volcanic activity no longer affected the climate, causing the destruction of sedimentary organic matter by oxidation.Liu, Y.-F., Qi, Z.-Z., Shou, L.-B., Liu, J.-F., Yang, S.-Z., Gu, J.-D., Mu, B.-Z., 2019. Anaerobic hydrocarbon degradation in candidate phylum ‘Atribacteria’ (JS1) inferred from genomics. The ISME Journal 13, 2377-2390. hydrocarbon-enriched environments, such as oil reservoirs and oil sands tailings ponds, contain a broad diversity of uncultured microorganisms. Despite being one of the few prokaryotic lineages that is consistently detected in both production water from oil reservoirs and stable hydrocarbon-degrading enrichment cultures originated from oil reservoirs, the physiological and ecological roles of candidate phylum “Atribacteria” (OP9/JS1) are not known in deep subsurface environments. Here, we report the expanded metabolic capabilities of Atribacteria as inferred from genomic reconstructions. Seventeen newly assembled medium-to-high-quality metagenomic assembly genomes (MAGs) were obtained either from co-assembly of two metagenomes from an Alaska North Slope oil reservoir or from previous studies of metagenomes coming from different environments. These MAGs comprise three currently known genus-level lineages and four novel genus-level groups of OP9 and JS1, which expands the genomic coverage of the major lineages within the candidate phylum Atribacteria. Genes involved in anaerobic hydrocarbon degradation were found in seven MAGs associated with hydrocarbon-enriched environments, and suggest that some Atribacteria could ferment short-chain n-alkanes into fatty acid while conserving energy. This study expands predicted metabolic capabilities of Atribacteria (JS1) and suggests that they are mediating a key role in subsurface carbon cycling.Loken, L.C., Crawford, J.T., Schramm, P.J., Stadler, P., Desai, A.R., Stanley, E.H., 2019. Large spatial and temporal variability of carbon dioxide and methane in a eutrophic lake. Journal of Geophysical Research: Biogeosciences 124, 2248-2266.: Lakes are conduits of greenhouse gases to the atmosphere; however, most efflux estimates for individual lakes are based on extrapolations from a limited number of locations. Within‐lake variability in carbon dioxide (CO2) and methane (CH4) arises from differences in water sources, mixing, atmospheric exchange, and biogeochemical transformations, all of which vary across multiple temporal and spatial scales. We asked, how variable are CO2 and CH4 across the surface of a single lake, how do spatial patterns change seasonally, and how well does the typical sampling location represent the entire lake surface? During the 2016 ice‐free period, we mapped surface water concentrations of CO2 and CH4 approximately weekly in Lake Mendota (USA) and modeled diffusive gas exchange. During stratification, CO2 was generally lower than atmospheric saturation (mean 19.81 μM) and relatively homogenous (mean coefficient of variation 0.12), whereas CH4 was routinely extremely supersaturated (mean 0.29 μM) with greater spatial heterogeneity (mean coefficient of variation 0.65). During fall mixis, concentrations of both gases increased and became more spatially variable, but their spatial arrangements differed. In this system, samples collected from the lake center reasonably well represented the spatially weighted mean CO2 concentration but overestimated annual CO2 efflux by 21%. For CH4, the lake center underestimated annual diffusive efflux by only 8.6% but poorly represented lakewide concentrations and fluxes on any given day. Upscaling from a single site to the whole lake requires consideration of spatial variation to assess lakewide carbon dynamics due to heterogeneity in within‐lake processing, transport to the lake surface, and exchange with the atmosphere.Plain language summary: Numerous physical, chemical, and biological properties vary across the surface of individual lakes. However, researchers frequently use the lake center to represent the entire lake and ignore spatial heterogeneity. Using a boat‐mounted sampling system, we mapped carbon dioxide and methane across the surface of Lake Mendota 26 times spanning the entire ice‐free season. We described the progression of each gas's spatial pattern and evaluated the consequences of using only the lake center to calculate emissions to the atmosphere. The lake surface alternated between periods of relative uniformity to periods or remarkable spatial heterogeneity, and the spatial patterns of the two gases did not always align. At the annual scale, samples at the lake center overestimated lakewide carbon dioxide efflux and underestimated methane efflux. These results have consequences for our understanding of lake carbon cycling and the contribution of lakes to atmospheric greenhouse gas budgets.López-Islas, A., Colín-García, M., Negrón-Mendoza, A., 2019. Stability of aqueous formaldehyde under γ irradiation: prebiotic relevance. International Journal of Astrobiology 18, 420-425 is a precursor of sugars, which are compounds essential in all forms of life and a necessary molecule for prebiotic processes. This work focuses on evaluating the stability of formaldehyde exposed to a high radiation field simulating prebiotic conditions on primitive Earth, such as the ocean or shallow waters. Formaldehyde may have been formed from reactions in the atmosphere and from rainout processes reached water bodies. In our experiments, we employed γ radiation and found that formaldehyde was labile towards radiation and decomposed even at low irradiation doses due to the fact that aldehyde/hydrate groups present in formaldehyde structure are very reactive under irradiation. However, after exposing this molecule to several doses of irradiation, we detected the formation of formic acid and glycolaldehyde – both of which are of prebiotic interest. We also observed formaldehyde regeneration by one of its radiolytic products: formic acid.Lu, G., Wei, C., Wang, J., Zhang, J., Quan, F., Tamehe, L.S., 2019. Variation of surface free energy in the process of methane adsorption in the nanopores of tectonically deformed coals: A case study of middle-rank tectonically deformed coals in the Huaibei coalfield. Energy & Fuels 33, 7155-7165. adsorption of coal is essentially a process of energy and material state transformation. It is a complex process especially for tectonically deformed coals (TDCs). In order to clarify this process, 12 middle-rank TDCs were screened for the experimental and theoretical study. On the basis of the liquid nitrogen adsorption experiment and methane isothermal adsorption experiment, the nanopore structure and the methane adsorption capacity of the TDC samples were analyzed. Using the theories of Polanyi adsorption potential and surface free energy reduction (SFER), the variation of energy in the process of methane adsorption in nanopores was explored. The following results were obtained. (1) The Langmuir volume has a stronger positive relationship with the specific surface area of the ultra-micropore, mild-micropore, and micropore than with those of the transitional pore. The adsorption potential decreases as the adsorption space grows; however, it rises as tectonic deformation enhances. The increase in the ratio of specific surface area for the mild-micropore and ultra-micropore indicates that the tectonic deformation can enhance both the available adsorption area and adsorption potential for methane in TDCs, eventually resulting in the increase of the Langmuir volume and the SFER. (2) The methane molecules preferentially occupy the sites with strong adsorption potential on the coal surface during the strong adsorption stage, resulting in the sharp increase of the methane adsorption volume and SFER. Then, the number of sites with strong adsorption potential decreases and the methane molecules have to settle at the energetically suboptimal sites during the weak adsorption stage, leading to the slight increase of methane adsorption volume and SFER. The above results may help to improve the accuracy of coalbed methane resource estimations and gas outburst prediction in the area where TDCs are developed.Luo, L., Chen, Z., Cheng, Y., Lv, J., Cao, D., Wen, B., 2019. Effects of dissolved organic carbon on desorption of aged phenanthrene from contaminated soils: A mechanistic study. Environmental Pollution 254, 113016. organic carbon (DOC) has a major influence upon sorption/desorption and transport of hydrophobic organic contaminants (HOCs) in soil environments. However, the molecular mechanisms of DOC sorption and its effects on aged HOC desorption in contaminated soils still remain largely unclear. Here, effects of three different DOC (one from commercial peat and two from biochars produced at 300?°C and 500?°C pyrolysis temperatures, respectively) and oxalate (as a reference) on abiotic desorption behavior of aged phenanthrene from three agricultural soils were investigated. Results showed that desorption of aged phenanthrene from soils was predominantly dependent on soil organic carbon content. The presence of DOC and oxalate resulted in higher desorption of phenanthrene compared to water alone, and the effects were positively related to soil organic carbon content and DOC/oxalate concentration. The facilitating effects of DOC were further increased during the second consecutive desorption, whereas oxalate had no such effect. Ultra-high-resolution Fourier transform-ion cyclotron resonance-mass spectrometry confirmed the molecular fractionation of DOC at the soil-water interface during DOC sorption. Specifically, the DOC molecules with O-rich moieties were preferentially adsorbed, whereas the molecules with phenolic and aromatic structures were selectively retained in the soil solutions through competitive displacement and co-sorption reactions during sorption. The enriched phenyl structures in the retained DOC facilitated its association with phenanthrene in the solutions and thus the release of phenanthrene from the soils. In contrast, oxalate replaced some organic carbon from the soils and thus released the associated phenanthrene into the solutions. Our findings highlight the importance of the molecular composition and structure of DOC for the desorption of phenanthrene in soil-water environments, which may help improve our understanding of the release and transport of organic compounds in the environments.Ly, T., Wright, J.R., Weit, N., McLimans, C.J., Ulrich, N., Tokarev, V., Valkanas, M.M., Trun, N., Rummel, S., Grant, C.J., Lamendella, R., 2019. Microbial communities associated with passive acidic abandoned coal mine remediation. Frontiers in Microbiology 10, 1955. doi: 10.3389/fmicb.2019.01955. mine drainage (AMD) is an environmental issue that can be characterized by either acidic or circumneutral pH and high dissolved metal content in contaminated waters. It is estimated to affect roughly 3000 miles of waterways within the state of Pennsylvania, with half being acidic and half being circumneutral. To negate the harmful effects of AMD, ~300 passive remediation systems have been constructed within the state of Pennsylvania. In this study, we evaluated the microbial community structure and functional capability associated with Middle Branch passive remediation system in central PA. Sediment and water samples were collected from each area within the passive remediation system and its receiving stream. Environmental parameters associated with the remediation system were found to explain a significant amount of variation in microbial community structure. This study revealed shifts in microbial community structure from acidophilic bacteria in raw AMD discharge to a more metabolically diverse set of taxa (i.e. Acidimicrobiales, Rhizobiales, Chthoniobacteraceae) towards the end of the system. Vertical flow ponds and the aerobic wetland showed strong metabolic capability for sulfur redox environments. These findings are integral to the understanding of designing effective passive remediation systems because it provides insight as to how certain bacteria (SRBs and SOBs) are potentially contributing to a microbially mediated AMD remediation process. This study further supports previous investigations that demonstrated the effectiveness of sulfate reducing bacteria (SRBs) in the process of removing sulfate and heavy metals from contaminated water.Lyu, Z., Zhang, L., Algeo, T.J., Zhao, L., Chen, Z.-Q., Li, C., Ma, B., Ye, F., 2019. Global-ocean circulation changes during the Smithian–Spathian transition inferred from carbon?sulfur cycle records. Earth-Science Reviews 195, 114-132. Triassic marine ecosystems experienced multiple environmental perturbations and a delayed biotic recovery following the end-Permian mass extinction. The Smithian–Spathian boundary (SSB), in the late Early Triassic, marks a major shift toward a less intensely warm climate, ameliorated marine environmental conditions, and the onset of a more sustained recovery of marine faunas. Accumulating geochemical evidence indicates that these developments were accompanied by large changes in global-ocean circulation during the Smithian–Spathian (S–S) transition. In the present study, tandem carbon and sulfur isotopic records were used to investigate changes in the marine carbon and sulfur cycles across the SSB and their potential relationship to global-ocean circulation changes. First, we conducted a carbon?sulfur isotope study at two deepwater SSB sections (West Pingdingshan and Jiarong) in South China. High-resolution δ13Ccarb-δ34SCAS profiles show large positive excursions and strong correlations through the S–S transition, suggesting control by co-burial of organic matter and pyrite. Second, we reviewed global carbon?sulfur isotope studies through the Smithian and Spathian substages. Similar to carbonate carbon isotopes, sulfate sulfur isotopes also show vertical gradient changes during the S–S transition. We link these changes to an expansion of oceanic oxygen-minimum zones (OMZs) in response to a cooling-driven re-invigoration of global-ocean circulation that triggered enhanced productivity on platform margins. OMZ expansion may have contributed to a second-order extinction among conodonts and ammonoids at the SSB, but the long-term shift toward more vigorous ocean circulation and better-ventilated watermasses is likely to have facilitated the overall recovery of marine biotas during the Spathian Substage of the late Early Triassic.Ma, L., Hurtado, A., Eguilior, S., Llamas Borrajo, J.F., 2019. Forecasting concentrations of organic chemicals in the vadose zone caused by spills of hydraulic fracturing wastewater. Science of The Total Environment 696, 133911. return water from hydraulic fracturing operations is characterised by high concentrations of salts and toxic organic compounds. This water is stored on the surface in storage tanks and/or ponds. Wastewater spills caused by inappropriate storage can lead to the contamination of various environmental compartments, thus posing a risk to human health. Such risk can be determined by estimating the concentrations of the substances in the storage system and the behaviour of the same in function of the characteristics of the environment in which they are released.To this end, here we addressed the evolution of the concentrations of pollutants in a tank used to store wastewater from hydraulic fracturing operations. To do this, we estimated both the volume of flowback and the concentrations of the pollutants found in these waters. We then examined the dynamic behaviour of spill-derived compounds in the various environmental compartments in function of the conditions of the medium (humid, semi-arid, and arid). This approach allowed us to rank the hazard posed by the chemical compounds in question, as well as to determine those parameters associated with both the compounds and external natural conditions that contribute to environmental risk. Our results shed greater light on the mechanism by which external environmental variables (especially recharge rate) influence the migration of organic compounds in the vadose zone, and contribute to the prediction of their concentrations. Also, by estimating the time that chemicals remain in contaminated areas, we identify the phases of contamination that pose the greatest risk to human health. In summary, the approach used herein allows the ranking of compounds on the basis of risk to human health and can thus facilitate the design of pollutant management strategies. Of note, our ranked list highlights the relevance of benzene.Ma, X., Yang, Y., Zhang, J., Xie, J., 2019. A major discovery in Permian volcanic rock gas reservoir exploration in the Sichuan Basin and its implications. Natural Gas Industry B 6, 419-425., a high-yield gas flow of 22.5 × 104 m3/d was achieved in the wildcat well Yongtan 1, deployed by PetroChina Southwest Oil and Gasfield Company, and an extrusive facies volcaniclastic gas reservoir was first discovered in the Sichuan Basin, which is a major breakthrough in the exploration of volcanic rock gas reservoirs. In order to further evaluate the exploration potential in Permian volcanic rock gas reservoirs in this basin, we systematically reviewed and summarized the exploration process of volcanic rocks in this study area, as well as the characteristics of gas reservoirs of well Yongtan 1, the controlling factors and modes of hydrocarbon accumulation. The following findings were obtained. (1) Over the past five decades of gas exploration of volcanic rocks, the change of exploration thought and progress in seismic prediction contribute to a major discovery in this study area, i.e., the well location deployment of Yongtan 1 was determined in the Jianyan area, where the volcanic anomalies of the Permian developed outbursts are well developed and the gas reservoir conditions are favorable. This also proves that another new gas exploration area in this basin was found. (2) From the data of Yongtan 1, we found high-quality volcanic porous reservoirs with a thickness of over 100 m developed in the Permian strata, the effusive volcanic rock types dominated by breccia and tuffaceous breccia, reservoir space composed of dissolution pores, interbreccia dissolution pores, and other pores, the porosity of which is 6.68%–13.22% and 10.26% on average, the permeability 0.01–4.43 mD and 2.35 mD on average. (3) This abnormally high pressure gas reservoir was buried 4500–6000 m deep underground with the middle formation pressure being 125.625 MPa and the pressure coefficient being up to 2.22. Methane content in the minor H2S-bearing produced gas flow reached up to 99.03%. (4) Volcanic rocks in the Jianyang–Zhongjiang–Santai area are developed, and they are adjacent to the Cambrian high-quality source rocks in the Deyang–Anyue rifting. The early extensional deep faults play a role in connecting source and storage. There are many sets of caprocks, such as the Upper Permian Longtan Formation and Lower Triassic layered thick paste rocks, providing conditions for forming large-scale tectonic–lithologic composite trap gas reservoirs, and the favorable exploration area reaches up to 6000 km2. In conclusion, this major discovery not only proves that Permian volcanic rocks in the Sichuan Basin has large potential for oil and gas exploration, but reaffirms the confidence in changing our exploration thought, speeding up new exploration zones and areas, and discovering more and bigger gas fields.Ma, Z.-H., Wei, X.-Y., Gao, H.-L., Liu, G.-H., Liu, Z.-Q., Liu, F.-J., Zong, Z.-M., 2019. Selective and effective separation of five condensed arenes from a high-temperature coal tar by extraction combined with high pressure preparative chromatography. Journal of Chromatography A 1603, 160-164. environmentally benign and cost-effective method was designed for isolating and purifying condensed arenes from acetone-extractable portion (AEP) of a high-temperature coal tar through a high pressure preparative chromatograph (HPPC) with different packings, including silica gel, octadecyl silane, octyl bonded silica gel, and diol bonded silica gel. In total, 196 compounds were detected with a gas chromatograph/mass spectrometer from AEP and its eluates. From the eluates, naphthalene, anthracene, phenanthrene, fluoranthene, and pyrene were successfully isolated and purified, and their structures were confirmed by their 1H and 13C nuclear magnetic resonance spectra in addition to their mass spectra. Extraction-HPPC device and solvent recovery process were designed and developed, which can potentially be applied to industrial production because the process is easy-to-operate and ecofriendliness. In addition, the solvents used can be easily recovered and reused, and neither waste water nor other pollutions are emitted.Makarov, A., Grinfeld, D., Ayzikov, K., 2019. Chapter 2 - Fundamentals of Orbitrap analyzer, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 37-61. chapter discusses fundamentals of the Orbitrap? mass spectrometry—the use of a purely electrostatic ion trap with harmonic properties to store ions and analyze their mass-to-charge distributions. The first section demonstrates principles of ion confinement in the quadro-logarithmic electrostatic field, where the ions perform hundreds of thousands of oscillations without losing their common phase. The discussion covers practical aspects of ion injection into the trap and the image current detection. The subsequent section introduces the reader to the Orbitrap aberration theory, gives a classification of electric field perturbations, and outlines the compensation methods. The next section concerns signal processing methods of the detected transients and covers both the traditional Fourier transform approaches and super-FT resolving methods. The chapter concludes with the overview of historical milestones of the Orbitrap technology and selected applications.Manea, E., Dell’Anno, A., Rastelli, E., Tangherlini, M., Nunoura, T., Nomaki, H., Danovaro, R., Corinaldesi, C., 2019. Viral infections boost prokaryotic biomass production and organic C cycling in hadal trench sediment. Frontiers in Microbiology 10, 1952. doi: 10.3389/fmicb.2019.01952. trenches are among the most remote and least explored ecosystems on Earth and can support high benthic microbial standing stocks and activities. However, information on the role of viruses in such ecosystems and their interactions with prokaryotic hosts is very limited. Here, we investigated activities of benthic viruses and prokaryotes and their interactions in three hadal trenches (Japan, Izu-Ogasawara and Mariana trenches) and in their surrounding abyssal sites. Our findings reveal that these hadal trenches, compared with the surrounding abyssal sites, support higher abundances and biomasses of prokaryotes. In addition, the high prokaryotic biomasses of hadal trenches could favour high rates of viral infection and cell lysis, especially in the Japan Trench. Hadal viruses can release large amounts of highly labile and promptly available organic material by inducing cell lysis, which could contribute to sustain benthic prokaryotes and decrease their dependency on the enzymatic digestion of the more refractory fraction of sediment organic matter. Our results suggest that this process can contribute to explain the discrepancy between high prokaryote biomass and apparent low efficiency in the utilization of the sedimentary organic matter in the hadal ecosystems. Hadal trenches may be characterized by highly dynamic viral component, which can enhance prokaryotic biomass production, thereby profoundly influencing the functioning of these remote and extreme ecosystems.Maria, E., Cran?on, P., Lespes, G., Bridoux, M.C., 2019. Spatial variation in the molecular composition of dissolved organic matter from the podzol soils of a temperate pine forest. ACS Earth and Space Chemistry 3, 1685-1696. podzols, the production and mobilization of dissolved organic matter (DOM) account for a considerable loss of carbon from the forest floor. The dynamics of DOM in the podzol soils of a pine forest result from complex interactions between water infiltrations, weathering, biological transformation, and retention-mobilization mechanisms. However, little is known about how the molecular composition of DOM changes spatially in the podzol soil as it moves from the upper horizons (organic (O) and eluvial (E)) to the illuvial horizon (B(h/s)) to the groundwater. In this study, DOM samples were collected in the upper (A1) and accumulation (Bh) horizons of a sandy permeable podzol with a hydrology occurring exclusively through drainage of shallow water (no surface runoff), as well as from the groundwater. Samples were concentrated on a Strata-X-AW solid-phase extraction cartridge and directly infused using electrospray ionization in the negative mode coupled with an LTQ-Orbitrap mass spectrometer. Over 2300 monoisotopic molecular formulas of CHO and CHON with molecular weights up to 600 Da, assigned mainly to lignin-like compounds (53%), tannins (22%), condensed aromatics (14%), protein-like compounds, lipids (3%), aminosugars/carbohydrates (1%), and unsaturated hydrocarbons, were identified in DOM from the upper podzol horizon (A1), indicating that leaching of plant debris dominates the DOM pool released in the soil seepage waters. Among all molecular formulas detected, 31% were unique to A1, while only 6.9% were only detected in Bh and 12.9% in Gw. Van Krevelen diagrams of these unique formulas clearly highlighted an evolution of the OM molecular composition along the podzol soil profile, from the upper horizon, through the accumulation horizon, to the groundwater with a shift from the high-oxygen, plant-derived compounds (tannins-like and lignin-like) to the low-oxygen classes (unsaturated and condensed hydrocarbon), suggesting a reduction process either microbially mediated or via preferential adsorption of oxygen-functionalized DOM compounds to mineral surfaces.Maris, A., Calabrese, C., Favero, L.B., Evangelisti, L., Usabiaga, I., Mariotti, S., Codella, C., Podio, L., Balucani, N., Ceccarelli, C., LeFloch, B., Melandri, S., 2019. Laboratory measurements and astronomical search for thioacetamide. ACS Earth and Space Chemistry 3, 1537-1549. observations allowed for the detection of two amides (formamide and acetamide) and some sulfur-containing molecules (among them, ethanethiol and thioformaldehyde) in the interstellar medium (ISM). To understand how the chemical complexity builds up in the ISM, thioacetamide is a next-step candidate. Therefore, laboratory measurements are necessary to attempt its identification in the millimeter wavelength spectral range. The rotational spectrum of thioacetamide was recorded in the 59.6–110.0 GHz frequency region (5.03–2.72 mm) using a Stark-modulated free-jet absorption spectrometer. The spectrum is complicated by the interaction of the methyl internal rotation with the overall molecular rotation, which splits the lines into two components. Nevertheless, 300 transition lines of the parent species and 42 transition lines of the 34S isotopologue were assigned, to yield the rotational constants, the quartic centrifugal distortion constants, the 14N nuclear quarupole coupling constants, and the internal rotation parameters. We searched for thioacetamide emission toward regions associated with the star-forming process, leading to a Sun-like star. More specifically, we used the IRAM 30 m ASAI observations toward the prestellar core L1544 and the outflow shock L1157-B1. The present paper allows us to put constrains on thioacetamide abundances in low-mass star-forming regions, paving the way to future deep astronomical searches.Marozava, S., Meyer, A.H., Pérez-de-Mora, A., Gharasoo, M., Zhuo, L., Wang, H., Cirpka, O.A., Meckenstock, R.U., Elsner, M., 2019. Mass transfer limitation during slow anaerobic biodegradation of 2-methylnaphthalene. Environmental Science & Technology 53, 9481-9490. they are theoretically conceptualized to restrict biodegradation of organic contaminants, bioavailability limitations are challenging to observe directly. Here we explore the onset of mass transfer limitations during slow biodegradation of the polycyclic aromatic hydrocarbon 2-methylnaphthalene (2-MN) by the anaerobic, sulfate-reducing strain NaphS2. Carbon and hydrogen compound specific isotope fractionation was pronounced at high aqueous 2-MN concentrations (60 μM) (εcarbon = ?2.1 ± 0.1‰/εhydrogen = ?40 ± 7‰) in the absence of an oil phase but became significantly smaller (εcarbon = ?0.9 ± 0.3‰/εhydrogen = ?6 ± 3‰) or nondetectable when low aqueous concentrations (4 μM versus 0.5 μM) were in equilibrium with 80 or 10 mM 2-MN in hexadecane, respectively. This masking of isotope fractionation directly evidenced mass transfer limitations at (sub)micromolar substrate concentrations. Remarkably, oil–water mass transfer coefficients were 60–90 times greater in biotic experiments than in the absence of bacteria (korg-aq2-MN = 0.01 ± 0.003 cm h–1). The ability of isotope fractionation to identify mass transfer limitations may help study how microorganisms adapt and navigate at the brink of bioavailability at low concentrations. For field surveys our results imply that, at trace concentrations, the absence of isotope fractionation does not necessarily indicate the absence of biodegradation.Martinelli, M., Mehrbod, M., Graham, U.M., Hu, Y., Gnanamani, M.K., Jacobs, G., 2019. Soft X-ray characterization of sulfur-poisoned cation-exchanged Pt/KL catalysts for aromatization of hexane, in: Rahimi, P., Ovalles, C., Zhang, Y., Adams, J.J. (Eds.), Chemistry Solutions to Challenges in the Petroleum Industry. American Chemical Society, Washington DC, pp. 243-260. percent Pt/KL catalysts containing ion-exchanged cations, for example, calcium (Ca), scandium (Sc), and manganese (Mn), were prepared by chemical vapor deposition. Catalysts were reduced at 500 °C in hydrogen and either cooled and fixed in wax directly, or subjected to H2S poisoning at 20.3 ppm for 2 h prior to cooling and fixing in wax. This prevented oxidation of catalyst samples, allowing for characterization by X-ray absorption near-edge spectroscopy (XANES) at the Soft X-ray Microcharacterization Beamline at the Canadian Light Source, Inc. K-edges of S, K, Ca, Sc, and Mn were examined following normalization of XANES spectra. There are two competing theories for the poisoning mechanism of Pt/KL catalysts. The first involves poisoning of charge-compensating cations located on Pt/KL, which is suggested to prevent the cation from assisting in ring closure of the adsorbed hexatriene intermediate on the Pt surface through an electrostatic interaction. The second mechanism involves direct poisoning of Pt surface by H2S. Once formed, Pt particles are proposed to migrate and agglomerate within KL channels, preventing diffusion of reactants and products to Pt clusters located within L-zeolite channels. XANES did not reveal evidence of an interaction between exchanged cations (e.g., Ca, Sc, or Mn) and sulfur, or between potassium cations and sulfur. Rather, XANES spectra at cation K-edges of freshly activated and activated/H2S-poisoned catalysts were virtually identical. Sulfur K-edge spectra showed line shapes consistent with platinum sulfide. In agreement with our prior study with Pt/KL catalysts, sulfur poisoning appears to involve direct poisoning of Pt, with detachment and agglomeration.Martinez, M., Garcia-Alonso, J.I., Parat, C., Encinar, J.R., Hécho, I.L., 2019. Anion-specific sulfur isotope analysis by liquid chromatography coupled to multicollector ICPMS. Analytical Chemistry 91, 10088-10094. accurate method has been developed to measure, in a single analytical run, δ34S in sulfite, sulfate and thiosulfate in water samples by liquid chromatography combined with multicollector inductively coupled plasma mass spectrometry (MC-ICPMS). The method is based on the anionic exchange separation of sulfur species prior to their online isotope ratio determination by MC-ICPMS. Mass bias correction was accomplished by a novel approach based on the addition of an internal sulfur-containing standard to the sample. This innovative approach was compared to the sample-standard bracketing procedure. On-column isotopic fractionation was observed and therefore corrected by external calibration. Isotopic ratios were calculated by linear regression slope (LRS), an advantageous method for transient signals, leading to a combined uncertainty of δ34S below 0.25‰ and a reproducibility below 0.5‰ for the injection of 1 μg of S. The method was successfully applied to the measurement of δ34S in synthetic solutions and environmental water samples. Matrix effects leading to δ34S overestimation were observed for sulfate in some samples with high sodium/sulfate mass ratios. The developed analytical procedure simplifies the δ34S analysis of liquid environmental samples since preparation steps are no longer required and allows the analysis of several sulfur-containing species in a single run.McDonald, M.J., 2019. Microbial Experimental Evolution – a proving ground for evolutionary theory and a tool for?discovery. EMBO reports 20, e46992. Microbial experimental evolution uses controlled laboratory populations to study the mechanisms of evolution. The molecular analysis of evolved populations enables empirical tests that can confirm the predictions of evolutionary theory, but can also lead to surprising discoveries. As with other fields in the life sciences, microbial experimental evolution has become a tool, deployed as part of the suite of techniques available to the molecular biologist. Here, I provide a review of the general findings of microbial experimental evolution, especially those relevant to molecular microbiologists that are new to the field. I also relate these results to design considerations for an evolution experiment and suggest future directions for those working at the intersection of experimental evolution and molecular biology.McKirdy, D.M., Gong, S., Corrick, A.J., Hall, P.A., Trefry, C., Ross, A.S., 2019. Are the n-alkane carbon isotopic profiles of South Australian coastal asphaltites indicative of their extent of weathering? Organic Geochemistry 136, 103893. bitumen (asphaltite) found on the ocean beaches of South Australia is considered to be a product of an adjacent, but as yet unlocated, submarine oil seep. Four large asphaltites recently stranded on three different beaches were sub-sampled (n?=?5–6). Samples were analysed to determine if their n-alkane δ13C profiles displayed systematic variation along a transect from the centre to the outer rim of the specimen. Previously reported 13C-enrichment in n-alkanes isolated from the outer portions of similar archival asphaltites was attributed to weathering. With one notable exception, these new specimens exhibited no unidirectional enrichment from interior (fresh) to exterior (weathered), although in every instance n-alkanes in the intermediate and outermost sub-samples were for the most part isotopically heavier than the same homologues in the central interior of the specimen. To be a viable measure of the extent of weathering in a population of coastal asphaltites, and hence also their relative exposure time in the ocean, this analytical protocol requires the specimens to have remained physically intact during their transit from the parent seep to shore. Whether this requirement has been met is impossible to determine, thereby limiting the effectiveness of the method to those specimens in which there is a consistent pattern of internal variation in their n-alkane carbon isotope profiles.McMahon, P.B., Vengosh, A., Davis, T.A., Landon, M.K., Tyne, R.L., Wright, M.T., Kulongoski, J.T., Hunt, A.G., Barry, P.H., Kondash, A.J., Wang, Z., Ballentine, C.J., 2019. Occurrence and sources of radium in groundwater associated with oil fields in the southern San Joaquin Valley, California. Environmental Science & Technology 53, 9398-9406. data from 40 water wells were used to examine the occurrence and sources of radium (Ra) in groundwater associated with three oil fields in California (Fruitvale, Lost Hills, South Belridge). 226Ra+228Ra activities (range = 0.010–0.51 Bq/L) exceeded the 0.185 Bq/L drinking-water standard in 18% of the wells (not drinking-water wells). Radium activities were correlated with TDS concentrations (p < 0.001, ρ = 0.90, range = 145–15,900 mg/L), Mn + Fe concentrations (p < 0.001, ρ = 0.82, range = <0.005–18.5 mg/L), and pH (p < 0.001, ρ = ?0.67, range = 6.2–9.2), indicating Ra in groundwater was influenced by salinity, redox, and pH. Ra-rich groundwater was mixed with up to 45% oil-field water at some locations, primarily infiltrating through unlined disposal ponds, based on Cl, Li, noble-gas, and other data. Yet 228Ra/226Ra ratios in pond-impacted groundwater (median = 3.1) differed from those in oil-field water (median = 0.51). PHREEQC mixing calculations and spatial geochemical variations suggest that the Ra in the oil-field water was removed by coprecipitation with secondary barite and adsorption on Mn–Fe precipitates in the near-pond environment. The saline, organic-rich oil-field water subsequently mobilized Ra from downgradient aquifer sediments via Ra-desorption and Mn/Fe-reduction processes. This study demonstrates that infiltration of oil-field water may leach Ra into groundwater by changing salinity and redox conditions in the subsurface rather than by mixing with a high-Ra source.Mejeha, O.K., Head, I.M., Sherry, A., McCann, C.M., Leary, P., Jones, D.M., Gray, N.D., 2019. Beyond N and P: The impact of Ni on crude oil biodegradation. Chemosphere 237, 124545. and P are the key limiting nutrients considered most important for the stimulation of crude oil degradation but other trace nutrients may also be important. Experimental soil microcosms were setup to investigate crude oil degradation in the context of Ni amendments. Amended Nickel as NiO, NiCl2, or, a porphyrin complex either inhibited, had no effect, or, enhanced aerobic hydrocarbon degradation in an oil-contaminated soil. Biodegradation was significantly (95% confidence) enhanced (70%) with low levels of Ni-Porph (12?mg/kg) relative to an oil-only control; whereas, NiO (200 and 350?mg/kg) significantly inhibited (36 and 87%) biodegradation consistent with oxide particle induced reactive oxygen stress. Microbial community compositions were also significantly affected by Ni. In 16S rRNA sequence libraries, the enriched hydrocarbon degrading genus, Rhodococcus, was partially replaced by a Nocardia sp. in the presence of low levels of NiO (12 and 50?mg/kg). In contrast, the highest relative and absolute Rhodococcus abundances were coincident with the maximal rates of oil degradation observed in the Ni-Porph-amended soils. Growth dependent constitutive requirements for Ni-dependent urease or perhaps Ni-dependent superoxide dismutase enzymes (found in Rhodococcus genomes) provided a mechanistic explanation for stimulation. These results suggest biostimulation technologies, in addition to N and P, should also consider trace nutrients such as Ni tacitly considered adequately supplied and available in a typical soil.Mikolasch, A., Donath, M., Reinhard, A., Herzer, C., Zayadan, B., Urich, T., Schauer, F., 2019. Diversity and degradative capabilities of bacteria and fungi isolated from oil-contaminated and hydrocarbon-polluted soils in Kazakhstan. Applied Microbiology and Biotechnology 103, 7261-7274. and fungi were isolated from eight different soil samples from different regions in Kazakhstan contaminated with oil or salt or aromatic compounds. For the isolation of the organisms, we used, on the one hand, typical hydrocarbons such as the well utilizable aliphatic alkane tetradecane, the hardly degradable multiple-branched alkane pristane, and the biaromatic compound biphenyl as enrichment substrates. On the other hand, we also used oxygenated derivatives of alicyclic and monoaromatic hydrocarbons, such as cyclohexanone and p-tert-amylphenol, which are known as problematic pollutants. Seventy-nine bacterial and fungal strains were isolated, and 32 of them that were clearly able to metabolize some of these substrates, as tested by HPLC-UV/Vis and GC-MS analyses, were characterized taxonomically by DNA sequencing. Sixty-two percent of the 32 isolated strains from 14 different genera belong to well-described hydrocarbon degraders like some Rhodococci as well as Acinetobacter, Pseudomonas, Fusarium, Candida, and Yarrowia species. However, species of the bacterial genus Curtobacterium, the yeast genera Lodderomyces and Pseudozyma, as well as the filamentous fungal genera Purpureocillium and Sarocladium, which have rarely been described as hydrocarbon degrading, were isolated and shown to be efficient tetradecane degraders, mostly via monoterminal oxidation. Pristane was exclusively degraded by Rhodococcus isolates. Candida parapsilosis, Fusarium oxysporum, Fusarium solani, and Rhodotorula mucilaginosa degraded cyclohexanone, and in doing so accumulate ε-caprolactone or hexanedioic acid as metabolites. Biphenyl was transformed by Pseudomonas/Stenotrophomonas isolates. When p-tert-amylphenol was used as growth substrate, none of the isolated strains were able to use it.Miles, S.M., Hofstetter, S., Edwards, T., Dlusskaya, E., Cologgi, D.L., G?nzle, M., Ulrich, A.C., 2019. Tolerance and cytotoxicity of naphthenic acids on microorganisms isolated from oil sands process-affected water. Science of The Total Environment 695, 133749. expansion of oil sands has made remediation of oil sands process-affected water (OSPW) critical. As naphthenic acids (NAs) are the primary contributors to toxicity, remediation is required. Bioremediation by native microorganisms is potentially effective, however, toxicity of NAs towards native microorganisms is poorly understood. The aim of this study was to isolate microorganisms from OSPW, assess tolerance to stressors, including naturally sourced NAs and examine exposure effect of NAs on cell membranes. Microorganisms were isolated from OSPW, including the first reported isolation of a fungus (Trichoderma harzianum) and yeast (Rhodotorula mucilaginosa). Isolates tolerated alkaline pH, high salinity, and NA concentrations far exceeding those typical of OSPW indicating toxic effects of OSPW are likely the result of interactions between OSPW components. Comparisons of toxicity determined that OSPW exhibited higher cytotoxicity than NAs. The fungal isolate was able to grow using commercial NAs as its sole carbon source, indicating high resistance to NAs' cytotoxic effects. Future studies will focus on the organisms' ability to degrade NAs, and subsequent effects on toxicity. Characterization of OSPW constituents should be investigated with focus on the synergistic toxic effects of dissolved compounds. A better understanding of OSPW toxicity would enable more effective and targeted bioremediation schemes by native microorganisms.Mishra, A., Medhi, K., Malaviya, P., Thakur, I.S., 2019. Omics approaches for microalgal applications: Prospects and challenges. Bioresource Technology 291, 121890. recent impetus of phycological research, microalgae have emerged as a potential candidate for various arena of application-driven research. Omics-based tactics are used for disentangling the regulation and network integration for biosynthesis/degradation of metabolic precursors, intermediates, end products, and identifying the networks that regulate the metabolic flux. Multi-omics coupled with data analytics have facilitated understanding of biological processes and allow ample access to diverse metabolic pathways utilized for genetic manipulations making microalgal factories more efficient. The present review discusses state-of-art “Algomics” and the prospect of microalgae and their role in symbiotic association by using omics approaches including genomics, transcriptomics, proteomics and metabolomics. Microalgal based uni- and multi-omics approaches are critically analyzed in wastewater treatment, metal toxicity and remediation, biofuel production, and therapeutics to provide an imminent outlook for an array of environmentally sustainable and economically viable microalgal applications.Mishra, S., Jha, N., Stebbins, A., Brookfield, M., Hannigan, R., 2019. Palaeoenvironments, flora, and organic carbon and nitrogen isotope changes across the non-marine Permian-Triassic boundary at Wybung Head, Australia. Palaeogeography, Palaeoclimatology, Palaeoecology 534, 109292. Permian-Triassic boundary section at Wybung Head, eastern Australia shows a rapid change from humid coal-bearing lowland braided stream through a thin clay and coal breccia and paleosols to semi-arid silty floodplain deposits. Identifiable plant remains and total organic matter disappear above the coal and clay breccia. Three characteristic palynofacies accumulated in a range from oxic to sub-oxic to anoxic conditions. The dominance of opaque phytoclasts in the entire sequence reflects deposition under oxic conditions, especially in the sequence lying above the Birdie Coal, the result of fluctuating water tables, high energy and desiccating conditions. In the Birdie Coal, however, at certain horizons, a water-saturated environment favored the preservation of organic matter such as pollen, spores, and structured organic matter. This latest Permian paleovegetation was dominated by opportunistic understory spore-bearing plants, with a canopy of pollen-bearing glossopterids, conifers and cordaitales. Total organic carbon drops from >30% in the coal, through <5% in the breccia to <1% in the paleosols and silts. The organic δ13C values are constant at ~ ?25.5‰ in the coal and coal breccia, but then decrease to less than ?27‰ in the paleosols and silts. These results confirm the rapid sedimentary, floral and organic carbon isotope changes across the non-marine Permian-Triassic boundary in eastern Australia. Our δ13Corg values suggest a significant and sustained negative δ13Corg excursion, with a magnitude of about 3‰, above the Birdie Coal. Unlike δ13Corg, there is no clear trend in δ15Norg values. The low C/N ratios of 10 and less, of the samples above +55?cm, are only found in modern burned soils with low bacteria/fungi ratios or in decaying wood. There is no obvious fungal spike in the Wybung Head section, may have been destroyed during the formation of this soil B horizon, as elsewhere a global fungal spike layer marks an interval of decreased terrestrial biomass and decaying vegetation associated with the Permian-Triassic crisis and boundary. Two negative excursions in the uppermost Permian and lowest Triassic can be correlated throughout Gondwana.Moir, M.E., 2019. The quantum mechanics of asphaltene aggregation, in: Rahimi, P., Ovalles, C., Zhang, Y., Adams, J.J. (Eds.), Chemistry Solutions to Challenges in the Petroleum Industry. American Chemical Society, Washington DC, pp. 89-111. is an understatement to say that asphaltenes are complex. There are at least 100,000 individual molecular formulae in any given asphaltene sample, each with an unknown number of isomers. Thus, it seems that developing an understanding of the physical behavior of asphaltenes based on quantum mechanics should be a fruitless task. But over the years, many researchers have attempted to do just that, to understand the intermolecular interactions of asphaltene molecules using the available theoretical tools. In this chapter we review the intermolecular forces at work in asphaltene aggregation, as they are currently understood. We also discuss the path forward to a more complete concept of asphaltene aggregation will be discussed.Morasch, M., Liu, J., Dirscherl, C.F., Ianeselli, A., Kühnlein, A., Le Vay, K., Schwintek, P., Islam, S., Corpinot, M.K., Scheu, B., Dingwell, D.B., Schwille, P., Mutschler, H., Powner, M.W., Mast, C.B., Braun, D., 2019. Heated gas bubbles enrich, crystallize, dry, phosphorylate and encapsulate prebiotic molecules. Nature Chemistry 11, 779–788. conditions must have been crucial for the assembly of the first informational polymers of early life, by supporting their formation and continuous enrichment in a long-lasting environment. Here, we explore how gas bubbles in water subjected to a thermal gradient, a likely scenario within crustal mafic rocks on the early Earth, drive a complex, continuous enrichment of prebiotic molecules. RNA precursors, monomers, active ribozymes, oligonucleotides and lipids are shown to (1) cycle between dry and wet states, enabling the central step of RNA phosphorylation, (2) accumulate at the gas–water interface to drastically increase ribozymatic activity, (3) condense into hydrogels, (4) form pure crystals and (5) encapsulate into protecting vesicle aggregates that subsequently undergo fission. These effects occur within less than 30?min. The findings unite, in one location, the physical conditions that were crucial for the chemical emergence of biopolymers. They suggest that heated microbubbles could have hosted the first cycles of molecular evolution.M?rchen, R., Lehndorff, E., Diaz, F.A., Moradi, G., Bol, R., Fuentes, B., Klumpp, E., Amelung, W., 2019. Carbon accrual in the Atacama Desert. Global and Planetary Change 181, 102993. Atacama Desert is the oldest and driest desert on Earth, nevertheless traces of life have been observed in several places, accumulating residues of organic matter (OM) in the desert soil. We evaluated to which degree the distribution of soil organic carbon (SOC) stocks depends on aridity. We questioned that these OM traces of life preferentially accumulate in topsoil and investigated whether there was also an enrichment of OM in deeper subsoil. We sampled four west-east directed transects with increasing distance to the coast, spanning the Atacama Desert from north to south, plus a hyperarid site at Yungay in the centre of the desert. With a nested sampling design we addressed topsoil heterogeneity at each sampling site (n?≤?18). For 12 of these sites soil profiles were dug to 0.6–2.0?m depth. The SOC concentrations were determined for each sample by temperature-dependent differentiation of total carbon.We found that with increasing distance to the coast (2.3 to 86.8?km) and thus aridity, SOC stocks decreased from 53.91?±?53.90 to 4.11?±?1.46 t SOC ha?1 in the topsoil. Hence, traces of life were ubiquitously preserved in both, arid and hyperarid desert areas, whereas a local hyperarid minimum of 1.02?±?0.18 t SOC ha?1 at 49.2?km distance, right in between the Andes and the coast, was found. Intriguingly, relatively large amounts of OM were found at depth below 15 cm, adding 74.0 to 94.3 % of subsoil SOC to the topsoil SOC stock. Furthermore, the subsoil SOC concentrations peaked between 40 and 150?cm depth in the soil, irrespectively of the presence or absence of visible vegetation. We conclude that carbon accrual in this arid to hyperarid system shifts from preferential carbon enrichment in topsoil to subsoil, therewith providing the potential for deep(er) biosphere food-webs and demonstrating the future need to dig into soil for discovering traces of life in comparable environments, including other planets such as Mars.Moreno-Perlin, T., Alpuche-Solís, ?.G., Badano, E.I., Etchebehere, C., Celis, L.B., 2019. Toward a solution for acid mine drainage treatment: Role of electron donors in sulfate reduction at low pH. Geomicrobiology Journal 36, 837-846. historically impacted by acid mine drainage was exposed to different initial pH and electron donors to investigate the effect that both conditions had on the performance and fingerprint of the community from naturally acidic sediments. Batch experiments were fed with either acetate, lactate, or glycerol at initial pH of 5, 4, or 3, under sulfate-reducing conditions. The performance results indicated that sulfide production efficiency was above 85% in the treatments fed with lactate and glycerol at pH 5 and 4. However, acetate consumption efficiency was greater than 85% only in the treatments with acetate at pH 5 and lactate at pH 5 and 4. Glycerol fed treatments successfully produced sulfide even at initial pH?=?3. Sulfide production rates were related to the initial pH in treatments fed with lactate and acetate and independent of the pH in the glycerol fed treatments. 16S rRNA gene T-RFLP analysis of the enriched communities indicated that the initial pH could explain the differences of the microbial community fingerprint obtained after 90?days. This study points out the fact that acidic stress is a heavy burden for the development of sulfate-reducing microorganisms, especially for those that use acetate as substrate.Moritz, F., Hemmler, D., Kanawati, B., Schnitzler, J.-P., Schmitt-Kopplin, P., 2019. Chapter 12 - Mass differences in metabolome analyses of untargeted direct infusion ultra-high resolution MS data, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 357-405. resolution mass spectrometers (UHR MS) including Fourier Transform ion cyclotron resonance (FT-ICR MS) and Orbitrap mass analyzers produce data of ever more increasing mass accuracy, resolution and information content. In its comparably long history of analyses on complex mixtures such as petroleum or natural organic matter, UHR-MS scientists have developed methods for mining and analysis of homologous hydrocarbon series, repetitive elemental compositional units that are characteristic for the chemistry of diverse complex organic matrices. The science of metabolomics considered the use of UHR-MS for the analysis of complete sets of metabolites since its infancy. However, the peculiarities of this type of UHR analytical instrumentation and the data it produces did not yet become a widely accepted source of biologically relevant information. This book chapter aims to assist the readers in their assessment of the great value that UHR-MS analyzers can produce for their own research. This book chapter's first section accordingly provides a short introduction into the history of metabolomics and attempts to gauge where UHR-MS is to be positioned amidst the various sub-classifications of metabolomic research. The second section then proceeds with introducing mass differences as the major means of mass spectrometric quality assessment, just to extend their use for the visual and computational localization of homologous molecular series and molecular formula assignment. After a review of major mass-difference based technologies in m/z signal identification, “Mass difference networks in the visualization and secondary analysis of UHR-MS data” section continues to line out the methods that are central for a systems biological analysis of metabolomic data. The chapter finishes by embedding mass differences into the context of the introduced methods and an example on their use for mining the chemical meaning of unknown metabolic features.Morozov, E.V., Yushmanov, P.V., Martyanov, O.N., 2019. Temperature-triggered rearrangement of asphaltene aggregates as revealed by pulsed-field gradient NMR. Energy & Fuels 33, 6934-6945. tendency of asphaltenes for aggregation followed by precipitation and deposition plays a crucial role in the petroleum industry since these processes present severe problems during the production, recovery, and processing of crude oils and fossil hydrocarbon feedstocks. The dynamics of oil asphaltene aggregates dissolved in chloroform at different concentrations varied in a wide range that was investigated at temperatures from 0 to 55 °C using the Pulsed-Field Gradient NMR technique. The components attributed to nanoaggregates and macroaggregates were successfully resolved, which allowed us to measure their diffusion coefficients. The diffusion coefficients for all types of aggregates grow as the asphaltene concentration decreases, whereas the partial weight of the aggregates increases with the increase of asphaltene concentration. The difference in diffusion behavior of the aggregates of different types was registered when passing the critical concentration range 10–20 g/L. The nano- and macroaggregates behave independently when the asphaltene concentration is higher than 20 g/L (concentrated regime), while below 20 g/L (semidiluted regime) the components related to the different types of aggregates cannot be properly resolved. It was found that regardless of the asphaltene concentration, the diffusion coefficients for nano- and macroaggregates demonstrate similar temperature behavior giving the straight lines in the Arrhenius coordinates which change their slopes when passing the temperature range 20–30 °C. The phenomenon evidences the thermally induced cleavage of noncovalent bonds with subsequent rearrangement of asphaltene aggregates that is observed for all concentration regimes covering the existence of asphaltene aggregates of all types. The data obtained are well consistent with the modern concept of asphaltene aggregate structure and fairly agree with the data obtained earlier. We believe these results will contribute essentially to a better understanding of the fundamental behavior of asphaltenes and their aggregates, providing a deep insight into aggregate transformation triggered by the temperature.Mu, C., Zhang, T., Abbott, B.W., Wang, K., Ge, S., Sayedi, S.S., Fan, C., Peng, X., 2019. Organic carbon pools in the subsea permafrost domain since the Last Glacial Maximum. Geophysical Research Letters 46, 8166-8173. level rise after the Last Glacial Maximum inundated several million square kilometers of Arctic permafrost, while estimates of organic carbon (OC) quantity and vulnerability to mineralization are exceedingly uncertain. We compiled geophysical measurements from Arctic continental shelves to estimate current subsea permafrost OC stocks. We found that marine transgression since the Last Glacial Maximum inundated approximately 3.92×106 km2 of permafrost, which contained 1,460±1,010 Pg OC in the top 25 m of sediment. We estimated that current subsea permafrost underlies an area of 2.30×106 km2 and contains 860±590 Pg OC, not including methane hydrates. Most of the ~600 Pg of OC that thawed after the marine transgression is still present on the continental shelves. Although our estimates of subsea OC storage remain highly uncertain due to the sparse and uneven distribution of data, they suggest that current estimates of subsea OC substantially underestimate a major component of the global carbon cycle.Müller, I.A., Rodriguez-Blanco, J.D., Storck, J.-C., do Nascimento, G.S., Bontognali, T.R.R., Vasconcelos, C., Benning, L.G., Bernasconi, S.M., 2019. Calibration of the oxygen and clumped isotope thermometers for (proto-)dolomite based on synthetic and natural carbonates. Chemical Geology 525, 1-17. is a very common carbonate mineral in ancient sediments, but is rarely found in modern environments. Because of the difficulties in precipitating dolomite in the laboratory at low temperatures, the controls on its formation are still debated after more than two centuries of research. Two important parameters to constrain the environment of dolomitization are the temperature of formation and the oxygen isotope composition of the fluid from which it precipitated. Carbonate clumped isotopes (expressed with the parameter Δ47) are increasingly becoming the method of choice to obtain this information. However, whereas many clumped isotope studies treated dolomites the same way as calcite, some recent studies observed a different phosphoric acid fractionation for Δ47 during acid digestion of dolomite compared to calcite. This causes additional uncertainties in the Δ47 temperature estimates for dolomites analyzed in different laboratories using different acid digestion temperatures.To tackle this problem we present here a (proto-)dolomite-specific Δ47-temperature calibration from 25 to 1100?°C for an acid reaction temperature of 70 °C and anchored to widely available calcite standards. For the temperature range 25 to 220?°C we obtain a linear Δ47-T relationship based on 289 individual measurements with R2 of 0.864:?47 CDES70°C=0.0428±0.0020×(106/T2)+0.1481±0.0160 (T in Kelvin)When including two isotopically scrambled dolomites at 1100?°C, the best fit is obtained with a third order polynomial temperature relationship (R2?=?0.924):‰?47 CDES70°C‰=?0.0002×(106/T2)3+0.0041×(106/T2)2+0.0115×(106/T2)+0.2218.Applying a calcite Δ47-T relationship produced under identical laboratory conditions results in 3 to 16?°C colder calculated formation temperatures for dolomites (with formation temperature from 0 to 100?°C) than using the (proto-)dolomite specific calibration presented here.For the synthetic samples formed between 70 and 220?°C we also determined the temperature dependence of the oxygen isotope fractionation relative to the water. Based on the similarity between our results and two other recent studies (Vasconcelos et al., 2005 and Horita, 2014) we propose that a combination of the three datasets represents the most robust calibration for (proto-)dolomite formed in a wide temperature range from 25 to 350?°C.103αCaMg?carbonates?Water=2.9923±0.0557×(106/T2)?2.3592±0.4116Because of the uncertainties in the phosphoric acid oxygen and clumped isotope fractionation for (proto-)dolomite, we promote the use of three samples that are available in large amounts as possible inter-laboratory reference material for oxygen and clumped isotope measurements. A sample of the middle Triassic San Salvatore dolomite from southern Switzerland, the NIST SRM 88b dolomite standard already reported in other Δ47 studies and a lacustrine Pliocene dolomite from La Roda (Spain).This study demonstrates the necessity to apply (proto-)dolomite specific Δ47-T relationships for accurate temperature estimates of dolomite formation, ideally done at identical acid digestion temperatures to avoid additional uncertainties introduced by acid digestion temperature corrections. In addition, the simultaneous analyses of dolomite reference material will enable a much better comparison of published dolomite clumped and oxygen isotope data amongst different laboratories.Mundy, L.J., Williams, K.L., Chiu, S., Pauli, B.D., Crump, D., 2019. Extracts of passive samplers deployed in variably contaminated wetlands in the Athabasca oil sands region elicit biochemical and transcriptomic effects in avian hepatocytes. Environmental Science & Technology 53, 9192-9202. contaminant monitoring in boreal wetlands situated in Alberta’s Athabasca oil sands region revealed increased concentrations of polycyclic aromatic compounds (PACs) in passive sampling devices deployed in wetlands close to bitumen surface mining operations. In this study, graded concentrations of semipermeable membrane device (SPMD) extracts, collected from 4 wetlands with variable burdens of PACs, were administered to chicken and double-crested cormorant (DCCO) embryonic hepatocytes to determine effects on 7-ethoxyresorufin-O-deethylase (EROD) activity and mRNA expression. Concentrations and composition of PACs detected in SPMDs varied among sites, and the proportion of alkyl PACs was greater than parent compounds at all sites. ΣPACs was the highest in SPMDs deployed within 10 km of mining activity (near-site wetland [5930 ng SPMD–1]) compared to those ～50 km south (far-site wetland [689 ng SPMD–1]). Measures of EROD activity and Cyp1a4 mRNA expression allowed the ranking of wetland sites based on aryl hydrocarbon receptor-mediated end points; EROD activity and Cyp1a4 mRNA induction were the highest at the near-site wetland. ToxChip PCR arrays (one chicken and one DCCO) provided a more exhaustive transcriptomic evaluation across multiple toxicological pathways following exposure to the SPMD extracts. Study sites with the greatest PAC concentrations had the most genes altered on the chicken ToxChip (12–15/43 genes). Exposure of avian hepatocytes to SPMD extracts from variably contaminated wetlands highlighted traditional PAC-related toxicity pathways as well as other novel mechanisms of action. A novel combination of passive sampling techniques and high-throughput toxicity evaluation techniques shows promise in terms of identifying hotspots of chemical concern in the natural environment.Murillo, W.A., Horsfield, B., Vieth-Hillebrand, A., 2019. Unraveling petroleum mixtures from the South Viking Graben, North Sea: A study based on δ13C of individual hydrocarbons and molecular data. Organic Geochemistry 137, 103900. of compositionally different petroleum occur in the Norwegian North Sea, one of the world’s major oil-producing regions. The objective of the present contribution was to appraise the source, maturity, in-reservoir mixing and alteration processes in a set of condensate and oil samples covering the main producing areas in the South Viking Graben (SVG). Furthermore, this study focused on unraveling complex mixtures of petroleum and quantifying mixing ratios of hydrocarbons generated from Jurassic source rocks. The present research was based on a multiparameter approach that comprised the molecular composition of light hydrocarbons and heterocyclic and polycyclic aromatic compounds, as well as the δ13C of individual hydrocarbons in oils, condensates and Upper and Middle Jurassic source rock extracts from the SVG. According to the relative contribution of oils from Type-III kerogen-rich source rocks, seven populations (A-G) of mixed petroleum were identified by combining source-related ratios of heterocyclic and non-heterocyclic aromatic hydrocarbons and δ13C values of n-alkanes, pristane (Pr) and phytane (Ph). The heterocyclic and polycyclic aromatic hydrocarbons provided a useful means to discriminate mixed hydrocarbons from source rocks of distinct organic matter type, depositional environment and lithology, in the SVG. The 13C-enrichments of (C10-C14) n-alkanes and Pr and Ph were good indicators of the scale of the terrigenous source contribution and allowed quantitative determination of the proportions of Jurassic source contributions enriched in Type-II and Type-III kerogens in complex petroleum mixtures from the southern part of the SVG.Muscarella, M.E., Boot, C.M., Broeckling, C.D., Lennon, J.T., 2019. Resource heterogeneity structures aquatic bacterial communities. The ISME Journal 13, 2183-2195. are strongly influenced by the bottom-up effects of resource supply. While many species respond to fluctuations in the concentration of resources, microbial diversity may also be affected by the heterogeneity of the resource pool, which often reflects a mixture of distinct molecules. To test this hypothesis, we examined resource–diversity relationships for bacterioplankton in a set of north temperate lakes that varied in their concentration and composition of dissolved organic matter (DOM), which is an important resource for heterotrophic bacteria. Using 16S rRNA transcript sequencing and ecosystem metabolomics, we documented strong relationships between bacterial alpha-diversity (richness and evenness) and the bulk concentration and the number of molecules in the DOM pool. Similarly, bacterial community beta-diversity was related to both DOM concentration and composition. However, in some lakes the relative abundance of resource generalists, which was inversely related to the DOM concentration, may have reduced the effect of DOM heterogeneity on community composition. Together, our results demonstrate the potential metabolic interactions between bacteria and organic matter and suggest that changes in organic matter composition may alter the structure and function of bacterial communities.Mustaj?rvi, L., Nybom, I., Eriksson-Wiklund, A.-K., Eek, E., Cornelissen, G., Sobek, A., 2019. How important is bioturbation for sediment-to-water flux of polycyclic aromatic hydrocarbons in the Baltic Sea? Environmental Toxicology and Chemistry 38, 1803-1810. the present study a recently developed benthic flow‐through chamber was used to assess the sediment‐to‐water flux of polycyclic aromatic hydrocarbons (PAHs) at 4 sites on the Swedish Baltic Sea coast. The flow‐through chamber allows for assessment of the potential effect of bioturbation on the sediment‐to‐water flux of hydrophobic organic contaminants. The sediments at the 4 investigated sites have both varying contamination degree and densities of bioturbating organisms. The flux of individual PAHs measured with the flow‐through chamber ranged between 21 and 510, 11 and 370, 3 and 9700, and 62 and 2300?ng?m–2 d–1 for the 4 sites. To assess the potential effect of bioturbation on the sediment‐to‐water flux, 3 flow‐through and closed chambers were deployed in parallel at each site. The activity of benthic organisms is attenuated or halted because of depletion of oxygen in closed benthic chambers. Therefore, the discrepancy in flux measured with the 2 different chamber designs was used as an indication of a possible effect of bioturbation. A potential effect of bioturbation on the sediment‐to‐water flux by a factor of 3 to 55 was observed at sites with a high density of bioturbating organisms (e.g., Marenzelleria spp., Monoporeia affinis, and Macoma balthica of approximately 860–1200 individuals m–2) but not at the site with much lower organism density (<200 individuals m–2). One site had a high organism density and a low potential effect of bioturbation, which we hypothesize to be caused by the dominance of oligochaetes/polychaetes at this site because worms (Marenzelleria spp.) reach deeper into the sediment than native crustaceans and mollusks.Nadhira, A., Sutton, M., D., Botting, J., P., Muir, L., A., Gueriau, P., King, A., Briggs, D., E. G., Siveter, D., J., Siveter, D., J., 2019. Three-dimensionally preserved soft tissues and calcareous hexactins in a Silurian sponge: implications for early sponge evolution. Royal Society Open Science 6, 190911. (Porifera), as one of the earliest-branching animal phyla, are crucial for understanding early metazoan phylogeny. Recent studies of Lower Palaeozoic sponges have revealed a variety of character states and combinations unknown in extant taxa, challenging our views of early sponge morphology. The Herefordshire Konservat–Lagerst?tte yields an abundant, diverse sponge fauna with three-dimensional preservation of spicules and soft tissue. Carduispongia pedicula gen. et sp. nov. possesses a single layer of hexactine spicules arranged in a regular orthogonal network. This spicule type and arrangement is characteristic of the reticulosans, which have traditionally been interpreted as early members of the extant siliceous Class Hexactinellida. However, the unusual preservation of the spicules of C. pedicula reveals an originally calcareous composition, which would be diagnostic of the living Class Calcarea. The soft tissue architecture closely resembles the complex sylleibid or leuconid structure seen in some modern calcareans and homoscleromorphs. This combination of features strongly supports a skeletal continuum between primitive calcareans and hexactinellid siliceans, indicating that the last common ancestor of Porifera was a spiculate, solitary, vasiform animal with a thin skeletal wall.Nan, H., Kuroda, K., Takahashi, K., Anderson, J.L., 2019. Examining the unique retention behavior of volatile carboxylic acids in gas chromatography using zwitterionic liquid stationary phases. Journal of Chromatography A 1603, 288-296. the first time, gas chromatographic (GC) stationary phases consisting of zwitterionic liquids (ZILs) possessing sulfonate functional groups were utilized for the analysis of volatile carboxylic acids (VCAs). The highly polar and acidic nature of VCAs significantly limits the number of currently available GC stationary phases, which are all largely based on acid-modified polyethylene glycol. In this study, it is shown that this class of ZILs exhibit strong retention of VCAs with excellent peak symmetry. Unique chromatographic selectivity toward VCAs is also demonstrated by tuning the structural features of the ZILs. The solvation properties of the three ZILs as well as a structurally similar conventional monocationic IL were characterized using the Abraham solvation parameter model.Narreddula, V.R., Boase, N.R., Ailuri, R., Marshall, D.L., Poad, B.L.J., Kelso, M.J., Trevitt, A.J., Mitchell, T.W., Blanksby, S.J., 2019. Introduction of a fixed-charge, photolabile derivative for enhanced structural elucidation of fatty acids. Analytical Chemistry 91, 9901-9909. acids are a structurally diverse category of lipids with a myriad of biochemical functions, which includes their role as building blocks of more complex lipids (e.g., glycerophospholipids and triacylglycerols). Increasingly, the analysis of fatty acids is undertaken using liquid chromatography–mass spectrometry (LC–MS), due to its versatility in the detection of lipids across a wide range of concentrations and diversity of molecular structures and masses. Previous work has shown that fixed-charge pyridinium derivatives are effective in enhancing the detection of fatty acids in LC–MS workflows. Herein, we describe the development of two novel pyridinium fixed-charged derivatization reagents that incorporate a photolabile aryl iodide that is selectively activated by laser irradiation inside the mass spectrometer. Photodissociation mass spectra of fatty acids conjugated to 1-(3-(aminomethyl)-4-iodophenyl)pyridin-1-ium (4-I-AMPP+) and 1-(4-(aminomethyl)-3-iodophenyl)pyridin-1-ium (3-I-AMPP+) derivatives reveal structurally diagnostic product ions. These spectra feature radical-directed dissociation of the carbon–carbon bonds within the fatty acyl chain, enabling structural assignments of fatty acids and discrimination of isomers that differ in site(s) of unsaturation, methyl branching or cyclopropanation. These derivatives are shown to be suitable for hyphenated LC–MS methods, and their predictable photodissociation behavior allows de novo identification of unusual fatty acids within a biological context.Neilen, A.D., Carroll, A.R., Hawker, D.W., O'Brien, K.R., Burford, M.A., 2019. Effects of photochemical and microbiological changes in terrestrial dissolved organic matter on its chemical characteristics and phytotoxicity towards cyanobacteria. Science of The Total Environment 695, 133901. studies have shown that under laboratory conditions, dissolved organic matter (DOM) leached from plants can be differentially more phytotoxic to cyanobacteria, compared to green algae. This study examined how DOM source and transformation processes (microbial and photochemical) affect its chemical composition and phytotoxicity towards a cultured species of cyanobacteria (Raphidiopsis raciborskii) using a factorial experimental design. To complement cyanobacterial bioassays, the chemical composition and associated changes in DOM were determined using spectroscopic (nuclear magnetic resonance (NMR) and absorbance) and elemental analyses. Sunlight exposed DOM from leaves of the terrestrial plants, Casuarina cunninghamiana and Eucalyptus tereticornis had the most phytotoxic effect compared to DOM not exposed to sunlight. This phytotoxic DOM was characterised by relatively low nitrogen content, containing highly coloured and relatively high molecular mass constituents. Both mixed effect model and PCA approaches to predict inhibition of photosynthetic yield indicated phytotoxicity could be predicted (P?<?0.001) based upon the following parameters: C: N ratio; gilvin, and lignin-derived phenol content of DOM. Parallel proton-detected 1D and 2D NMR techniques showed that glucose anomers were the major constituents of fresh leachate. With ageing, glucose anomers disappeared and products of microbial transformation appeared, but there was no indication of the appearance of additional phytotoxic compounds. This suggests that reactive oxygen species may be responsible, at least partially, for DOM phytotoxicity. This study provides important new information highlighting the characteristics of DOM that link with phytotoxic effects.Nie, H., Jin, Z., Sun, C., He, Z., Liu, G., Liu, Q., 2019. Organic matter types of the Wufeng and Longmaxi formations in the Sichuan Basin, South China: Implications for the formation of organic matter pores. Energy & Fuels. matter (OM) pores are crucial to porosity in many shale gas reservoirs, but the origin and types of OM pores remain controversial. In this paper, the OM types are systematically identified and analyzed in the Wufeng–Longmaxi Formations from wells JY 1 and JY 2 in the Jiaoshiba gas field, Sichuan Basin. The results indicate that the OM comprises several hydrocarbon-generating organisms, such as various algae (multi- and unicellular algae, colonial algae, acritarch, etc.), graptolite, sponge spicule, and other fossil fragments, as well as several amorphous OM types, such as solid bitumen and strongly compacted algae. The OM pores have inherited the morphology and structure of multicellular algae and are commonly hundreds of nanometers, some of which even reach micrometer size, exhibiting irregular, bubble-like, spherical, and/or elliptical shapes. In the unicellular algae, only a small amount of OM pores are observed, which are isolated and distributed randomly. The OM pores, either irregular or oval, are tens to more than 100 nm, which are developed by the arrangement gap between the unicellular algae, and some are generated inside the unicellular algae by hydrocarbon generation and expulsion. Two types of OM pores developed in solid bitumen, including bitumen–spherulite pores and vesicular pores. The bitumen–spherulite pores are formed by the arrangement of nanoscale bitumen–spherulite with a pore diameter of nanometer scale. The vesicular pores are formed by gas generation and expulsion after oil cracking, and the shape is mostly sporadic, isolated with various sizes ranging from 500 nm to 3 μm. The OM pores in graptolite, sponge spicule, radiolarian, and other fossil fragments are much fewer in quantity and smaller in size. The OM pores may have only developed on the surface of graptolite. The pores are commonly developed in the walls of the fossil fragments and in the solid bitumen by filling in the biological cavity of the sponge spicule. Therefore, it is concluded that the OM types are the pivotal causes of different OM pore types and properties. Multicellular algae are most beneficial to OM pore development, serving as the major producer of OM pores. In the profile of the Wufeng–Longmaxi shales, the vertical variation of OM types and OM pores are diverse in different graptolitic zones. The dominant hydrocarbon-generating organisms in the WF2–LM4 graptolitic zone are multicellular algae and graptolite, followed by a small number of unicellular algae, sponge spicule, radiolarian, and other fossil fragments. The OM pores are mainly developed in multicellular algae and graptolite, with only a few developed in solid bitumen and unicellular algae. In the LM5–LM8 graptolitic zone, however, the hydrocarbon-generating organisms are primarily unicellular algae, with little multicellular algae, graptolite, sponge spicule, and other fossil fragments. The OM pores are mainly developed in unicellular algae and solid bitumen. The new findings provide evidence to support the proposal that multicellular algae are the main hydrocarbon-generating organisms controlling the OM pore development. Moreover, the WF2–LM4 graptolitic zone is the target interval for shale gas exploration and development in the Upper Ordovician and Lower Silurian Formations in the Sichuan Basin and its surrounding areas.Nielsen, C., 2019. Early animal evolution: a morphologist's view. Royal Society Open Science 6, 190638. hypotheses for the early radiation of the metazoans are vividly discussed in recent phylogenomic studies, the ‘Porifera-first’ hypothesis, which places the poriferans as the sister group of all other metazoans, and the ‘Ctenophora-first’ hypothesis, which places the ctenophores as the sister group to all other metazoans. It has been suggested that an analysis of morphological characters (including specific molecules) could throw additional light on the controversy, and this is the aim of this paper. Both hypotheses imply independent evolution of nervous systems in Planulozoa and Ctenophora. The Porifera-first hypothesis implies no homoplasies or losses of major characters. The Ctenophora-first hypothesis shows no important synapomorphies of Porifera, Planulozoa and Placozoa. It implies either independent evolution, in Planulozoa and Ctenophora, of a new digestive system with a gut with extracellular digestion, which enables feeding on larger organisms, or the subsequent loss of this new gut in the Poriferans (and the re-evolution of the collar complex). The major losses implied in the Ctenophora-first theory show absolutely no adaptational advantages. Thus, morphology gives very strong support for the Porifera-first hypothesis.Nikolaev, E.N., Kostyukevich, Y.I., Vladimirov, G., 2019. Chapter 4 - Fundamentals and simulations in FT-ICR-MS, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 89-111. transforms ion cyclotron resonance (FT-ICR) mass spectrometry method introduced by Alan Marshall and Melvin Comisarow in 1974 is based on the measurement of the frequency of ion rotation in the magnetic field—cyclotron frequency. Ion mass to charge (m/q) ratio is inversely proportional to the cyclotron frequency and it is possible to determine the m/q ratio if we know this frequency and the magnetic field strength B. Since introduction of FT-ICR until now this technique demonstrates the highest mass resolution and mass measurement accuracy. The main part of the FT-ICR spectrometer is a measuring cell which is a Penning trap1. In this cell ions get trapped by electric field in the direction along magnetic field vector and by magnetic field in perpendicular direction. By applying RF electric field containing resonant frequency in the plane of ion cyclotron motion we are exciting ion's synchronous cyclotron motion. Rotating ions induce image charges in detection electrodes resulting in the current in electrical circuit of a signal amplifier. In the process of analysis of complex mixtures such as oil and humic acids more than 106 ions can be trapped in the ion trap and their cyclotron frequencies can be measured simultaneously. The ion–ion interactions considerably influence the ion motion resulting in shifting measured frequencies and m/q values. Further improvement of the main FT-ICR characteristics such as mass resolution, mass accuracy and dynamic range could be promoted by deeper understanding of ion motion dynamics in ion traps taking into account ion–ion interactions.Niu, X.-Z., Harir, M., Schmitt-Kopplin, P., Croué, J.-P., 2019. Sunlight-induced phototransformation of transphilic and hydrophobic fractions of Suwannee River dissolved organic matter. Science of The Total Environment 694, 133737. chemical changes of both transphilic (SWR-TPH) and hydrophobic (SWR-HPO) fractions of Suwannee River dissolved organic matter (DOM) were followed by ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). Irradiated SWR-TPH exhibited increase of chemodiversity, loss of some aromatic compounds, and almost no change in terms of average values of m/z, O/C and double bond equivalents (DBE). Irradiated SWR-HPO showed decrease of chemodiversity, average values of m/z, O/C and DBE. Irradiation of SWR-HPO produced oxygenated (O/C?>?0.7) and aliphatic new compounds and removed some aromatics and carboxyl-rich alicyclic molecules (CRAM). Comparatively, CHO-compounds of SWR-TPH were relatively stable with a minor class of aromatic compounds disappeared under sunlight irradiation. Photochemical processing of SWR-HPO generated highly oxygenated new compounds that were readily present in SWR-TPH, implying that sunlight changes the hydrophobicity of DOM and that SWR-HPO is a photochemical precursor for SWR-TPH. This study contributed to the developing knowledge on organic matter phototransformation, particularly the transformation pattern of SWR-TPH that was never described previously; it also demonstrated the role of sunlight in producing SWR-TPH compounds from SWR-HPO and consequently driving the transformation of organic matter.Niyonsaba, E., Wehde, K.E., Yerabolu, R., Kilaz, G., Kentt?maa, H.I., 2019. Determination of the chemical compositions of heavy, medium, and light crude oils by using the Distillation, Precipitation, Fractionation Mass Spectrometry (DPF MS) method. Fuel 255, 115852. have previously demonstrated that the Distillation, Precipitation, Fractionation Mass Spectrometry (DPF MS) method can be used to characterize crude oil at the molecular level by fractionating the crude oil into six different chemical classes and analyzing each class by using an optimized mass spectrometry method. In this study, the chemical compositions of five crude oil samples, including heavy, medium, and light crude oils with different API gravities, were determined using the DPF MS method. The gravimetric weight percentages of the six compound classes within each crude oil sample were also determined. In general, the heavier crude oils contained more asphaltenes and heteroaromatic compounds and less heavy, alkyl aromatic and volatile saturated hydrocarbons than the lighter crude oils. However, the only correlation found for API gravity and the gravimetric weight percentages of the entire compound classes was for the heteroaromatic compound class: crude oils with lower API gravities contained more heteroaromatic compounds. Determination of the total nitrogen content by using a controlled combustion experiment revealed only a poor correlation between the total nitrogen content and API gravity. No obvious correlations were found between API gravity and the amounts of the compounds with different elemental compositions in the whole crude oils. However, consideration of differences in the chemical compositions within the different compound classes revealed trends related to the API gravity. For example, a linear correlation was found for the decrease in the API gravity and the increase in the gravimetric weight percentage of the most abundant nitrogen-containing compounds (with the CcHhN elemental composition) in the heteroaromatic compound class, the class that contains most of these compounds. On the other hand, as the API gravity decreases, the nitrogen content outside the aromatic cores (or in another aromatic core) of the compounds in the heteroaromatic compound class increases. Further, as the API gravity decreases, the extent of unsaturation increases for the compounds in the heteroaromatic compound class. These findings correlate the API gravity of crude oil to the chemical composition of the heteroaromatic compound class. No correlations were found between API gravity and the chemical compositions of the other compound classes or the whole crude oil.Notini, L., Byrne, J.M., Tomaszewski, E.J., Latta, D.E., Zhou, Z., Scherer, M.M., Kappler, A., 2019. Mineral defects enhance bioavailability of goethite toward microbial Fe(III) reduction. Environmental Science & Technology 53, 8883-8891. defects have been shown to facilitate electron transfer between Fe(II) and goethite (α-FeOOH) in abiotic systems. It is unclear, however, whether defects also facilitate microbial goethite reduction in anoxic environments where electron transfer between cells and Fe(III) minerals is the limiting factor. Here, we used stable Fe isotopes to differentiate microbial reduction of goethite synthesized by hydrolysis from reduction of goethite that was further hydrothermally treated to remove surface defects. The goethites were reduced by Geobacter sulfurreducens in the presence of an external electron shuttle, and we used ICP-MS to distinguish Fe(II) produced from the reduction of the two types of goethite. When reduced separately, goethite with more defects has an initial rate of Fe(III) reduction about 2-fold higher than goethite containing fewer defects. However, when reduced together, the initial rate of reduction is 6-fold higher for goethite with more defects. Our results suggest that there is a suppression of the reduction of goethite with fewer defects in favor of the reduction of minerals with more defects. In the environment, minerals are likely to contain defects and our data demonstrates that even small changes at the surface of iron minerals may change their bioavailability and determine which minerals will be reduced.Nutman, A.P., Bennett, V.C., Friend, C.R.L., Kranendonk, M.V., 2019. The Eoarchean legacy of Isua (Greenland) worth preserving for future generations. Earth-Science Reviews 198, 102923. Eoarchean (>3600?Ma, or millions of years ago) folded and metamorphosed Isua supracrustal belt and the adjacent orthogneiss exposures of Greenland contain rare low deformation lenses that display some uniquely-preserved components of Earth's oldest rock record. These include world's oldest (but contested) stromatolites in dolomitic carbonates, conglomerates, pillow basalts demonstrating submarine eruption, slivers of upper mantle rocks, formation of earliest continental crust by multistage tonalite + diorite emplacement followed by intracrustal granite production. All these diverse occurrences are keys to establish early Earth's processes at the start of the geological record. Although some of these features are preserved at several localities, other critical ones are exposed on only a few m2 of rock at single localities or are of historical significance. None of these sites are currently protected, and there is a reliance on responsible sampling to keep them intact for future generations. Given the high interest in the Archean Eon, combined with the increased ease of fieldwork in remote localities, many significant ‘Deep Time’ localities in not only Greenland but worldwide are in danger of eradication. Here, five key Isua area geological sites are presented, with an explanation of their significance and worthiness for initially reliance on already-collected samples, but hopefully ultimately government protection. This highlights an increasing problem of destruction of in situ evidence of Earth's unique early geological heritage and the need for collaboration in protecting and archiving of these key scientific resources.Omae, K., Fukuyama, Y., Yasuda, H., Mise, K., Yoshida, T., Sako, Y., 2019. Diversity and distribution of thermophilic hydrogenogenic carboxydotrophs revealed by microbial community analysis in sediments from multiple hydrothermal environments in Japan. Archives of Microbiology 201, 969-982. hydrothermal environments, carbon monoxide (CO) utilisation by thermophilic hydrogenogenic carboxydotrophs may play an important role in microbial ecology by reducing toxic levels of CO and providing H2 for fuelling microbial communities. We evaluated thermophilic hydrogenogenic carboxydotrophs by microbial community analysis. First, we analysed the correlation between carbon monoxide dehydrogenase (CODH)–energy-converting hydrogenase (ECH) gene cluster and taxonomic affiliation by surveying an increasing genomic database. We identified 71 genome-encoded CODH–ECH gene clusters, including 46 whose owners were not reported as hydrogenogenic carboxydotrophs. We identified 13 phylotypes showing?>?98.7% identity with these taxa as potential hydrogenogenic carboxydotrophs in hot springs. Of these, Firmicutes phylotypes such as Parageobacillus, Carboxydocella, Caldanaerobacter, and Carboxydothermus were found in different environmental conditions and distinct microbial communities. The relative abundance of the potential thermophilic hydrogenogenic carboxydotrophs was low. Most of them did not show any symbiotic networks with other microbes, implying that their metabolic activities might be low.Ovalles, C., 2019. Subsurface Upgrading of Heavy Crude Oils and Bitumen. CRC Press. 304 pp. crude oils and bitumen represent more than 50% of all hydrocarbons available on the planet. These feedstocks have a low amount of distillable material and high level of contaminants that make their production, transportation, and refining difficult and costly by conventional technologies. Subsurface Upgrading of Heavy Crude Oils and Bitumen is of interest to the petroleum industry mainly because of the advantages compared to aboveground counterparts. The author presents an in-depth account and a critical review of the progress of industry and academia in underground or In-Situ upgrading of heavy, extra-heavy oils and bitumen, as reported in the patent and open literature. This work is aimed to be a standalone monograph, so three chapters are dedicated to the composition of petroleum and fundamentals of crude oil production and refining.Key Features:Offers a multidisciplinary scope that will appeal to chemists, geologists, biologists, chemical engineers, and petroleum engineers Presents the advantages and disadvantages of the technologies considered Discusses economic and environmental considerations for all the routes evaluated and offers perspectives from experts in the field working with highlighted technologiesOvalles, C., Rogel, E., Hurt, M., Duma, V., Morazan, H., Hench, K., Moir, M.E., 2019. Nitrogen speciation: Application to reactivity of feeds to hydroprocessing and catalyst deactivation, in: Rahimi, P., Ovalles, C., Zhang, Y., Adams, J.J. (Eds.), Chemistry Solutions to Challenges in the Petroleum Industry. American Chemical Society, Washington DC, pp. 261-280. is one of the hardest heteroatoms to remove from petroleum and its fractions. For this reason, nitrogen speciation has useful applications in feed reactivity to hydroprocessing and understanding catalyst deactivation. In the first part of this chapter, the objective is to characterize the nitrogen species present in the asphaltenes of vacuum residues to gain an understanding of the processability of these feedstocks to hydroprocessing. The results by X-ray photoelectron spectroscopy and mass spectrometry (MS) showed that the hydrodenitrogenation rate constant is inversely proportional to the percentages of pyrrolic nitrogen in the asphaltenes and whole residue. The correlations were relatively weak (0.42 and 0.71, respectively), which was attributed to differences in the degree of aromatic condensation, size, and alkyl-substitutions on the N-aromatic rings of the feeds evaluated. The second part of the chapter is focused on the deep solvent extraction of a spent hydrocracking catalyst to characterize the species adsorbed on the surface, with the final goal of increasing our understanding of the deactivation mechanism. The solvent extractions were carried out by conventional Soxhlet technique using dichloromethane under 1 atm of nitrogen for ~24 h. Then, the Soxhlet-extracted solid was solvent-extracted again using an accelerated solvent extraction apparatus and CH2Cl2 at 120 °C and 1500 psi of nitrogen for 1 h. The organic extracts were characterized by elemental analysis, asphaltene solubility profile, and electron spray ionization and atmospheric pressure photoionization MS. Based on the literature and the MS results, a general mechanism for the conversion of N-compounds was proposed. Basic N-species with double bond equivalence values less than 10 can be preferentially adsorbed onto the strong acid sites of the catalyst for an extended amount of time, which, along with the heavy polynuclear aromatics, leads to coke formation and catalyst deactivation.Owusu, E.B., Tsegab, H., Sum, C.W., Padmanabhan, E., 2019. Organic geochemical analyses of the Belata black shale, Peninsular Malaysia; implications on their shale gas potential. Journal of Natural Gas Science and Engineering 69, 102945. study discusses the shale gas potential of Carboniferous Belata black shales within Peninsular Malaysia. Organic geochemical analyses of the shales show a good hydrocarbon source with total organic carbon (TOC) content ranging from 1.90 wt. % to 4.05?wt. %. TOC versus S2 plot shows that the derived dominant kerogen in the Belata black shale samples is of Type IV; gas prone. Recorded low hydrogen index value ranges between 0 and 0.38 (mgHC/gTOC) and the vitrinite reflectance analyses revealed that the shales are generally overmatured with a mean Ro of 3.85 as supported by the burial history models. Although these shales are located away from the granitic intrusion, the regional metamorphism caused by the regional orogenesis and subduction of the Peninsular has affected and could be the cause of the shale over maturity. The findings suggest a minimal potential for working petroleum system in onshore Peninsular Malaysia within the studied stratigraphic intervals.Panitz, C., Fr?sler, J., Wingender, J., Flemming, H.-C., Rettberg, P., 2019. Tolerances of Deinococcus geothermalis biofilms and planktonic cells exposed to space and simulated martian conditions in low Earth orbit for almost two years. Astrobiology 19, 979-994. biofilms represent one of the oldest known confirmations of life on the Earth. The success of microbes in biofilms results from properties that are inherent in the biofilm, including enhanced interaction, protection, and biodiversity. Given the diversity of microbes that live in biofilms in harsh environments on the Earth, it is logical to hypothesize that, if microbes inhabit other bodies in the Universe, there are also biofilms on those bodies. The Biofilm Organisms Surfing Space experiment was conducted as part of the EXPOSE-R2 mission on the International Space Station. The experiment was an international collaboration designed to perform a comparative study regarding the survival of biofilms versus planktonic cells of various microorganisms, exposed to space and Mars-like conditions. The objective was to determine whether there are lifestyle-dependent differences to cope with the unique mixture of stress factors, including desiccation, temperature oscillations, vacuum, or a Mars-like gas atmosphere and pressure in combination with extraterrestrial or Mars-like ultraviolet (UV) radiation residing during the long-term space mission. In this study, the outcome of the flight and mission ground reference analysis of Deinococcus geothermalis is presented. Cultural tests demonstrated that D. geothermalis remained viable in the desiccated state, being able to survive space and Mars-like conditions and tolerating high extraterrestrial UV radiation for more than 2 years. Culturability decreased, but was better preserved, in the biofilm consortium than in planktonic cells. These results are correlated to differences in genomic integrity after exposure, as visualized by random amplified polymorphic DNA–polymerase chain reaction. Interestingly, cultivation-independent viability markers such as membrane integrity, ATP content, and intracellular esterase activity remained nearly unaffected, indicating that subpopulations of the cells had survived in a viable but nonculturable state. These findings support the hypothesis of long-term survival of microorganisms under the harsh environmental conditions in space and on Mars to a higher degree if exposed as biofilm.Parinos, C., Hatzianestis, I., Chourdaki, S., Plakidi, E., Gogou, A., 2019. Imprint and short-term fate of the Agia Zoni II tanker oil spill on the marine ecosystem of Saronikos Gulf. Science of The Total Environment 693, 133568. this study we investigate the spatial and temporal imprint of the September 2017 Agia Zoni II tanker heavy fuel oil spill on the marine ecosystem of Saronikos Gulf (Greece). Based on the chemical fingerprinting approach, by means of gas chromatography - flame ionization detector, gas chromatography–mass spectrometry and the use of various diagnostic ratios, we characterize changes in the composition of the spilled oil at various sampling sites and evaluate major mechanisms affecting its fate i.e. dissolution/dispersion, evaporation, biodegradation, photo-oxidation and sedimentation during the first six months from the spill. Overall, the main effects of the incident were confined to the coastal zone during the first three months after the spill, where an extended petroleum imprint was recorded in many cases, with the determined concentrations of the total petroleum hydrocarbons and polycyclic aromatic hydrocarbons falling within the highest range of concentrations previously reported for similar oil spill incidents worldwide. In the first three months following the spill the oil was affected by a combination of volatilization, rapid biodegradation and photodegradation, the later playing a role in its early days weathering. Concerning sediments, an imprint related to the incident was recorded in a few cases, being, however, mild in respect to the high chronic petroleum-associated anthropogenic background of the impacted area.Park, J., Dall’Osto, M., Park, K., Kim, J.-H., Park, J., Park, K.-T., Hwang, C.Y., Jang, G.I., Gim, Y., Kang, S., Park, S., Jin, Y.K., Yum, S.S., Simó, R., Yoon, Y.J., 2019. Arctic primary aerosol production strongly influenced by riverine organic matter. Environmental Science & Technology 53, 8621-8630. sources of primary and secondary aerosols in the Arctic are still poorly known. A number of surface seawater samples—with varying degrees of Arctic riverine and sea ice influences—were used in a sea spray generation chamber to test them for their potential to produce sea spray aerosols (SSA) and cloud condensation nuclei (CCN). Our interdisciplinary data showed that both sea salt and organic matter (OM) significantly influenced the SSA production. The number concentration of SSA in the coastal samples was negatively correlated with salinity and positively correlated with a number of OM tracers, including dissolved and chromophoric organic carbon (DOC, CDOM), marine microgels and chlorophyll a (Chl-a) but not for viral and bacterial abundances; indicating that OM of riverine origin enhances primary aerosol production. When all samples were considered, transparent exopolymer particles (TEP) were found to be the best indicator correlating positively with the ratio number concentration of SSA/salinity. CCN efficiency was not observed to differ between the SSA from the various samples, despite differences in organic characteristics. It is suggested that the large amount of freshwater from river runoff have a substantial impact on primary aerosols production mechanisms, possibly affecting the cloud radiative forcing.Pascal, R., Chen, I.A., 2019. From soup to peptides. Nature Chemistry 11, 763-764. are biosynthesized from α-amino acids using hefty biological machinery, but the origin of this process on the early Earth is unclear. Now, a bottom-up approach for forming peptides, taking place under mild, prebiotically-plausible conditions, has been developed. This strategy uses α-aminonitrile precursors, bypassing α-amino acids entirely.In 1953, the Miller–Urey experiment demonstrated the formation of α-amino acids in a mixture of water and gases under simulated lightning1, kicking off the field of prebiotic chemistry. The primary role of α-amino acids is as subunits of proteins, and therefore a prebiotically plausible method to convert monomers to peptides has been sought over the intervening decades. Chemical clues found in the Miller–Urey experiment implicated the well-known Strecker reaction — the formation of energy-rich α-aminonitriles from aldehyde, ammonia and cyanide, which can be subsequently hydrolysed to amino acids2. Direct polymerization of α-aminonitriles has long been an attractive hypothesis for the origin of peptides3, given the seemingly roundabout alternative of hydrolysis to amino acids, followed by reactivation for polymerization. However, despite several attempts by different researchers (including one of us4), experimental conversion of α-aminonitriles to peptides was not found, and attention shifted toward activation of amino acids using N-carboxyanhydrides (NCAs) and related compounds. Yet NCA polymerization also presents significant challenges for prebiotic chemistry, such as controlling side reactions, and the problem of peptide synthesis remained without a conclusive solution.Now, in a recent report in Nature, Matthew Powner and co-workers5 reboot the α-aminonitrile hypothesis to produce quantitative yields of peptides in a gentle aqueous procedure. Remarkably, the reaction is successful with all 20 proteinogenic side chains without protecting groups. A peptide chain is initiated by quantitative acylation of an α-aminonitrile (Fig. 1a), which activates the nitrile for an iterative, one-pot, three-step ligation cycle (Fig. 1b, c): first, thiolysis of the nitrile to produce the corresponding thioamide; second, hydrolysis of the thioamide to the thioacid; and third, oxidation of the thioacid and reaction with an incoming α-aminonitrile monomer, leaving a nitrile available to undergo another ligation cycle. A conceptual difference between this scheme and NCA chemistry is the fact that the elongating peptides, not the monomers, are electrophilically activated. Important features of each of these steps contribute to the high efficiency of the overall process.In the first step of the cycle, a simple reagent (H2S) converts the α-amidonitrile to the α-amidothioamide. It is worth noting that the initial acylation is crucial, as the corresponding reaction involving non-acylated aminonitriles is much less efficient. Presumably, the electron-withdrawing character of the acetamido group strongly facilitates the nucleophilic reaction of sulfide with the nitrile.A technical breakthrough occurs in the second step of the cycle, hydrolysis of the thioamide. In stark contrast to α-aminothioamides, the hydrolysis of which yields a mixture of products, hydrolysis of the α-acetamidothioamide selectively produces a C-terminal thioacid. This surprising facility, which highlights the importance of the N-terminal modification, realizes a decades-old suggestion of Liu and Orgel6. The thioacid can subsequently be converted into an acyl transfer agent by oxidation with ferricyanide or electrophilic activation.Last but not least, the third step, elongation through nucleophilic attack by α-aminonitriles, exploits the low pKa (about 5.3) of protonated aminonitriles to achieve selectivity. At an intermediate pH (~5–9), the aminonitriles outcompete stronger (more basic) amine nucleophiles that might otherwise terminate the polymer. The team further show that a single elongation step could add more than one monomer if the nucleophile itself were a peptidonitrile. These features enable the creation of oligomers of significant length.What is behind the success of this peptide-forming chemistry using α-aminonitriles? The nitrile group combines thermodynamic instability and kinetic stability, creating a system held ‘far from equilibrium by kinetic barriers’ that might undergird the self-organization of life7. However, the sluggish kinetics of α-aminonitrile reactions (for example, hydrolysis) also constitutes an obstacle, such that use of efficient reagents (H2S) or catalysts is paramount. High yields along each step of this pathway combined to produce excellent overall yield, and wise avoidance of the amino acid, a thermodynamic trap, meant that relatively gentle conditions were adequate for activation.Any study of prebiotic chemistry must contend with questions of yield and prebiotic plausibility. These reactions proceed with impressively high yield (nearly quantitative in most cases) and high selectivity. In terms of prebiotic plausibility, the reactants (α-aminonitriles, H2S, ferricyanide) would be considered reasonable by most workers in the field. A common issue is the need for interventions by the chemist, who purifies intermediates and adds reagents at the proper times. In this case, the ligation cycle occurred efficiently in a one-pot reaction without purification of intermediates. However, H2S and ferricyanide must be added sequentially during the cycle to avoid mutual reaction. Understanding how such dynamic chemical and energetic inputs might drive prebiotic chemistry remains an important area of consideration for the field as a whole.This highly efficient peptide chemistry raises the possibility of addressing several interesting features. Chirality, and specifically the emergence of a homochiral system, is a central puzzle for the origin of peptides. Electrophilic activation of the C-terminus typically results in epimerization of the α-carbon through chirally unstable intermediates. In contrast, Powner and colleagues show that stereochemistry of the electrophile is conserved during the gentle ligation cycle. Thus, the chirality of the peptides is inherited from the α-aminonitrile substrates. A tantalizing question is whether the chirality of the electrophile favours a specific chirality of the nucleophile. At moderate pH values, α-aminonitriles exist at equilibrium with their precursors (Fig. 1d), a process that causes racemization. If peptide elongation is stereo-selective and slow, relative to the α-aminonitrile equilibrium, racemization of the unreacted α-aminonitrile pool could potentially lead to runaway enantiomeric excess8. Mechanistic questions are also of interest, such as why hydrolysis of the α-amidothioamide to the corresponding thioacid is so efficient. General features of this pathway, including surprising tolerance to side chains, one-pot aqueous conditions and high yields may motivate synthetic peptide chemists to explore these reactions further.An important lesson from this and other seminal work is that, although the fundamental strategies may be preserved9, details of biochemistry may mislead us about prebiotic chemistry. Much like the metaphor of ‘my grandfather’s axe’10, the ancient origin of peptides may not resemble the modern biochemistry of protein translation in seemingly major ways. Amino acids, now used as substrates in protein translation, may be a red herring, much like the biosynthesis of ribonucleotides through ribose11. Nevertheless, bottom-up pathways must eventually reconnect to their biological descendants. Now, given the starting point described by Powner and co-workers, discovering such connections will surely create a fascinating scientific journey toward synthesizing life.References1. Miller, S. L. Science 117, 528–529 (1953).2. Miller, S. L. J. Am. Chem. Soc. 77, 2351–2361 (1955).3. Hanafusa, H. & Akabori, S. Bull. Chem. Soc. Jpn. 32, 626–630 (1959).4. Pascal, R. & Rousset, A. in Frontiers of Life (eds Tr?n Thanh V?n, J., Tr?n Thanh V?n, K., Mounolou, J. C., Schneider, J. & Mc Kay, C.) 467–468 (Editions Frontières, Gif-sur-Yvette, 1992).5. Canavelli, P., Islam, S. & Powner, M. W. Nature 571, 546–549 (2019).6. Liu, R. & Orgel, L. E. Nature 389, 52–54 (1997).7. Eschenmoser, A. Orig. Life Evol. Biosph. 24, 389–423 (1994).8. Blackmond, D. Cold Spring Harb. Perspect. Biol. 11, a032540 (2019).9. Sutherland, J. D. Nat. Rev. Chem. 1, 0012 (2017).10 Hud, N., Cafferty, B. J., Krishnamurthy, R. & Williams, L. D. Chem. Biol. 20, 466–474 (2013).11. Szostak, J. W. Nature 459, 171–172 (2009).Paterson, J.S., Smith, R.J., McKerral, J.C., Dann, L.M., Launer, E., Goonan, P., Kleinig, T., Fuhrman, J.A., Mitchell, J.G., 2019. A hydrocarbon-contaminated aquifer reveals a Piggyback-the-Persistent viral strategy. FEMS Microbiology Ecology 95. environments hold the largest reservoir of microbes in the biosphere. They play essential roles in transforming nutrients, degrading contaminants and recycling organic matter. Here, we propose a previously unrecognised fundamental microbial process that influences aquifer bioremediation dynamics and that applies to all microbial communities. In contrast to previous models, our proposed Piggyback-the-Persistent (PtP) mechanism occurs when viruses become more dominated by those exhibiting temperate rather than lytic lifestyles driven by persistent chemicals (in our case chlorinated-hydrocarbon pollutants) that provide long-term carbon sources and that refocus the aquifer carbon cycle, thus altering the microbial community. In this ultra-oligotrophic system, the virus:microbial ratio (VMR) ranges from below the detection limit of 0.0001 to 0.6, well below the common aquatic range of 3–10. Shortest-average-path network analysis revealed VMR and trichlorethene (TCE) as nodes through which ecosystem information and biomass most efficiently pass. Novel network rearrangement revealed a hierarchy of Kill-the-Winner (KtW), Piggyback-the-Winner (PtW) and PtP nodes. We propose that KtW, PtW and PtP occur simultaneously as competing strategies, with their relative importance depending on conditions at a particular time and location with unusual nutrient sources, such as TCE, appearing to contribute to a shift in this balance between viral mechanisms.Pearson, A., Hurley, S.J., Elling, F.J., Wilkes, E.B., 2019. CO2-dependent carbon isotope fractionation in Archaea, Part I: Modeling the 3HP/4HB pathway. Geochimica et Cosmochimica Acta 261, 368-382. 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) pathway of carbon fixation is found in thermophilic Crenarchaeota of the order Sulfolobales and in aerobic, ammonia-oxidizing Thaumarchaeota. Unlike all other known autotrophic carbon metabolisms, this pathway exclusively uses HCO3? rather than CO2 as the substrate for carbon fixation. Biomass produced by the 3HB/4HP pathway is relatively 13C-enriched compared to biomass fixed by other autotrophic pathways, with total biosynthetic isotope effects (εAr) of ca. 3‰ in the Sulfolobales and ca. 20‰ in the Thaumarchaeota. Explanations for the difference between these values usually invoke the dual effects of thermophily and growth at low pH (low [HCO3-]) for the former group vs. mesophily and growth at pH?>?7 (high [HCO3-]) for the latter group. Here we examine the model taxa Metallosphaera sedula and Nitrosopumilus maritimus using an isotope flux-balance model to argue that the primary cause of different εAr values more likely is the presence of carbonic anhydrase in M. sedula and its corresponding absence in N. maritimus. The results suggest that the pool of HCO3- inside N. maritimus is out of isotopic equilibrium with CO2 and that the organism imports <?10% HCO3- from the extracellular environment. If correct and generalizable, the aerobic, ammonia-oxidizing marine Thaumarchaeota are dependent on passive CO2 uptake and a slow rate of intracellular conversion to HCO3-. Values of εAr should therefore vary in response to growth rate (μ) and CO2 availability, analogous to eukaryotic algae, but in the opposite direction: εAr becomes smaller as [CO2(aq)] increases and/or μ decreases. Such an idea represents a testable hypothesis, both in the laboratory and in natural systems. Sensitivity to μ and CO2 implies that measurements of εAr may hold promise as a pCO2 paleobarometer.Pedreira-Segade, U., Hao, J., Montagnac, G., Cardon, H., Daniel, I., 2019. Spontaneous polymerization of glycine under hydrothermal conditions. ACS Earth and Space Chemistry 3, 1669-1677. abiotic polymerization of nucleotides and amino acids is a prerequisite for the emergence of life. It has been proposed that hydrothermal conditions might favor the polymerization of amino acids. In the present study, we analyzed by in situ Raman spectroscopy in a diamond anvil cell the fate of the simplest and most abundant amino acid, glycine, under hydrothermal conditions at 200 °C and pressures ranging between 50 and 3500 MPa. We also tested the effect of magnetite on the reactivity of glycine. The polymerization of glycine is highly favored under pressure and in the presence of magnetite. Linear dimers are more abundant than the cyclic ones up to a threshold pressure of 500 MPa. Above 800 MPa, amino acids stop reacting and the system is “frozen”. Our findings suggest that pressure and mineral–water interface strongly favor the formation of linear peptides. The optimum conditions for polymerization obtained in the present study suggest that the prebiotic chemical evolution of amino acids was not restricted to hydrothermal vents at oceanic ridges but might also occur much deeper in the first 15–30 km of the crust, widely expanding the prebiotic reactive zone.Peng, L., Zhang, C., Ma, H., Pan, H., 2019. Estimating irreducible water saturation and permeability of sandstones from nuclear magnetic resonance measurements by fractal analysis. Marine and Petroleum Geology 110, 565-574. the relationships between the pore structure and bulk properties such as irreducible water saturation (Swir) and permeability (k) of rocks is a crucial problem in geoscience. In this study, two types of fractal dimension were determined from nuclear magnetic resonance (NMR) T2 relaxation time distribution and models for estimating Swir and k using fractal theory were proposed. In view of the data of sandstone samples from upper Paleozoic formation in China, we found a good agreement between the predicted Swir values based on fractal analysis and the experimental measurements, and the estimated k values based on the proposed model are within one order of magnitude of measured k. Additionally, another four frequently used k estimation models were compared with our proposed model, and the result support that the proposed approach has great potential in investigating k while certain limitation still exists. This procedure was applied on another set of sandstone samples collected from a different location, and the predicted permeability values are reliable. Our study suggests that the proposed Swir estimation model using NMR T2 data and fractal dimensions provides useful insights into characterizing the pore space properties of sedimentary rocks. Our work demonstrates that we can use NMR data to infer Swir directly, and the estimated Swir value can be well integrated in permeability prediction model, which improves the applications of NMR in characterizing the properties related to rock pores.Pennisi, E., 2019. Tentacled microbe hints at how simple cells became complex. Science 365, 631. 12 years of dogged effort, a team in Japan has grown an organism from seafloor mud that it says could explain how simple microbes evolved into eukaryotes—organisms with complex, nucleated cells, including animals, plants, and ourselves. The microbe sports unusual branched appendages, leading the group to suggest that an ancestral version long ago used similar tentacles to corral and envelop the symbiotic bacteria that gave rise to mitochondria, the energy-producing organelles characteristic of eukaryotic cells.“This is the work that many people in the field have been waiting for,” says Thijs Ettema, an evolutionary microbiologist at Wageningen University in the Netherlands. The finding has not yet been published in a peer-reviewed journal, but on Twitter, other scientists have described a preprint on the work as the “paper of the year” and the “moon landing for microbial ecology.”The tree of life has three major branches: eukaryotes, plus bacteria and archaea, which both lack nuclei, mitochondria, and internal membranes. Biologists have long debated the origins of those branches, with some proposing that they sprang from a single common ancestor and others saying eukaryotes branched off archaea, making those microbes our direct ancestors.That “two domain idea” was bolstered when Ettema and colleagues sieved fragments of DNA from seafloor mud that revealed a new class of microbes with some genetic features resembling eukaryotes: the so-called Asgard archaea. But to explore that possible link, researchers needed to isolate and grow them—a tall order, as the archaea live in oxygen-deprived environments deep in the seabed and grow very slowly.Hiroyuki Imachi and Ken Takai, microbiologists at the Japan Agency for Marine-Earth Science and Technology in Yokosuka, and their colleagues persisted. For 2000 days, they kept mud from a core sample extracted from a depth of 2500 meters off the coast of Japan in bioreactors fed continuously with methane, a gas common in deep-sea mud. The team then incubated samples of the mud in glass tubes supplied with a wide variety of nutrients and other substances. A year later, they detected microbes in one of the tubes.DNA analyses indicated the tube held an Asgard archaeon. It took about 20 days for its numbers to double—bacteria commonly double in less than an hour—but eventually, the team grew enough of the organism to study it. “It was really a gargantuan task,” says David Baum, an evolutionary biologist at the University of Wisconsin in Madison.The Japanese researchers, who declined to comment while a journal reviews their manuscript, named the microbe Prometheoarchaeum syntrophicum, after the Greek titan Prometheus, who created humans out of mud. The researchers confirmed last week in their preprint, posted on bioRxiv, that some of the microbe's genes look like those found in eukaryotes. It's as if the microbe “were primed to become eukaryotes,” Ettema says.Electron microscope images revealed another suggestive feature: multiple branched appendages. The team hypothesizes that early in the history of life, the protrusions of an ancient member of the same archaeon family encircled the bacterial ancestor of mitochondria—an organism that could convert oxygen to energy. The researchers propose that as the concentration of oxygen increased on early Earth, the oxygen-using partners gave a Prometheoarchaeum-like host an advantage, and eukaryotic life took off.“This is exactly what we predicted,” Baum says. In 2014, he and a colleague published this idea, called the “inside out” theory. Previously, most researchers had assumed that the mitochondria were pulled into their archaeal hosts—the “outside in” theory, with the cell's internal membrane-bound compartments evolving from cell membrane folded inward. Baum proposed instead that appendages on the original host cell encased the protomitochondria, then merged to form the body of the early eukaryotic cell. Prometheoarchaeum's tentacles support the idea, he says.Ettema cautions that the archaeal ancestor to eukaryotic cells may not have looked and acted just like Prometheoarchaeum. Moreover, DNA studies indicate that other archaea are more closely related to eukaryotes than this one. He expects, however, that the team's work will help him and others grow related archaea: “I'm sure it will not take 12 years to get the next Asgard into culture.”As impressive as the work is, the culturing of this Asgard—or others—doesn't answer whether there are two kingdoms or three, says Patrick Forterre, a microbiologist at the Pasteur Institute in Paris. Based on his group's extensive DNA studies of the microbes, Forterre argues that Asgard archaea are not close kin to eukaryotes. He maintains that its eukaryotelike genes were borrowed from the real eukaryotic ancestors, which evolved from a common ancestor to both archaea and eukaryotes. “They don't look like [an] ‘intermediate’ cell between prokaryote and eukaryote but 100% as a classical (but very small) archaeon,” he wrote in an email.But even if Asgard archaea don't prove to be the ancestor of eukaryotes, the new work “reveals all kinds of exciting biology,” says Willem van Schaik, a microbiologist at the University of Birmingham in the United Kingdom. “It feels like this will go into microbial textbooks immediately.”Pereira, I., de Aguiar, D.V.A., Vasconselos, G., Vaz, B.G., 2019. Chapter 16 - Fourier transform mass spectrometry applied to petroleomics, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 509-528. Fourier transform mass spectrometry (FTMS) revolutionized MS analysis by providing the possibility of determining the elemental compositions of thousands of chemical components simultaneously from accurate mass measurements. Fourier transform ion cyclotron (FT-ICR) and Orbitrap are remarkable mass analyzers which are part of the FTMS group. Combining FT-ICR and Orbitrap with a plenty of ionization methods, such as electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI), atmospheric pressure photoionization (APPI), and other ionization sources, enables a myriad of polar and non-polar compounds present in ultra-complex mixtures to be routinely identified and assigned with unmatched mass resolution and accuracy. Crude oil is an ultra-complex mixture and has been classified as the most complex organic mixture in the world regarding a number of chemical constituents in a single sample. The field of science that studies crude oil at the molecular level is called petroleomics, and its progress has been intimately tied to advances in MS ionization sources and instrumentation. Here, we describe the state of the art of several ionization methods that are used with FTMS for crude oil analysis as well as the latest applications of FT-ICR and Orbitrap analyzers in petroleomics.Pérez, N., Velazco-Vargas, J.L., Martin, O., Cardenas, R., Martínez-Frías, J., 2019. The mass impacts on chemosynthetic primary producers: potential implications on anammox communities and their consequences. International Journal of Astrobiology 18, 440-444. potential of a mass asteroid impact on Earth to disturb the chemosynthetic communities at global scale is discussed. Special emphasis is made on the potential influence on anammox communities and their implications in the nitrogen biogeochemical cycle. According to our preliminary estimates, anammox communities could be seriously affected as a consequence of global cooling and the large process of acidification usually associated with the occurrence of this kind of event. The scale of affectations could vary in a scenario like the Chicxulub as a function of the amount of soot, depth of the water column and the deposition rate for sulphates assumed in each case. The most severe affectations take place where the amount of soot and sulphates produced during the event is higher and the scale of time of settlements for sulphates is short, of the order of 10 h. In this extreme case, the activity of anammox is considerably reduced, a condition that may persist for several years after the impact. Furthermore, the impact of high levels of other chemical compounds like sulphates and nitrates associated with the occurrence of this kind of event are also discussed.Pi, X., Zhao, S., Wang, W., Liu, D., Xu, C., Han, G., Kuang, T., Sui, S.-F., Shen, J.-R., 2019. The pigment-protein network of a diatom photosystem II–light-harvesting antenna supercomplex. Science 365, eaax4406.: Diatoms play important roles in global primary productivity and biogeochemical cycling of carbon, in part owing to the ability of their photosynthetic apparatus to adapt to rapidly changing light intensity. We report a cryo–electron microscopy structure of the photosystem II (PSII)–fucoxanthin (Fx) chlorophyll (Chl) a/c binding protein (FCPII) supercomplex from the centric diatom Chaetoceros gracilis. The supercomplex comprises two protomers, each with two tetrameric and three monomeric FCPIIs around a PSII core that contains five extrinsic oxygen-evolving proteins at the lumenal surface. The structure reveals the arrangement of a huge pigment network that contributes to efficient light energy harvesting, transfer, and dissipation processes in the diatoms.Editor's summary: A light-harvesting array in diatoms. Photosynthetic organisms use huge arrays of pigments to draw light energy into the core of photosystem II. The arrangement of these pigments influences how much energy reaches the reaction center. Pi et al. determined the structure of photosystem II from a diatom in complex with an antenna of fucoxanthin–chlorophyll a/c binding proteins (FCPs) (see the Perspective by Büchel). The specialized pigments in this complex allow microalgae to harvest light within a wide range of the visible spectrum. The FCPs are arranged in a pattern analogous to light-harvesting complexes in plants.Structured Abstractintroduction. Photosystem II (PSII) is a pigment-protein complex and catalyzes light-induced water splitting in photosynthesis, converting light energy from the Sun into chemical energy and providing molecular oxygen to the atmosphere. To make full use of light energy, photosynthetic organisms have developed light-harvesting complexes (LHCs) to gather light energy and transfer it to photosynthetic reaction centers. Many LHCII subunits are associated with a core PSII, forming PSII-LHCII supercomplexes. LHC proteins vary across lineages of photosynthetic organisms and enable groups of organisms to cope with different light environments. In addition to light-harvesting, LHCs also have a role in dissipation of excess energy under strong light illumination so as to avoid damage to photosystems caused by intense light.Rationale: LHCIIs of green-lineage photosynthetic organisms bind chlorophyll (Chl) a/b as their main pigments, whereas some organisms of the red lineage bind Chl a/c as their main pigments. Diatoms are one of the main groups in the red lineage and contribute ~20% of all primary productivity on Earth. The light-harvesting antennas of diatoms are known as Chl a/c and fucoxanthin (Fx) binding proteins, or FCPs, and enable diatoms to efficiently use blue-green light available under water. The distinct pigment composition and organization of the PSII-FCPII supercomplex confers on diatoms the capacity to efficiently dissipate excess energy when necessary. A structure of PSII-FCPII of diatoms greatly expands our understanding of the energy harvesting and dissipation mechanisms in a dominant photosynthetic organism.Results: We used single-particle cryo–electron microscopy analysis to elucidate a structure of the PSII-FCPII supercomplex from the diatom Chaetoceros gracilis at a resolution of 3.0 ?. The supercomplex contains two protomers with 24 subunits in the PSII core and 11 subunits in FCPII, giving rise to a total of 70 subunits with an overall molecular weight of 1.4 MDa. The PSII core is largely similar to that of cyanobacteria and higher plants, but we found five extrinsic proteins that play a role in the oxygen-evolving reaction. Two additional transmembrane subunits located at the periphery of the PSII core help to connect the PSII core with the FCPII subunits. The major FCPII is organized into two tetramers: one is tightly associated whereas the other is moderately associated with the PSII core. In addition, three FCP monomers are associated with each PSII core; among them, two connect the moderately associated FCPII tetramer with the PSII core whereas one is associated at the periphery of the moderately associated FCPII tetramer. These arrangements differ from those found in the PSII-LHCII supercomplexes of the green-lineage organisms, and the locations of the tightly and moderately associated FCP tetramers are opposite to those of the strongly and moderately associated trimers found in PSII-LHCII. On the other hand, locations of the two monomeric FCPs (FCP-D and FCP-E) resemble those of CP24 and CP29 in higher-plant PSII-LHCIIs in that both of them connect the moderately associated FCP tetramer or LHCII trimer with the PSII core.Conclusion: Our PSII-FCPII structure reveals the arrangement of a huge number of pigments (Chls a/c and Fxs) that contribute to energy transfer and dissipation in this supercomplex. Theoretical and time-resolved spectroscopic studies can be designed on the basis of this structure and, in combination with reexamination of existing results, will reveal more details of these reactions. The diatom PSII core also contains transmembrane and extrinsic subunits that may provide clues to changes occuring in the PSII core during evolution.Plancq, J., Couto, J.M., Ijaz, U.Z., Leavitt, P.R., Toney, J.L., 2019. Next-generation sequencing to identify lacustrine haptophytes in the Canadian prairies: Significance for temperature proxy applications. Journal of Geophysical Research: Biogeosciences 124, 2144-2158.: The Great Plains of North America often experience prolonged droughts that have major economic and environmental impacts. Temperature reconstructions are thus crucial to help decipher the mechanisms responsible for drought occurrences. Long‐chain alkenones (LCAs), lipids produced by three major phylogenetic groups (Groups I, II, and III) of haptophyte algae within the order Isochrysidales, are increasingly used for temperature reconstructions in lacustrine settings. However, to select the most appropriate calibration of the LCA‐based temperature proxy, it is first essential to identify the LCA‐producing haptophyte species present. Here we used next‐generation sequencing to target the 18S rRNA haptophyte gene from sediments with distinct LCA profiles to identify the LCA‐producer(s) from five Canadian prairie lakes. In total, 374 operational taxonomic units (OTUs) were identified across the studied samples, of which 234 fell within the Phylum Haptophyta. Among the most abundant OTUs, three were characterized as LCA‐producers, one falling within the Group I haptophytes and two within the Group II haptophytes. The OTU from Group I haptophytes was associated with a single, highly specific LCA profile, whereas Group II OTUs showed higher variability in LCA distributions. Our study revealed that most of the LCA‐producing OTUs thriving in the Canadian lakes are included within the genus Isochrysis, which helps guide selection of the most appropriate calibration for down‐core temperature reconstructions. Our findings also suggest that the temperature dependency is likely consistent within different taxa from Group I and Group II haptophytes, but that other environmental parameters may influence the accuracy of the calibration.Plain Language Summary: The Great Plains of North America are extremely sensitive to changes in temperature and moisture and often experience prolonged periods of droughts and floods that have major impacts on agriculture production and ecosystem function. Temperature reconstructions are thus crucial to help decipher the climate mechanisms responsible for drought and flood occurrences. In the present study, we identified the algae that biosynthesize a very specific class of lipids, the long‐chain alkenones (LCAs). LCAs have been successfully used for decades to reconstruct past temperature changes in marine environments, but it is important to identify the algae producing these lipids in lakes before we can use them as a paleo‐thermometer for aquatic environments. Here, we used new DNA‐based techniques to identify three main distinct species in five lakes of the Canadian Prairies. One species produces a highly specific LCA distribution and was found in freshwater lakes, while the two other species were found in more saline lakes. By comparing our findings with previous works, we also discovered that environmental parameters other than temperature may influence the accuracy of historical temperature reconstructions.Plant, G., Kort, E.A., Floerchinger, C., Gvakharia, A., Vimont, I., Sweeney, C., 2019. Large fugitive methane emissions from urban centers along the U.S. East Coast. Geophysical Research Letters 46, 8500-8507.: Urban emissions remain an underexamined part of the methane budget. Here we present and interpret aircraft observations of six old and leak‐prone major cities along the East Coast of the United States. We use direct observations of methane (CH4), carbon dioxide (CO2), carbon monoxide (CO), ethane (C2H6), and their correlations to quantify CH4 emissions and attribute to natural gas. We find the five largest cities emit 0.85 (0.63, 1.12) Tg CH4/year, of which 0.75 (0.49, 1.10) Tg CH4/year is attributed to natural gas. Our estimates, which include all thermogenic methane sources including end use, are more than twice that reported in the most recent gridded EPA inventory, which does not include end‐use emissions. These results highlight that current urban inventory estimates of natural gas emissions are substantially low, either due to underestimates of leakage, lack of inclusion of end‐use emissions, or some combination thereof.Plain Language Summary: Recent efforts to quantify fugitive methane associated with the oil and gas sector, with a particular focus on production, have resulted in significant revisions upward of emission estimates. In comparison, however, there has been limited focus on urban methane emissions. Given the volume of gas distributed and used in cities, urban losses can impact national‐level emissions. In this study we use aircraft observations of methane, carbon dioxide, carbon monoxide, and ethane to determine characteristic correlation slopes, enabling quantification of urban methane emissions and attribution to natural gas. We sample nearly 12% of the U.S. population and 4 of the 10 most populous cities, focusing on older, leak‐prone urban centers. Emission estimates are more than twice the total in the U.S. EPA inventory for these regions and are predominantly attributed to fugitive natural gas losses. Current estimates for methane emissions from the natural gas supply chain appear to require revision upward, in part possibly by including end‐use emissions, to account for these urban losses.Porto, C.F.C., Pinto, F.E., Souza, L.M., Madeira, N.C.L., Neto, ?.C., de Menezes, S.M.C., Chinelatto, L.S., Freitas, C.S., Vaz, B.G., Lacerda, V., Rom?o, W., 2019. Characterization of organosulfur compounds in asphalt cement samples by ESI(+)FT-ICR MS and 13C NMR spectroscopy. Fuel 256, 115923., it is presented a methodology for the characterization of organosulfur compounds in asphalt cement (AC) samples employing solid-phase extraction (SPE) associated with methylation reactions and positive-ion mode electrospray Fourier transform ion cyclotron resonance mass spectrometry (ESI(+)FT-ICR MS) and carbon-13 nuclear magnetic resonance (13C NMR) spectroscopy. Three AC samples were submitted to an SPE separation, and the fractions obtained the original AC samples, and their maltenes were methylated and analyzed using the ESI(+)FT-ICR MS. The ESI(+)FT-ICR MS ionized the sulfur fractions much better than the original samples, detecting organosulfur compounds with a broader average molecular mass distribution (Mw). Several types of sulfur compounds were detected, such as sulfides, disulfides, thiophenes, and dibenzothiophenes. Besides, the ESI(+)FT-ICR data were compared with the 13C NMR (from model molecules analyses) and ESI(+)-Orbitrap MS. The organosulfur chemical profile was correlated to the physical properties of AC samples. It was verified that the samples with higher aromatic-character were less susceptible to aging test, while the one with more saturated-character presented more significant variation in their physical properties after the aging test.Pratami, F.L.P., Chandra, S., Angtony, W., 2019. A new look on reserves prediction of unconventional shale gas plays: moving from static parameters to dynamic, operation-based reserves’ calculation. Journal of Petroleum Exploration and Production Technology 9, 2205-2220. conventional oil and gas are now in a scarcer condition than they have ever been, attentions have shifted into unconventional resources. These unconventional resources, although abundant in nature, cannot be produced by conventional means economically. Therefore, efforts must be done to calculate reserves in such a fashion that uncertainties can be acknowledged, reducing errors and inaccuracies in the process. Researchers in the past have argued that uncertainties in reserve estimation cannot be measured by a single number and as the scale of reserve grows bigger, so will the uncertainties be. Two novel methods are developed from the basis of operation-based reserves’ calculation, where development strategies namely hydraulic fracturing plans will be a deciding factor in determining reserves. These two methods are adapted from Monte Carlo-based approach, in which the first method will be using random numbers that are generated for listed properties to calculate ranged probability of reserves. The second approach is based on simple well-testing procedures that can also be referred to fracture design. The procedures are then compared to define practicality and situational capability of each method prepared. The models presented are dynamically flexible, due to the fact that they are integrated into development scenarios of the reserves.Pryor, W.R., Esposito, L.W., Jouchoux, A., West, R.A., Grodent, D., Gérard, J.C., Radioti, A., Lamy, L., Koskinen, T., 2019. Cassini UVIS detection of Saturn's north polar hexagon in the grand finale orbits. Journal of Geophysical Research: Planets 124, 1979-1988. Cassini's final orbits in 2016 and 2017 provided unprecedented spatial resolution of Saturn's polar regions from near-polar spacecraft viewing geometries. Long-wavelength channels of Cassini's Ultraviolet Imaging Spectrograph instrument detected Saturn's UV-dark north polar hexagon near 180 nm at planetocentric latitudes near 75°N. The dark polar hexagon is surrounded by a larger, less UV-dark collar poleward of planetocentric latitude 65°N associated with the dark north polar region seen in ground-based images. The hexagon is closely surrounded by the main arc of Saturn's UV aurora. The UV-dark material was locally darkest on one occasion (23 January 2017) at the boundary of the hexagon; in most Ultraviolet Imaging Spectrograph images the dark material more uniformly fills the hexagon. The observed UV-dark stratospheric material may be a hydrocarbon haze produced by auroral ion-neutral chemistry at submicrobar pressure levels. Ultraviolet Imaging Spectrograph polar observations are sensitive to UV-absorbing haze particles at pressures lower than about 10?20 mbar.Purwasena, I.A., Astuti, D.I., Syukron, M., Amaniyah, M., Sugai, Y., 2019. Stability test of biosurfactant produced by Bacillus licheniformis DS1 using experimental design and its application for MEOR. Journal of Petroleum Science and Engineering 183, 106383. enhanced oil recovery (MEOR) is a proven tertiary recovery technique. Biosurfactant is a microbial bioproduct that plays an important role in MEOR applications. This study aimed to test biosurfactant stability using a design experiment based on response surface methodology. First, isolation and screening for potential biosurfactant-producing bacteria from crude oil samples was performed, followed by their characterization. A biosurfactant core flooding experiment was also conducted to examine bacterial activity on MEOR. Thirty-one sequential isolates of bacteria were screened based on qualitative and semi-qualitative parameters. One selected biosurfactant-producing bacterium was identified as Bacillus licheniformis DS1 based on phylogenetic analysis of the 16S rRNA gene. This bacterium had the highest emulsification activity (Ei24?=?65.19%) in light crude oil and could reduce the interfacial tension between oil and water with an effective critical-micelle concentration of 157.5?mg/L. The biosurfactant was observed as a growth-associated metabolite type and the Fourier transform infrared spectrum revealed that the biosurfactant produced belonged to a group of lipopeptides. The biosurfactant has good stability in maintaining emulsification activity at pH 4–10, high temperatures up to 120?°C, and with an NaCl concentration up to 10% (w/v). Based on response surface methodology using the Box–Behnken experimental design, the optimum condition for the most stable biosurfactant is pH 12, a 40?°C temperature and 10% salinity, with an Ei24 value of 94.28%. Core flooding experiments with biosurfactant resulted in 5.4% additional oil recovery. Therefore, this biosurfactant shows a high potential application for MEOR.Putra, W., Hakiki, F., 2019. Microbial?enhanced oil recovery: interfacial tension and biosurfactant-bacteria growth. Journal of Petroleum Exploration and Production Technology 9, 2353-2374. oil recovery (MEOR) is a method that utilises bacteria or bioproducts to increase oil recovery at the tertiary stage. Clostridium sp. produces biosurfactant that alters rock–fluid properties and increases oil detachment. The interaction between bacteria and surfactant is interesting relation to study. We revisit and develop models for biosurfactant-producing bacteria’s growth and the interfacial tension (IFT) response. The biosurfactant-producing bacteria growth model (BBG model) mimics the predator–prey interaction and the IFT response model derived from analogy. Both models form an integrated model called coupled-simultaneous model. We deliver the suitability of these models to experimental datasets by conducting parameter estimation. The decreased number of parameter in BBG model is with the help of rate estimation model. It estimates the bacteria growth rate and biosurfactant production rate. This research introduces a graphical method to narrow parameters initial guess in the IFT model. The method comes with a proposed index to compare surfactant performance called as surfactant performance index (SPI). The paper exposes the logic of each parameter, physics behind the models, and addresses the mathematical artefacts. The significant findings are valuable to anticipate bacterial performance for MEOR.Qie, W., Algeo, T.J., Luo, G., Herrmann, A., 2019. Global events of the Late Paleozoic (Early Devonian to Middle Permian): A review. Palaeogeography, Palaeoclimatology, Palaeoecology 531, 109259. Late Paleozoic (Early Devonian to Middle Permian) was an interval of profound changes in Earth-surface systems, reflected in dynamic interplay among the biosphere, hydrosphere, atmosphere, and geosphere. Major events transpired, including the colonization of landmasses by vascular plants, the assembly of the supercontinent Pangea, two first-order mass extinctions (the Frasnian-Famennian and Devonian-Carboniferous boundary events), and the most severe icehouse climate mode of the Phanerozoic (the Late Paleozoic Ice Age, LPIA). The goals of the present review are (1) to summarize major global developments in climate, oceanography, and paleobiology during the Late Paleozoic, (2) to examine the roles of land plant evolution, global tectonics, and large igneous province magmatism in driving these developments, and (3) to serve as an introduction to the 23 contributions to this special issue of Palaeogeography, Palaeoclimatology, Palaeoecology, indicating how they advance our knowledge of various scientific issues related to these developments.Qin, R., Lillico, D., How, Z.T., Huang, R., Belosevic, M., Stafford, J., Gamal El-Din, M., 2019. Separation of oil sands process water organics and inorganics and examination of their acute toxicity using standard in-vitro bioassays. Science of The Total Environment 695, 133532. sands process water (OSPW) contains complex components of inorganics and organics. This is the first study that separated OSPW inorganic and organic fractions and examined their relative acute toxicity when compared with the original whole OSPW using an in-vitro cell-based bio-indicator system. The separation of OSPW inorganic and organic fractions would be conducive to the understanding of the toxic contribution of organic and inorganic fractions as well as the identification and treatment of organic fractions. In this research, we demonstrated that the highest organic fraction extraction was obtained using HLB solid phase extraction with 95.4?±?0.7% of dissolved organic carbon (DOC) and 90.0?±?5.3% of naphthenic acid (NA) recovered from OSPW, which were higher than those obtained using the traditional dichloromethane liquid-liquid extraction (48.8?±?0.2% of DOC and 81.0?±?2.6% of NA recovery) or other SPE cartridges tested. We also reported the first isolation method for OSPW inorganic fraction by removing 96.1?±?0.2% of DOC in OSPW using granular activated carbon. The difference of other parameters such as pH, alkalinity, conductivity, and concentration of detected ions between OSPW and isolated inorganic fraction was negligible. The acute toxicity of whole OSPW, separated OSPW inorganic fraction and organic fraction, and the reconstituted fractions were assessed using in-vitro bioassays with RAW 264.7 mouse macrophage cell lines. OSPW organic fraction demonstrated significant cytotoxicity at 14?mg/L O2-NA and affected the cellular metabolic activity at 10?mg/L of O2-NAs. No significant cytotoxicity or effect on cellular metabolic activity was observed for whole OSPW, OSPW inorganic fraction and the reconstituted fractions. Overall, this study provides the procedure for the isolation of the major components of OSPW (i.e., organics and inorganics), which allows the assessment of their relative toxicological effects using a standard in-vitro bioassay and would allow more accurate characterization and treatment study for each fraction in OSPW.Qin, Z., Arshadi, M., Piri, M., 2019. Micro-scale experimental investigations of multiphase flow in oil-wet carbonates. I. In situ wettability and low-salinity waterflooding. Fuel 257, 116014. this study, the impacts of temperature, initial water saturation, and aging time on wettability alteration during dynamic aging process were investigated at the pore scale, using a state-of-the-art high-temperature, high-pressure miniature core-flooding system integrated with a high-resolution micro-CT scanner. Furthermore, pore-scale displacement mechanisms impacting the waterflooding oil recovery under varying oil-wet conditions were probed. Subsequently, we investigated the wettability alteration and its corresponding impact on pore-scale displacement mechanisms during low-salinity waterflooding (LSWF). The results showed that the aging-induced wettability alteration reached an equilibrium condition after approximately seventeen days. With higher temperature, lower initial water saturation, and longer aging time, we observed greater in situ contact angles indicative of more oil-wet rock surfaces. Once brine was injected to displace oil, since the majority of pore elements were oil-wet after the aging process, pore-scale piston-like displacements (brine-to-oil drainage) had the largest contribution to the oil recovery. Based on our observations, the waterflooding-based oil recovery decreases as the porous medium becomes more oil-wet. This phenomenon is due to the higher threshold brine pressures of the displacements in more oil-wet conditions, which restricts brine invasion into medium and small size pores. Furthermore, wettability alteration towards neutral-wetness and the consequent reduction in threshold brine pressure required for the fluid to invade the midsize oil-filled pores, result in higher oil recovery by LSWF compared to high-salinity waterflooding (HSWF). The in situ analyses indicate that reservoirs with wide pore size distributions (a large number of midsize pores) could be better candidates for applications of LSWF EOR technique.Qin, Z., Arshadi, M., Piri, M., 2019. Micro-scale experimental investigations of multiphase flow in oil-wet carbonates. II. Tertiary gas injection and WAG. Fuel 257, 116012. reservoirs are typically oil-wet, which can lead to low oil production during the oil recovery processes such as base waterflooding. The residual oil in these reservoirs is the target of many EOR techniques such as tertiary gas injection and Water-Alternating-Gas (WAG) flooding. Currently, there is scarce research investigating the pore-scale displacement physics governing the afore-mentioned EOR techniques in oil-wet carbonates. In this study, three sets of miniature core-flooding experiments were performed in carbonate samples at elevated pressure and temperature conditions using a three-phase core-flooding system integrated with a high-resolution X-ray micro-CT scanner. Pore-scale displacement events governing tertiary gas injection and WAG under weakly oil-wet conditions were examined. The prevailing oil mobilization mechanisms during the tertiary gas injection were further investigated under varying wettability conditions. The results revealed that gas-to-oil-to-brine double displacement is the main displacement chain for oil production by tertiary gas injection. During this process, the greater was the degree of oil-wetness of the rock, the larger became the additional oil recovery that could be achieved. This was due to the increase in the frequency of gas-to-oil-to-brine double displacements and the superior connectivity of the oil phase under stronger oil-wet conditions. Furthermore, WAG flooding significantly increased the displacement efficiency of both gas and brine phases because of the shielding effect of the trapped gas ganglia. In the first WAG cycle, oil was produced through a series of direct and double displacements. Multiple displacements started taking place and further contributed to oil recovery as more WAG cycles were implemented.Qu, C.-S., Qiu, L.-W., Cao, Y.-C., Yang, Y.-Q., Yu, K.-H., 2019. Sedimentary environment and the controlling factors of organic-rich rocks in the Lucaogou Formation of the Jimusar Sag, Junggar Basin, NW China. Petroleum Science 16, 763-775. Lucaogou Formation in the Jimusar Sag of the eastern Junggar Basin is an important sedimentary stratum accumulating huge amounts of lacustrine tight oil in China, where organic-rich rocks are commonly observed. Focusing on the Lucaogou Formation, a precise analysis of the inorganic and organic petrology and the inorganic geochemistry characteristics was conducted. The paleoclimate and paleoenvironment during sedimentation of the Lucaogou Formation were established, and the key factors that were controlling the accumulation of organic matter during this time were identified. The results of this study suggest that during the sedimentation of the Lucaogou Formation, the paleoclimate periodically changed from a humid environment to an arid environment. As a result, the salinity of the water and the redox environment fluctuated. During the sedimentation period, the lake showed sufficient nutrient supplies and a high primary productivity. The interval studies in the Lucaogou Formation were divided into five sedimentary cycles, where the first, second, and fifth sedimentary cycles consisted of cyclical paleoclimate fluctuations varied from a humid environment to an arid environment and shifted back to a humid environment with levels of salinity from low to high and decreased again. The third and fourth cycles have cyclical fluctuations from a humid to an arid environment and corresponding salinity variation between low and high levels. During the period when organic-rich rocks in the Lucaogou Formation deposited in the Jimusar Sag, the paleoclimate and the water body were suitable for lower aquatic organisms to flourish. As a result, its paleoproductivity was high, especially during the early period of each cycle. A quiet deep water body is likely to form an anoxic environment at the bottom and is also good for accumulation and preservation of organisms. Fine-grained sediments were accumulated at a low deposition rate, with a low dilution of organic matter. Therefore, high paleoproductivity provided a sufficient volume of organisms in the studied area in a quiet deep water body with an anoxic environment and these were the key factors controlling formation of organic-rich rocks.Quan, V.T.H., Giao, P.H., 2019. Geochemical evaluation of shale formations in the northern Song Hong basin, Vietnam. Journal of Petroleum Exploration and Production Technology 9, 1839-1853. exploration and production of conventional reservoirs have been strongly developed over the years in Vietnam since 1987. However, with the decrease in petroleum production in recent years, a certain attention has started to be given to the unconventional reservoirs. This study presents the results of a comprehensive geochemical evaluation of three main shale formations in the northern Song Hong basin (also known as the Red River basin) of Vietnam. Over 200 cutting samples of Lower Miocene, Oligocene and Triassic shales from two onshore and two offshore wells were collected and tested for total organic carbon (TOC), hydrocarbon generation potential (S2), hydrogen index (HI), production index (PI), Tmax and vitrinite reflectance (Ro). Lower Miocene shales are characterized by HI of 94 to 591 mgHC/gTOC, TOC of 0.14 to 1.65 wt% and S2 of 0.34 to 4.62 mg HC/g rock, indicating a poor-to-fair source rock of mixed gas-prone kerogen types II and III. Their Tmax of 425 to 437 °C and Ro of 0.35 to 0.66% suggested an immaturity to early-maturity HC generation. Oligocene shales have HI of 164 to 602 mgHC/gTOC, TOC of 0.52 to 3.18 wt% and S2 of 0.63 to 5.61 mg HC/g rock, indicating a fair-to-good potential source rock with a gas- and oil-prone kerogen of mixed types II and III. Their Tmax values of 427 to 476 °C and Ro of 0.43 to 1.73% suggested an optimum thermal maturity. Triassic shales are characterized by HI <?50 mgHC/gTOC, TOC from 1.04 to 14.10 wt% and S2 from 0.03 to 1.11 mg HC/g rock, showing little remaining source or no potential for hydrocarbon generation in the late to post-mature stages with Ro of 1.79 to 2.10%. The newly obtained geochemical data and analysis results of this study are expected to improve the knowledge on the main source rocks in the northern Song Hong basin, in particular in the onshore part and to provide with the useful background information for further assessment of shale gas potential in Vietnam.Raab, A., Feldmann, J., 2019. Biological sulphur-containing compounds – Analytical challenges. Analytica Chimica Acta 1079, 20-29. review covers analytical methods applied to the determination of none volatile sulphur-containing biological compounds. The classes of S-compounds include amino acids, proteins, lipids, carbohydrates and sulphur-containing metabolites. Techniques covered include element specific detectors as well as molecular specific detectors from X-ray absorption near-edge structure (XANES) to elemental and molecular mass spectrometers. The major techniques used are inductively coupled plasma mass spectrometry (ICP-MS) and high-resolution electrospray mass spectrometry (ESI-MS) in their various forms. Both techniques either individually or combined require the sample to be present in liquid form and therefore involve sample preparation usually extraction and depending on sample and molecular class studied potentially also derivatisation in addition to generally requiring chromatographic separation. Over recent years, detection limits achieved by elemental methods and computational methods to extract signals of sulphur-containing compounds out of the mass of data produced by molecular high-resolution mass spectrometers made significant gains. Still the determination of sulphur-containing compounds is challenging, but nowadays the methods have been developed well enough to allow application to real samples for absolute quantification of biomolecules such as proteins or lipids.Rae, A.S.P., Collins, G.S., Morgan, J.V., Salge, T., Christeson, G.L., Leung, J., Lofi, J., Gulick, S.P.S., Poelchau, M., Riller, U., Gebhardt, C., Grieve, R.A.F., Osinski, G.R., 2019. Impact-induced porosity and microfracturing at the Chicxulub impact structure. Journal of Geophysical Research: Planets 124, 1960-1978.: Porosity and its distribution in impact craters has an important effect on the petrophysical properties of impactites: seismic wave speeds and reflectivity, rock permeability, strength, and density. These properties are important for the identification of potential craters and the understanding of the process and consequences of cratering. The Chicxulub impact structure, recently drilled by the joint International Ocean Discovery Program and International Continental scientific Drilling Program Expedition 364, provides a unique opportunity to compare direct observations of impactites with geophysical observations and models. Here, we combine small‐scale petrographic and petrophysical measurements with larger‐scale geophysical measurements and numerical simulations of the Chicxulub impact structure. Our aim is to assess the cause of unusually high porosities within the Chicxulub peak ring and the capability of numerical impact simulations to predict the gravity signature and the distribution and texture of porosity within craters. We show that high porosities within the Chicxulub peak ring are primarily caused by shock‐induced microfracturing. These fractures have preferred orientations, which can be predicted by considering the orientations of principal stresses during shock, and subsequent deformation during peak ring formation. Our results demonstrate that numerical impact simulations, implementing the Dynamic Collapse Model of peak ring formation, can accurately predict the distribution and orientation of impact‐induced microfractures in large craters, which plays an important role in the geophysical signature of impact structures.Plain Language Summary: The Chicxulub crater, Mexico, is widely known for its association with the extinction of the nonavian dinosaurs at the end of the Cretaceous period. The crater was first identified due to its gravitational and magnetic anomalies. Potential impact structures are often identified, in part, on the basis of geophysical anomalies, most commonly including a circular gravity low. Gravity is slightly weaker at craters because the impact cratering process removes mass from the impact site. In this study, we examine the cause of the Chicxulub gravity anomaly by combining observations from recent drilling of the crater, geophysical data measured across the crater, and numerical impact simulations. We demonstrate that porosity in rocks beneath the crater floor is primarily accommodated by fracturing during the impact cratering process, that the orientation of those fractures are consistent with predictions from numerical impact simulations, and that impact‐induced porosity is one of the primary causes of gravity anomalies in large impact craters.Rafiei, M., Kennedy, M., 2019. Weathering in a world without terrestrial life recorded in the Mesoproterozoic Velkerri Formation. Nature Communications 10, 3448. the terrestrial surface drives biogeochemical cycles on Earth through chemical weathering reactions mediated by the biological influence of soils. Prior to the expansion of life on to land, abiotic weathering may have resulted in different boundary conditions affecting the composition of the biosphere. Here we show a striking difference in weathering produced minerals preserved in the Mesoproterozoic Velkerri Formation. While the bulk chemistry and mineralogy is dominated by illite similar to many modern mudstones, application of a novel microbeam technology reveals that the initial detrital minerals were composed of mica (28%) and feldspar (45%) with only a trace amount (<2%) of typical soil formed clay minerals. The majority of illite and the high Al2O3 fraction previously interpreted as a weathering signal, is present as a replacement of feldspar and mica. These sediments record physical erosion with limited pedogenic clay mineral formation implying fundamentally different weathering pathways.Rahimi, P., 2019. Properties of Canadian bitumen and bitumen-derived crudes, and their impacts on refinery processing, in: Rahimi, P., Ovalles, C., Zhang, Y., Adams, J.J. (Eds.), Chemistry Solutions to Challenges in the Petroleum Industry. American Chemical Society, Washington DC, pp. 223-240. production of bitumen and heavy oil from the Western Canadian Sedimentary Basin, including the Cold Lake, Athabasca, and Peace River regions, has increased in the last 10 years and currently reaches to approximately 2.7 million bbl/d. Although a large portion of the produced bitumen is processed in Alberta, a significant amount is transported by pipeline and rail to different refineries in Canada and the United States. Due to their high viscosity and density, bitumen and heavy oils must be blended with diluents (dilbit) or synthetic oil (synbit) to meet pipeline specifications for density (940 kg/m3) and viscosity (350 cSt at 11 °C). Other processing options such as partial upgrading are being considered to reduce or eliminate the diluent requirement for bitumen transportation to the market. Canadian heavy crudes are also categorized as “opportunity crudes” partly because of a relatively high total acid number (TAN) content, although there are no public data available on the refinery corrosivity of these crudes. Although the large discount of Canadian heavy crudes such as Western Canadian Select compared to West Texas Intermediate may be due to lack of pipeline capacity, part of the price reduction is imposed because of the quality and perceived refinery processing issues that may occur as a result of processing Canadian heavy crudes. In this chapter, I review the properties of Canadian heavy oils and bitumen revealing how these oils, in fact, have superior quality compared to light and tight oils and create less operational problems in refinery processes. Data will be presented showing that the conversion chemistry leading to lighter products is facilitated because of the presence of hydrogen donors as well as hydrogen transfer molecules in Canadian bitumen. Canadian bitumen has one of the highest stabilities among the heavy oils in the world. In refinery processing, Canadian dilbits have shown to have the lowest fouling tendencies and as such can be blended with light or tight oils to reduce fouling from these crudes in refinery operations. Finally, I will demonstrate that at a high temperature (300 °C), heavy gas oil (HVGO) derived from Canadian bitumen, despite relatively high TAN, has lower activity toward Fe powder compared to HVGO derived from a known corrosive crude with a lower TAN.Rahimi, P., Ovalles, C., Zhang, Y., Adams, J.J., 2019. Chemistry Solutions to Challenges in the Petroleum Industry, in: Rahimi, P., Ovalles, C., Zhang, Y., Adams, J.J. (Eds.). American Chemical Society, Washington DC, 348 pp. the last few years, we have witnessed some dramatic changes in the petroleum industry. While production of heavy and extra heavy oils has been reduced from Venezuela and Mexico, Canada has been increasing its oil output. In the United States, light tight oil (LTO) production has reached close to 11 million barrels with approximately 2 million barrels exported throughout the world. Determination of crude assay from LTO such as Bakken and Eagle Ford can be challenging, partly due to significant variation in quality of these crudes within time and producing region. These variations can be much more severe than changes in typical reservoirs in terms of well location and depth. LTO crudes may contain unusual contaminants, be incompatible with other crudes—especially high asphaltene crudes—and have a high vapor pressure of H2S. These properties create challenges in transportation, blending, and processing in refineries. As a result, significant research initiatives have started to address these challenging issues and mitigate the abovementioned technical problems.In Alberta, almost half of the 3 million barrels of heavy oil/bitumen produced are processed using either hydrogen addition or carbon rejection technologies such as hydroprocessing Delayed Coking. These technologies produce synthetic crude oil, which needs to be further processed in refineries to produce transportation fuels. The other half of Alberta production is blended with 25%–30% diluent and transported to the United States where refineries are equipped to process heavy crudes. While there are challenges in processing heavy crudes—including high total acid number (TAN), high asphaltenes content and metals—these crudes can provide not only economic opportunities but also operational incentives comparedwith the light and LTOprocessing.However, solving one problem upstream may cause additional processing challenges downstream at the refinery. In the case of heavy oils and bitumen, the diluent is often needed to reduce viscosity for transportation via pipeline. However, from economic and environmental standpoints, the use of diluent is ideally reduced or eliminated by partially upgrading. Reducing the viscosity of heavy oils by partial upgrading requires thermal treatment, which also results in the formation of less stable asphaltenes and olefins/diolefins that may cause operational issues in downstream processing. In addition to the traditional challenges of heavy oils (high viscosity, asphaltenes, sulfur,TAN, bottoms, etc.), the looming International Maritime Organization mandate for the reduction of sulphur in marine fuel from the current 3.5wt% to 0.5wt% will present yet another technical challenge. The 13 chapters in this book touch upon some of these issues that the petroleum industry is facing today and provide chemistry solutions to mitigate these problems. These chapters are divided into four sections dealing with production, asphaltene characterization and aggregation, bitumen/heavy oil processability, and detection and removal of contaminants during petroleum processing. The following is a brief excerpt of each chapter to familiarize the readers with the different topics.Cairns, A.J., Hull, K.L., Sayed, M. From design to practice: Development of new acid platforms to address upstream oil and gas production challenges, 3-21.Hernandez, H.W., Perrard, A., Mendoza Gonzalez, E., Ehlert, W., Trabelsi, S. Advantages of using a microemulsion to remove crude oil residue from solid surfaces, 23-36.Zhang, Y. Similarities in diverse polycyclic aromatic hydrocarbons of asphaltenes and heavy oils revealed by noncontact atomic force microscopy: Aromaticity, bonding, and implications for reactivity, 39-65.Hoepfner, M.P., Yang, Y. Ultra-small-angle X-ray scattering as a probe of petroleum heterogeneities from the nano- to the macroscale, 67-87.Moir, M.E. The quantum mechanics of asphaltene aggregation, 89-111.Sivaramakrishnan, K., de Klerk, A., Prasad, V. Viscosity of Canadian oilsands bitumen and its modification by thermal conversion, 115-199.Rogel, E., Hench, K., Hajdu, P., Ingham, H. The role of compatibility in determining the blending and processing of crude oils, 201-222.Rahimi, P. Properties of Canadian bitumen and bitumen-derived crudes, and their impacts on refinery processing, 223-240.Martinelli, M., Mehrbod, M., Graham, U.M., Hu, Y., Gnanamani, M.K., Jacobs, G. Soft X-ray characterization of sulfur-poisoned cation-exchanged pt/kl catalysts for aromatization of hexane, 243-260.Ovalles, C., Rogel, E., Hurt, M., Duma, V., Morazan, H., Hench, K., Moir, M.E. Nitrogen speciation: Application to reactivity of feeds to hydroprocessing and catalyst deactivation, 261-280.Dutta, M., Pathiparampil, A., Quon, D., Tan, J., Poirier, L., Berhane, L., Lopez-Linares, F.. Total chloride analysis in petroleum crude samples: Challenges and opportunities, 281-310.Ren, F., Zhu, Y., Liu, Q., Wu, H.. Characteristics of morphology and mobility of iron species on iron-poisoned fluid catalytic cracking catalyst particles, 327-335.Rahman, M.A., Halfar, J., Adey, W.H., Nash, M., Paulo, C., Dittrich, M., 2019. The role of chitin-rich skeletal organic matrix on the crystallization of calcium carbonate in the crustose coralline alga Leptophytum foecundum. Scientific Reports 9, 11869. organic matrix (OM) contained in marine calcifiers has a key role in the regulation of crystal deposition, such as crystalline structure, initiation of mineralization, inhibition, and biological/environmental control. However, the functional properties of the chitin-rich skeletal organic matrix on the biological aspect of crystallization in crustose coralline algae have not yet been investigated. Hence, the characterization of organic matrices in the biomineralization process of this species was studied to understand the functions of these key components for structural formation and mineralization of calcium carbonate crystals. We purified skeletal organic matrix proteins from this species and explored how these components are involved in the mineralization of calcium carbonate crystals and environmental control. Intriguingly, the analytical investigation of the skeletal OM revealed the presence of chitin in the crustose coralline alga Leptophytum foecundum. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the OM revealed a high molecular mass protein as 300-kDa. Analysis of glycosylation activity exposed two strong glycoproteins as 300-kDa and 240-kDa. Our study of the biominerals of live collected specimens found that in addition to Mg-calcite up to 30% aragonite were present in the skeleton. Our experiment demonstrated that the chitin-rich skeletal OM of coralline algae plays a key role in the biocalcification process by enabling the formation of Mg-calcite. In addition, this OM did not inhibit the formation of aragonite suggesting there is an as yet unidentified process in the living coralline that prevents the formation of aragonite in the living skeletal cell walls.Ran, W., Wang, H., Liu, Y., Qi, M., Xiang, Q., Yao, C., Zhang, Y., Lan, X., 2019. Storage of starch and lipids in microalgae: Biosynthesis and manipulation by nutrients. Bioresource Technology 291, 121894. accumulate starch and lipid as storage metabolites under nutrient depletion, which can be used as sustainable feedstock for biorefinery. Omics analysis coupled with enzymatic and genetic verifications uncovered a partial picture of pathways and important enzymes or regulators related to starch and lipid biosynthesis as well as the carbon partitioning between them under nutrient depletion conditions. Depletion of macronutrients (N, P, and S) resulted in considerable enhancement of starch and/or lipid content in microalgae, but the accompanying declined photosynthesis hampered the achievements of high concentrations. This review summarized the current knowledge on the pathways and the committed steps as well as their carbon allocation involved in starch and lipid biosynthesis, and focused on the manipulation of different nutrients and the alleviation of oxidative stress for enhanced storage metabolites production. The biological and engineering approaches to cope with the conflict between biomass production and storage metabolites accumulation are proposed.Rangel-Alvarado, R.B., Willis, C.E., Kirk, J.L., St Louis, V.L., Amyot, M., Bélanger, D., Ariya, P.A., 2019. Athabasca oil sands region snow contains efficient micron and nano-sized ice nucleating particles. Environmental Pollution 252, 289-295. Athabasca Oil Sands Region (AOSR) in Alberta, Canada, is an important source of atmospheric pollutants, such as aerosols, that have repercussions on both the climate and human health. We show that the mean freezing temperature of snow-borne particles from AOSR was elevated (?7.1?±?1.8?°C), higher than mineral dust which freezes at?～??15?°C and is recognized as one of the most relevant ice nuclei globally. Ice nucleation of nanosized snow samples indicated an elevated freezing ability (?11.6?±?2.0?°C), which was statistically much higher than snow-borne particles from downtown Montreal. AOSR snow had a higher concentration (～2 orders of magnitude) of >100?nm particles than Montreal. Triple quadrupole ICP-(QQQ)-MS/MS analysis of AOSR and Montreal snow demonstrated that most concentrations of metals, including those identified as emerging nanoparticulate contaminants, were much more elevated in AOSR in contrast to Montreal: 34.1, 34.1, 16.6, 5.8, 0.3, 0.1, and 9.4?mg/m3 for Cr, Ni, Cu, As, Se, Cd, and Pb respectively, in AOSR and 1.3, 0.3, 2.0, <0.03, 0.1, 0.03, and 1.2?mg/m3 in Montreal snow. High-resolution Scanning Transmission Electron Microscopy/Energy-dispersive X-ray Spectroscopy (STEM-EDS) imaging provided evidence for various anthropogenic nano-materials, including carbon nanotubes resembling structures, in AOSR snow up to 7–25?km away from major oil sands upgrading facilities. In summary, particles characterized as coming from oil sands are more efficient at ice nucleation. We discuss the potential impacts of AOSR emissions on atmospheric and microphysical processes (ice nucleation and precipitation) both locally and regionally.Ranjbar Jafarabadi, A., Dashtbozorg, M., Mitra, S., Riyahi Bakhtiari, A., Mohamadjafari Dehkordi, S., Cappello, T., 2019. Historical sedimentary deposition and ecotoxicological impact of aromatic biomarkers in sediment cores from ten coral reefs of the Persian Gulf, Iran. Science of The Total Environment 696, 133969. present study determines the levels, vertical distributions, source apportionment and ecological risk of polycyclic aromatic hydrocarbons (PAHs) in ten sediment cores of coral reef in the Persian Gulf, Iran, one of the important oil polluted marine areas in the world. The main purpose of this study was to determine the spatio-vertical distribution pattern of PAHs pollution at the four hot spot zones on the Gulf: dense industrial, medium industrial, urbanized and non-impacted zones over the past few years. Sediment quality and ecological risk were also assessed in order to determine the pollutants of concern. In detail, 23 parent (PPAHs) and 16 alkylated PAHs (APAHs), along with retene and perylene, were determined in sediment cores (0–40?cm depth). The vertical distribution of all PAHs showed a wide variation among sampling stations and depths, with a decreasing trend of concentration from surface to bottom, and a peak at 12?cm. Total concentrations of PPAHs and APAHs ranged from 35 to 1927?ng?g?1 dw and 19 to 1794?ng?g?1 dw respectively, with the highest concentrations at the industrial zone. The diagnostic ratio for PAHs and perylene (3 to 1277?ng?g?1 dw) indicated mixed sources of PAHs, with dominance of petrogenic origins at the industrial zone and natural diagenetic inputs, respectively. The PAH concentration depicted a significant decreasing trend along the length of the core with an abrupt increase within the core length 12–20?cm. Temporal variations in contaminants can be linked to economic, coastal developments and industrial growth. Overall, the baseline data on geographical distribution, congener profiles, sources and vertical deposition of PAHs in the Persian Gulf area would be useful to establish proper monitoring plans for this sensitive ecosystem.Razghandi, M., Hemmati-Sarapardeh, A., Rashidi, F., Dabir, B., Shamshirband, S., 2019. Smart models for predicting under-saturated crude oil viscosity: a comparative study. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects 41, 2326-2333. this study, radial basis function (RBF) and multilayer perceptron (MLP) neural networks were proposed for accurate prediction of under-saturated oil viscosity. To this end, more than 600 viscosity data were collected from various geological locations worldwide which cover oil API gravity from 6.5 (extra heavy crude oils) to 53 (very light crude oils), reservoir temperature from 300.15 to 445.15?K, and reservoir pressure from 1.68 to 105.52 MPa. Statistical and graphical comparison of the proposed models with other existing models indicates that the prediction accuracy and applicability extent of the suggested models are much better compared to the previously published ones by providing average absolute relative errors of 3.09% and 3.88% for MLP and RBF models, respectively.Rédei, C., Felinger, A., 2019. Modeling the competitive adsorption of sample solvent and solute in supercritical fluid chromatography. Journal of Chromatography A 1603, 348-354. retention behavior of a series of n-alkylbenzene homologues as well as the effect of different sample solvents on chromatographic efficiency were studied in supercritical fluid chromatography. After testing various columns, an alkylamide stationary phase was selected for detailed studies. The results showed that even a small amount of methanol originating only from the sample, overloaded the column and competitive adsorption was induced between the analytes and the sample solvent for adsorption on the stationary phase. This was indicated by the changes in column efficiency, retention and peak widths. The concentration of the analytes in the sample was negligible compared to the amount of methanol – but their adsorption was influenced by the solvent – while the adsorption of methanol remained unaffected by the n-alkylbenzenes. First, the competition was described by determining the single-component adsorption isotherms for both the analytes and their solvent, then competitive isotherms were calculated. Based on the peak profiles, bi-Langmuir and competitive bi-Langmuir isotherms were assumed. The solvent effect was modeled by a numerical method created in-house where the differential mass balance equation given by the equilibrium–dispersive (ED) model was integrated using the Rouchon algorithm. The experimental observations were confirmed by in silico experiments and additional cases involving two hypothetical analytes were studied as well.Ren, F., Zhu, Y., Liu, Q., Wu, H., 2019. Characteristics of morphology and mobility of iron species on iron-poisoned fluid catalytic cracking catalyst particles, in: Rahimi, P., Ovalles, C., Zhang, Y., Adams, J.J. (Eds.), Chemistry Solutions to Challenges in the Petroleum Industry. American Chemical Society, Washington DC, pp. 327-335. is growing concern about iron contamination in fluid catalytic cracking catalysts due to the processing of opportunity crude on pursuing higher margin of the refinery profit. Sinopec Research Institute of Petroleum Processing has conducted extensive research on the effect of iron poisoning on fluid catalytic cracking catalysts. Recent studies reveal new results to obtain a better understanding of iron poisoning mechanisms. The morphology and elemental distribution on the severely iron-poisoned equilibrium catalysts (Ecats) are characterized by scanning electron microscopy (SEM), scanning electron microscopy with energy dispersive spectrometer (SEM-EDS), and electron probe micro analyzer (EPMA) techniques. In this study, a new morphology gully-part was found on the surface of the catalyst particle, and its iron concentration is much higher than on nodules. Ni and the Si/Al mass ratio exhibit the same trend as Fe content on Ecats. Iron can migrate from Ecats or iron-contaminated fresh catalyst to the surface of metal trap particles under redox or hydrothermal conditions, which can be directly observed by SEM-EDS and EPMA techniques. Si and Ni were also found transferred with iron, which proved that the formation of eutectic material is composed of at least three elements such as Fe2Ni~1Six.Ren, M., Feng, X., Huang, Y., Wang, H., Hu, Z., Clingenpeel, S., Swan, B.K., Fonseca, M.M., Posada, D., Stepanauskas, R., Hollibaugh, J.T., Foster, P.G., Woyke, T., Luo, H., 2019. Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution. The ISME Journal 13, 2150-2161. archaea (AOA) of the phylum Thaumarchaeota are widespread in marine and terrestrial habitats, playing a major role in the global nitrogen cycle. However, their evolutionary history remains unexplored, which limits our understanding of their adaptation mechanisms. Here, our comprehensive phylogenomic tree of Thaumarchaeota supports three sequential events: origin of AOA from terrestrial non-AOA ancestors, colonization of the shallow ocean, and expansion to the deep ocean. Careful molecular dating suggests that these events coincided with the Great Oxygenation Event around 2300 million years ago (Mya), and oxygenation of the shallow and deep ocean around 800 and 635–560 Mya, respectively. The first transition was likely enabled by the gain of an aerobic pathway for energy production by ammonia oxidation and biosynthetic pathways for cobalamin and biotin that act as cofactors in aerobic metabolism. The first transition was also accompanied by the loss of dissimilatory nitrate and sulfate reduction, loss of oxygen-sensitive pyruvate oxidoreductase, which reduces pyruvate to acetyl-CoA, and loss of the Wood–Ljungdahl pathway for anaerobic carbon fixation. The second transition involved gain of a K+ transporter and of the biosynthetic pathway for ectoine, which may function as an osmoprotectant. The third transition was accompanied by the loss of the uvr system for repairing ultraviolet light-induced DNA lesions. We conclude that oxygen availability drove the terrestrial origin of AOA and their expansion to the photic and dark oceans, and that the stressors encountered during these events were partially overcome by gene acquisitions from Euryarchaeota and Bacteria, among other sources.Ren, W., Guo, J., Zeng, F., Wang, T., 2019. Modeling of high-pressure methane adsorption on wet shales. Energy & Fuels 33, 7043-7051. is present in most shale reservoirs and has a negative effect on methane adsorption. A modified Langmuir model was developed to model methane adsorption on wet shales. This model was validated against published adsorption data on wet shales. We also studied the effect of adsorbed water on methane adsorption. The Langmuir pressure increases with increasing water content, which could be explained by the fact that absorbed water molecules weaken the methane-shale interaction and reduce the mobility of adsorbed methane molecules. The maximum methane adsorption capacities of all investigated samples decrease approximately linearly with increasing water content when the water saturation is lower than 70%. The methane adsorption capacities of wet shales are controlled by TOC content, kerogen maturity, and the content of clay minerals, which is due to the fact that adsorbed water molecules have a large impact on the methane adsorption capacities of clay minerals but little effect on that of high maturity kerogen. The hydrophobic fraction of organic matter is a primary control on methane storage by adsorption under reservoir conditions.Renner, G., Sauerbier, P., Schmidt, T.C., Schram, J., 2019. Robust automatic identification of microplastics in environmental samples using FTIR microscopy. Analytical Chemistry 91, 9656-9664. analysis of microplastics is mainly performed using Fourier transformation infrared spectroscopy/microscopy (FTIR/ μFTIR). However, in contrast to most aspects of the analysis process, for example, sampling, sample preparation, and measurement, there is less known about data evaluation. This particularly critical step becomes more and more important if a large number of samples has to be handled. In this context, it is concerning that the commonly used library searching is not suitable to identify microplastics from real environmental samples automatically. Therefore, many spectra have to be rechecked by the operator manually, which is very time-consuming. In this study, a new fully automated robust microplastics identification method is presented that assigns over 98% of microplastics correctly. The main concept of this new method is to detect and numerically describe the individual vibrational bands within an FTIR absorbance spectrum by curve fitting, which leads to a very compact and highly characteristic peak list. This list allows very accurate and robust library searching. The developed approach is based on the already published microplastics identification algorithm (μIDENT) and extends and improves the field of application to μFTIR data with a special focus on relevant broad, overlapped, or complex vibrational bands.Renson, V., Navarro-Castillo, M., Cucina, A., Culleton, B.J., Kennett, D.J., Neff, H., 2019. Origin and diet of inhabitants of the Pacific Coast of Southern Mexico during the Classic Period - Sr, C and N isotopes. Journal of Archaeological Science: Reports 27, 101981. paper presents the results of a multi-proxy analysis of human remains from the Classic Period in the Pacific Coast region of Southern Mexico. The strontium isotopic composition of bone, dentine and enamel samples is combined with C and N isotope determinations on remains from four individuals recovered from burials dated to 595–950 CE. The possible impact of diagenesis, in this context probably related to the use of modern fertilizers, on the results is also evaluated. The combination of Sr, C and N isotope results show that the individuals examined here were likely local people who were consuming maize-based terrestrial food. The discrepancy observed between the strontium isotopic composition of these four individuals and the local strontium signature is best explained by a contribution from sea salt as well as the alkali solution used in the nixtamalization process. This study emphasizes the importance of considering the diet together with the strontium isotopes when attempting to understand migration, especially in coastal environments. It also shows that pre-treatment with acetic acid does not remove all trace of diagenesis.Retelletti Brogi, S., Jung, J.Y., Ha, S.-Y., Hur, J., 2019. Seasonal differences in dissolved organic matter properties and sources in an Arctic fjord: Implications for future conditions. Science of The Total Environment 694, 133740. Arctic Ocean is undergoing drastic changes due to the effects of climate change. Arctic fjords are preferred systems to study these changes as they respond quickly to variations in ocean, land and atmosphere conditions. In this study, we investigated for the first time the seasonal variability of dissolved organic matter (DOM) properties and its origin in an Arctic fjord, which allows for an assessment of the future potential effects of climate change in this environment. We conducted an integrated analysis of the concentrations, optical properties (absorption and fluorescence), and molecular size distributions of DOM in two seasons (October 2017 and April 2018) and in eight to ten stations in Kongsfjorden (Svalbard) along with the related environmental parameters such as chlorophyll-a, inorganic nutrients, particulate organic carbon (POC), temperature, and salinity. Our results showed that, in both seasons, the DOM in the fjord was predominately of autochthonous origin with a seasonally variable terrestrial input. The dissolved organic carbon (DOC) concentrations were consistently higher in October than in April at each station. Fluorescence spectroscopy revealed a marked seasonal variability depending on the DOM fluorophore types and size fractions. In October, humic-like and tryptophan-like substances were dominant whereas in April, tyrosine-like compounds represented, on average, 58% of the DOM fluorescence. This study points out the key role of spring sea ice melting in determining the DOM properties of the fjord in spring.Rettberg, P., Antunes, A., Brucato, J., Cabezas, P., Collins, G., Haddaji, A., Kminek, G., Leuko, S., McKenna-Lawlor, S., Moissl-Eichinger, C., Fellous, J.-L., Olsson-Francis, K., Pearce, D., Rabbow, E., Royle, S., Saunders, M., Sephton, M., Spry, A., Walter, N., Wimmer Schweingruber, R., Treuet, J.-C., 2019. Biological contamination prevention for outer solar system moons of astrobiological interest: What do we need to know? Astrobiology 19, 951-974. ensure that scientific investments in space exploration are not compromised by terrestrial contamination of celestial bodies, special care needs to be taken to preserve planetary conditions for future astrobiological exploration. Significant effort has been made and is being taken to address planetary protection in the context of inner Solar System exploration. In particular for missions to Mars, detailed internationally accepted guidelines have been established. For missions to the icy moons in the outer Solar System, Europa and Enceladus, the planetary protection requirements are so far based on a probabilistic approach and a conservative estimate of poorly known parameters. One objective of the European Commission-funded project, Planetary Protection of Outer Solar System, was to assess the existing planetary protection approach, to identify inherent knowledge gaps, and to recommend scientific investigations necessary to update the requirements for missions to the icy moons.Riva, M., Ehn, M., Li, D., Tomaz, S., Bourgain, F., Perrier, S., George, C., 2019. CI-Orbitrap: An analytical instrument to study atmospheric reactive organic species. Analytical Chemistry 91, 9419-9423. acknowledged as key components in the formation of new particles in the atmosphere, the accurate characterization of gaseous (highly) oxygenated organic compounds remains challenging and requires analytical developments. Earlier studies have successfully used the nitrate ion (NO3–) based chemical ionization (CI) coupled to atmospheric pressure interface time-of-flight mass spectrometry (CI-APi-TOF) for monitoring these compounds. Despite many breakthroughs in recent years, the CI-APi-TOF has many limitations, preventing for instance the unambiguous ion identification of overlapping peaks. To tackle this analytical challenge, we developed a CI interface coupled to an ultrahigh-resolution Orbitrap mass spectrometer (CI-Orbitrap). We show that the CI-Orbitrap has similar sensitivity and selectivity as the CI-APi-TOF, but with over an order of magnitude higher mass resolving power (up to 140?000). Equally importantly, the CI-Orbitrap allows tandem mass spectrometry, providing the possibility for structural elucidation of the highly oxygenated organic molecules (HOM). As a proof of concept, we characterized HOM formed during the ozonolysis of two biogenic compounds (α-pinene and limonene), under different environmental conditions in a flow reactor. The CI-Orbitrap exhibited high sensitivity to both HOM and radical species, while easily separating ions of different elemental composition in cases where the more common TOF applications would not have been able to distinguish all ions. Our tandem mass spectrometry analyses revealed distinct fingerprint spectra for all the studied HOM. Overall, the CI-Orbitrap is an extremely promising instrument, and it provides a much-needed extension to ongoing research on HOM, with potential to impact also many other fields within atmospheric chemistry.Rivera-Barrera, D., Rueda-Chacón, H., Molina V, D., 2019. Prediction of the total acid number (TAN) of Colombian crude oils via ATR–FTIR spectroscopy and chemometric methods. Talanta 206, 120186. as the attack by naphthenic and hydrogen sulfide have caused corrosion problems in the petroleum industry due to they affect the crude oil heating furnaces and distillation towers at temperatures between 220 and 400?°C. The total acid number (TAN) measurement has been used as a test to quantify the acid compounds in crude oils and has shown to be a reliable indicator of their corrosion degree. However, the standard method for the TAN measurement, ASTM D-644, involves long times, environment unfriendly wastes and high costs for each analysis. A more appropriate method for the TAN determination is implemented in this paper, by correlating Fourier transform infrared spectroscopy (FTIR) spectral data of the samples with the standard method measurements using multivariate regression models. In particular, the intensities and frequencies of their mid-infrared attenuated total reflectance (MIR-ATR) spectra (4000-400?cm?1) are used as independent variables of several principal component regression (PCR) and partial least squares regression (PLSR) models. The latter are employed to correlate the spectra with their respective TAN values so as to obtain a suitable prediction model. Twenty-six (26) samples of Colombian crude oils are used for the study with a TAN ranging from 0.1 to 6.8?mg KOH/g crude oil (ASTM D-664). The models are evaluated according to the coefficient of determination (R2), the root mean square error of calibration (RMSEC) and of prediction (RMSEP). The best model is obtained via PLSR using as few as four components (i.e. factors), which attains a calibration R2 of 0.981 and an RMSEC of 0.317?mg KOH/g crude oil, while for prediction it attains an R2 of 0.996 and an RMSEP of 0.160?mg KOH/g crude oil. It is observed that the functional groups COOH, CH3 and CH2 contribute the most to the prediction models. The designed methodology is faster and environmentally friendly since it does not require sample pretreatment and the use of toxic reagents, and of low-cost compared with the standard procedure since FTIR measurements can be easily taken anywhere using a hand-held or portable spectrometer and a laptop.Rodríguez-López, L., Cardenas, R., Parra, O., González-Rodríguez, L., Martin, O., Urrutia, R., 2019. On the quantification of habitability: merging the astrobiological and ecological schools. International Journal of Astrobiology 18, 412-415. this paper, we connect ideas of the astrobiological and ecological schools to quantify habitability. We show how habitability indexes, devised using the astrobiologically inspired Quantitative Habitability Theory (QHT), can be embedded into ecological models of trophic levels. In particular, we address the problem of spatial-temporal scales. It turns out that the versatility of QHT allows to treat spatial and temporal scales typical of ecological studies. As a habitability index, we propose a new version of our Aquatic Primary Habitability, devised by some of us and formerly applied to saltwater ecosystems (both ocean and coastal) and now applied to freshwater. Although the aim of the paper is to outline the methodology rather than realism, initial steps for parameterization are considered for lakes of South-Central Chile.Rogel, E., Hench, K., Hajdu, P., Ingham, H., 2019. The role of compatibility in determining the blending and processing of crude oils, in: Rahimi, P., Ovalles, C., Zhang, Y., Adams, J.J. (Eds.), Chemistry Solutions to Challenges in the Petroleum Industry. American Chemical Society, Washington DC, pp. 201-222. materials precipitating from hydrocarbon systems either in the field or during refining operations are a major concern in the petroleum industry. During refinery operations, the deposition of unwanted materials or fouling on heat transfer equipment induces the loss of thermal efficiency. Carbonaceous materials can also deposit on reactors, downstream vessels, and catalyst surfaces. The financial implications caused by the formation of these deposits are huge. This work summarizes the current state of knowledge on compatibility testing in predicting fouling and minimizing operational and economic consequences. Asphaltene stability, factors that affect such stability, and how to measure it are described in detail using experimental data. The theoretical basis for the successful blending of fluids is discussed as well as recently developed correlations between compatibility parameters and fouling behavior. Several examples of how this technique is applied to different situations encountered on refineries are also presented.Romero-Sarmiento, M.-F., 2019. A quick analytical approach to estimate both free versus sorbed hydrocarbon contents in liquid-rich source rocks. American Association of Petroleum Geologists Bulletin 103, 2031-2043. and sorbed low-to-medium molecular weight thermovaporized hydrocarbons (<C20) are the main organic compounds released at the temperature range corresponding to the Rock-Eval? Shale PlayTMSh0 parameter (100°C–200°C), whereas medium and high molecular weight thermovaporized compounds (< C30) are the predominant components that are thermal released in the temperature range corresponding to the Shale Play Sh1 parameter (200°C–350°C). Now, an analytical methodology is proposed here to predict the quantity of free versus sorbed hydrocarbons still present in any liquid-rich sedimentary rock. The method compares shale play parameters (Sh0 and Sh1) obtained from both whole-rock samples and their corresponding organic matter (OM) concentrates isolated by standard nonoxidizing acid treatments and drying procedures. The hydrocarbon content obtained from whole rock (HCTotal,rock) is mainly considered as the total amount of free liquid hydrocarbons (HCFree) and sorbed liquid hydrocarbons (HCSorbed,OM) still contained in the investigated rock sample.HCTotal rock = FIDsignalrockSh0+Sh1/Massrock x TOCrockThe hydrocarbon content obtained from OM concentrates, however, only reflects the sorbed liquid hydrocarbons.HCSorbed,OM = FIDsignalOMSh0+Sh1/MassOM x TOCOMIn these equations, TOCrock is the total organic carbon of the rock sample; TOCOM corresponds to the TOC content of the OM concentrate sample; Massrock is the initial mass of the rock sample; MassOM is the initial mass of the OM concentrate sample; FIDsignalrockSh0+Sh1 is the flame ionization detection (FID) signal that corresponds to the global surface area under each thermal peak (Sh0 and Sh1) generated by the Rock-Eval FID; FIDsignalOMSh0+Sh1 corresponds to the global surface area under each thermal peak (Sh0 and Sh1) measured by the Rock-Eval FID between 100°C and 350°C after the themovaporization of the OM concentrate sample. Free liquid hydrocarbons are finally calculated as the difference between these last two values (HCFree &equals; HCTotal,rock ? HCSorbed,OM). This paper illustrates the application of this methodology on rock samples derived from the Vaca Muerta Formation (Argentina). Along the selected vertical profile, the lower rock interval contains approximately 60% of sorbed liquid hydrocarbons, whereas the upper sample contains more than 90% free liquid hydrocarbons. The parameters FreeHCSh0 and FreeHCSh0+Sh1 could be used to identify potential producible free liquid hydrocarbons intervals in early exploration campaigns.Rossi, V., McNamara, M.E., Webb, S.M., Ito, S., Wakamatsu, K., 2019. Tissue-specific geometry and chemistry of modern and fossilized melanosomes reveal internal anatomy of extinct vertebrates. Proceedings of the National Academy of Sciences, 201820285.: Recent reports of nonintegumentary melanosomes in fossils hint at functions for melanin beyond color production, but the biology and evolution of internal melanins are poorly understood. Our results show that internal melanosomes are widespread in diverse fossil and modern vertebrates and have tissue-specific geometries and metal chemistries. Tissue-specific chemical signatures can persist in fossils despite some diagenetic overprint, allowing the reconstruction of internal soft-tissue anatomy in fossil vertebrates, and suggest that links between melanin and metal regulation have deep evolutionary origins in vertebrates.Abstract: Recent discoveries of nonintegumentary melanosomes in extant and fossil amphibians offer potential insights into the physiological functions of melanin not directly related to color production, but the phylogenetic distribution and evolutionary history of these internal melanosomes has not been characterized systematically. Here, we present a holistic method to discriminate among melanized tissues by analyzing the anatomical distribution, morphology, and chemistry of melanosomes in various tissues in a phylogenetically broad sample of extant and fossil vertebrates. Our results show that internal melanosomes in all extant vertebrates analyzed have tissue-specific geometries and elemental signatures. Similar distinct populations of preserved melanosomes in phylogenetically diverse vertebrate fossils often map onto specific anatomical features. This approach also reveals the presence of various melanosome-rich internal tissues in fossils, providing a mechanism for the interpretation of the internal anatomy of ancient vertebrates. Collectively, these data indicate that vertebrate melanins share fundamental physiological roles in homeostasis via the scavenging and sequestering of metals and suggest that intimate links between melanin and metal metabolism in vertebrates have deep evolutionary origins.Rowe, L., Peller, J., Mammoser, C., Davidson, K., Gunter, A., Brown, B., Dhar, S., 2019. Stability of non-proteinogenic amino acids to UV and gamma irradiation. International Journal of Astrobiology 18, 426-435 tps://10.1017/S1473550418000381Almost all living organisms on Earth utilize the same 20 amino acids to build their millions of different proteins, even though there are hundreds of amino acids naturally occurring on Earth. Although it is likely that both the prebiotic and the current environment of Earth shaped the selection of these 20 proteinogenic amino acids, environmental conditions on extraterrestrial planets and moons are known to be quite different than those on Earth. In particular, the surfaces of planets and moons such as Mars, Europa and Enceladus have a much greater flux of UV and gamma radiation impacting their surface than that of Earth. Thus, if life were to have evolved extraterrestrially, a different lexicon of amino acids may have been selected due to different environmental pressures, such as higher radiation exposure. One fundamental property an amino acid must have in order to be of use to the evolution of life is relative stability. Therefore, we studied the stability of three different proteinogenic amino acids (tyrosine, phenylalanine and tryptophan) as compared with 20 non-proteinogenic amino acids that were structurally similar to the aromatic proteinogenic amino acids, following ultraviolet (UV) light (254, 302, or 365 nm) and gamma-ray irradiation. The degree of degradation of the amino acids was quantified using an ultra-high performance liquid chromatography-mass spectrometer (UPLC-MS). The result showed that many non-proteinogenic amino acids had either equal or increased stability to certain radiation wavelengths as compared with their proteinogenic counterparts, with fluorinated phenylalanine and tryptophan derivatives, in particular, exhibiting enhanced stability as compared with proteinogenic phenylalanine and tryptophan amino acids following gamma and select UV irradiation.Ruan, H., Qin, Y., Heyne, J., Gieleciak, R., Feng, M., Yang, B., 2019. Chemical compositions and properties of lignin-based jet fuel range hydrocarbons. Fuel 256, 115947. aviation fuels remain the only near, mid, and likely long term solution for lowering the carbon emissions of commercial and military aviation. Determination of sustainable aviation fuel’s chemical compositions and prediction of their properties is a critical first step for further research and development leading to the final certification process. Our analytical results showed that the lignin-based jet fuel (US patent 9,518,076 B2) consists of mainly paraffinic hydrocarbon species. They can be further classified into several classes, including n-paraffins, iso-paraffins, mono-, di-, and tri-cycloparaffins of which the majority contains carbon numbers in the range of 7–20. The very high concentration of polycycloparaffins along with the relatively low content of monocycloparaffins contribute to the high boiling point of the sample. Reducing the boiling point will require cracking and further hydrotreating of the lignin-based jet fuel range hydrocarbons to increase monocycloparaffins ratio close to the coal-based jet fuel compositions (e.g., JP-900). Also, this lignin-based jet fuel contains very low aromatics concentration which illuminates favorable energy content, energy density, possible low emissions, and very high-performance characteristics might meet drop-in specifications.Ruan, Z., Sun, Q., Zhang, Y., Jiang, J.-D., 2019. Oleisolibacter albus gen. nov., sp. nov., isolated from an oil-contaminated soil. International Journal of Systematic and Evolutionary Microbiology 69, 2220-2225. Gram-stain-negative, aerobic, flagellated, rod-shaped bacterium, designated strain NAU-10T, was isolated from an oil-contaminated soil collected in PR China. Strain NAU-10T could grow at 10–42?°C (optimum, 30?°C), pH 5.0–9.0 (pH 7.0) and in the presence of 0–2.5?% (w/v) NaCl (0.5?% in Luria–Bertani broth). The major fatty acids were C18?:?1 ? ω 7c (38.6?%), C17?:?1 ? ω 6c (9.8?%), C18?:?1 2-OH (9.1?%), summed feature 3 (8.7?%), C16?:?0 3-OH (7.2?%) and C16?:?0 (6.7?%). The major respiratory quinones were Q9 and Q10. The total polar lipids were lipid, aminolipid, phospholipid, phosphatidylglycerol and phosphatidylethanolamine. Strain NAU-10T shared the highest 16S rRNA gene sequence similarities with Rhodocista pekingensis 3-pT (95.9?%), Niveispirillum cyanobacteriorum TH16T (95.3?%) and Niveispirillum fermenti CC-LY736T (95.3?%), and constituted a sub-cluster within the family Rhodospirillacea . The DNA G+C?content of strain NAU-10T was 68.2?mol% based on its draft genome sequence. Genome annotation of strain NAU-10T predicted the presence of 4309 genes, of which 4237 are coding proteins and 72 are RNA genes. Based on its phenotypic and chemotaxonomic characteristics, as well as the analysis of the 16S rRNA gene sequences, it was concluded that strain NAU-10T represents a novel genus, for which the name Oleisolibacter gen. nov., is proposed. The type species of this genus is Oleisolibacter albus with the type strain NAU-10T (=KCTC 62417T=CCTCC AB 2018015T). The GenBank/EMBL/DDBJ accession numbers for the draft genome sequence and 16S rRNA gene sequence of strain NAU-10T are QGNJ00000000 and MH244128, respectively.Rychlik, M., Kanawati, B., Roullier-Gall, C., Hemmler, D., Liu, Y., Alexandre, H., Gougeon, R.D., Gmelch, L., Gotthardt, M., Schmitt-Kopplin, P., 2019. Chapter 21 - Foodomics assessed by Fourier transform mass spectrometry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 651-677. its ultrahigh resolution power and excellent mass accuracy, Fourier transform ion cyclotron resonance mass spectrometry is the perfct tool to analyze the “foodome” as the set of all polar small molecular compounds present in an investigated food sample. We present here selected applications of this technique in unraveling the metabolome in complex foods (thermally affected, fermentation products, distillates) such exemplified with Maillard reaction products or with wines and spirits. Technical considerations for high resolution mass analyzers are provided from a practical point of view. Moreover, aspects of food safety and nutritional quality are covered by presenting applications to the mycobolome of Alternaria fungi and vitamins of the folate group, respectively.Safi, E., Telling, J., Parnell, J., Chojnacki, M., Patel, M.R., Realff, J., Blamey, N.J.F., Payler, S., Cockell, C.S., Davies, L., Boothroyd, I.M., Worrall, F., Wadham, J.L., 2019. Aeolian abrasion of rocks as a mechanism to produce methane in the Martian atmosphere. Scientific Reports 9, 8229. changes in methane background levels and methane spikes have been detected in situ a metre above the Martian surface, and larger methane plumes detected via ground-based remote sensing, however their origin have not yet been adequately explained. Proposed methane sources include the UV irradiation of meteoritic-derived organic matter, hydrothermal reactions with olivine, organic breakdown via meteoroid impact, release from gas hydrates, biological production, or the release of methane from fluid inclusions in basalt during aeolian erosion. Here we quantify for the first time the potential importance of aeolian abrasion as a mechanism for releasing trapped methane from within rocks, by coupling estimates of present day surface wind abrasion with the methane contents of a variety of Martian meteorites, analogue terrestrial basalts and analogue terrestrial sedimentary rocks. We demonstrate that the abrasion of basalt under present day Martian rates of aeolian erosion is highly unlikely to produce detectable changes in methane concentrations in the atmosphere. We further show that, although there is a greater potential for methane production from the aeolian abrasion of certain sedimentary rocks, to produce the magnitude of methane concentrations analysed by the Curiosity rover they would have to contain methane in similar concentrations as economic reserved of biogenic/thermogenic deposits on Earth. Therefore we suggest that aeolian abrasion is an unlikely origin of the methane detected in the Martian atmosphere, and that other methane sources are required.Saifuddin, M., Bhatnagar, J.M., Segrè, D., Finzi, A.C., 2019. Microbial carbon use efficiency predicted from genome-scale metabolic models. Nature Communications 10, 3568. by soil bacteria and fungi is one of the largest fluxes of carbon (C) from the land surface. Although this flux is a direct product of microbial metabolism, controls over metabolism and their responses to global change are a major uncertainty in the global C cycle. Here, we explore an in silico approach to predict bacterial C-use efficiency (CUE) for over 200 species using genome-specific constraint-based metabolic modeling. We find that potential CUE averages 0.62?±?0.17 with a range of 0.22 to 0.98 across taxa and phylogenetic structuring at the subphylum levels. Potential CUE is negatively correlated with genome size, while taxa with larger genomes are able to access a wider variety of C substrates. Incorporating the range of CUE values reported here into a next-generation model of soil biogeochemistry suggests that these differences in physiology across microbial taxa can feed back on soil-C cycling.Saleem, A., Bell, M.A., Kimpe, L.E., Korosi, J.B., Arnason, J.T., Blais, J.M., 2019. Identifying novel treeline biomarkers in lake sediments using an untargeted screening approach. Science of The Total Environment 694, 133684. uses sedimentary biomarkers as proxies to reconstruct long-term changes in environmental conditions from lake sediment cores. This work describes an untargeted metabolomics-based approach and uniquely applies it to the field of paleolimnology to identify novel sediment biomarkers to track long-term patterns in treeline dynamics. We identified new potential biomarkers across the Canadian northern Arctic, non-alpine, treeline using high-resolution accurate mass spectrometry, and pattern recognition analysis. This method was applied to 120 sediment core extracts from 14 boreal, 25 forest-tundra, and 21 tundra lakes to assess long-term fluctuations in treeline position. High resolution accurate mass spectrometry resolved many compounds from complex mixtures with low mass accuracy errors. This generated a large dataset that required metabolomics styled statistical analyses to identify potential biomarkers. In total, 29 potential biomarkers discriminated between boreal and tundra lakes. Tetrapyrrole-type phorbides and squalene derivatives dominated in boreal regions, while biohopane-type lipids were in the tundra regions. Tetrapyrroles were in both surface and subsurface sediments of boreal lakes indicating these compounds can survive long-term burial in sediments. At the ecozone level, tetrapyrroles were more abundant in boreal Taiga Shield, and Taiga Plains. Boreal plant extracts belonging to Pinaceae and Ericaceae also contained tetrapyrroles. Squalene derivatives demonstrated long-term preservation, but wider distribution than tetrapyrroles. Hopanoids were present in tundra and forest-tundra lake regions, specifically the Low Arctic and Taiga Shield, and were absent in all boreal lake sediments. Herein, we describe a method that can systematically identify new paleolimnological biomarkers. Novel biomarkers would facilitate multi-proxy paleolimnological studies and potentially lead to more accurate paleoenvironmental reconstructions.Salter, T.L., Wootton, L., Brown, W.A., 2019. Thermal processing and interactions of ethyl formate in model astrophysical ices containing water and ethanol. ACS Earth and Space Chemistry 3, 1524-1536. desorption (TPD) and reflection absorption infrared spectroscopy (RAIRS) have been used to investigate the interactions between ethyl formate and water and ethyl formate and ethanol in model astrophysical ices adsorbed on a graphitic model grain surface. Experiments show that the ethyl formate forms hydrogen bonds to both water and ethanol via the oxygen lone pairs. This leads to the observation of shifts in the vibrational wavenumber of the C═O and C—O—C modes of ethyl formate, which can potentially be used to identify the environment of this complex organic molecule in astronomical observations. TPD data show that the interaction of ethyl formate with water is stronger than that with ethanol with an additional species being observed in the TPD spectrum corresponding to the desorption of ethyl formate directly bonded to the water ice surface. The desorption energy of ethyl formate adsorbed on water ice was found to be 48.5 kJ mol–1, compared to 43.2 kJ mol–1 for pure ethyl formate monolayers. Ethyl formate also traps in water ice and undergoes volcano desorption at the water amorphous to crystalline phase transition temperature. In contrast to the water, ethanol has very little effect on the desorption of ethyl formate with the two species behaving independently even in a codeposited ice.Salzmann, C.G., 2019. Water and methane stay together at extreme pressures. Proceedings of the National Academy of Sciences 116, 16164-16166. Large lakes of liquid methane nestle between mountain ranges of solid water ice in the polar regions of Jupiter’s moon Titan (1, 2). This strange world illustrates in a quite dramatic fashion that the isoelectronic CH4 and H2O molecules display profoundly different physical properties including a 182 °C difference in their melting points at ambient pressure. Unlike methane, water molecules form strong hydrogen bonds with up to 4 neighbors, which explains the high melting point of ice compared to that of solid methane. Rearrangements of those hydrogen bonds, which take place as temperature and pressure are varied, give rise to a large family of complex network structures beyond the “ordinary” hexagonal form of ice, ice Ih (3). However, the structural diversity of H2O does not end with the pure phases of ice. Water molecules can form cages around hydrophobic species such as methane to form clathrate hydrates (4, 5). These important inclusion compounds have been suggested as model systems for studying hydrophobic interactions (4), and they are also relevant for a wide range of industrial, geological, atmospheric, and cosmological settings (6, 7). Methane clathrate hydrate (MH) is one of the most thoroughly studied materials in this context with 3 distinct structural forms identified so far experimentally at different pressures (5). Schaack et al. (8) now report in PNAS the existence of a fourth hydrate of methane (MH-IV) that forms above ～40 GPa and remains stable up to at least 150 GPa. Intriguingly, the water network of MH-IV takes on a very familiar form, that of ice Ih, but it is densely packed with methane molecules at a 2:1 H2O:CH4 ratio.Sandoval, G.A.B., Thompson, R.L., Sad, C.M.S., Teixeira, A., Soares, E.J., 2019. Influence of adding asphaltenes and gas condensate on CO2 hydrate formation in water–CO2–oil systems. Energy & Fuels 33, 7138-7146. hydrate formation is a huge flow assurance problem in offshore production of oil and gas. However, there have been some reported cases in oil-dominated systems where the hydrates do not form, even though the high-pressure and low-temperature environments induce favorable thermodynamic conditions. The reason for this unexpected result seems to be related to the presence of natural chemical compounds in crude oils that prevent the hydrates’ nucleation and agglomeration. Because the number of works in this specific topic are scarce, in the present work, we study the role played by saturates (hydrocarbon compounds) and asphaltenes (heterocyclic compounds), which are commonly present in crude oil, on hydrates that are formed from CO2 molecules in water–CO2–oil systems. Our tests were carried out in an assembly composed of a rotational rheometer with a magnetic pressure cell, which was connected to a high-pressure system. Our main results are displayed in terms of viscosity as a function of time at constant shear rate, pressure, and temperature. In this kind of experiment, hydrate formation is associated with a jump of viscosity. Our data suggest that asphaltenes retard the CO2 hydrate nucleation and formation in the crude oils studied in this work.Santak, P., Conduit, G., 2019. Predicting physical properties of alkanes with neural networks. Fluid Phase Equilibria 501, 112259. train artificial neural networks to predict the physical properties of linear, single branched, and double branched alkanes. These neural networks can be trained from fragmented data, which enables us to use physical property information as inputs and exploit property-property correlations to improve the quality of our predictions. We characterize every alkane uniquely using a set of five chemical descriptors. We establish correlations between branching and the boiling point, heat capacity, and vapor pressure as a function of temperature. We establish how the symmetry affects the melting point and identify erroneous data entries in the flash point of linear alkanes. Finally, we exploit the temperature and pressure dependence of shear viscosity and density in order to model the kinematic viscosity of linear alkanes. The accuracy of the neural network models compares favorably to the accuracy of several physico-chemical/thermodynamic methods.Santisi, S., Catalfamo, M., Bonsignore, M., Gentile, G., Di Salvo, E., Genovese, M., Mahjoubi, M., Cherif, A., Mancini, G., Hassanshahian, M., Pioggia, G., Cappello, S., 2019. Biodegradation ability of two selected microbial autochthonous consortia from a chronically polluted marine coastal area (Priolo Gargallo, Italy). Journal of Applied Microbiology 127, 618-629. aims of this study were: (i) the characterization of the structure of the indigenous microbial community associated with the sediments under study; (ii) the isolation and characterization of microbial consortia able to degrade the aged hydrocarbons contaminating the sediments, and (iii) the assessment of related biodegradation capability of selected consortia. Samples of surface sediments were collected in Priolo Gargallo harbour (Sicily, Italy). The samples were analysed for physical, chemical (GC‐FID analysis) and microbiological characteristics (qualitative (16S rDNA clone library) and quantitative (DAPI, CFU and MPN count) analysis). The sediment samples were used for the selection of two microbial consortia (indicated as PSO and PSM) with high biodegradation capacity for crude oil (～95%) and PAHs (～63%) respectively. Genetic analysis showed that Alcanivorax and Cycloclasticus were the dominant genera in both the PSO and PSM consortia. Oil‐polluted environments naturally develop an elevated biorecovery potential. The presence of a highly specialized microbial flora (adapted to support the contamination) and their stimulation through favourable induced conditions provides a promising recovery strategy. The chance to identify and select indigenous bacteria and/or consortia with a high biodegradation capacity is fundamental for the development and optimization of bioaugmentation strategies especially for those concerning in situ applications. Saputra, I.W.R., Park, K.H., Zhang, F., Adel, I.A., Schechter, D.S., 2019. Surfactant-assisted spontaneous imbibition to improve oil recovery on the Eagle Ford and Wolfcamp shale oil reservoir: Laboratory to field analysis. Energy & Fuels 33, 6904-6920. resources being left behind at the end of the short production life of an unconventional liquid-rich reservoir (ULR) well has inspired many to investigate methods to improve the recovery. One eminent method is through the addition of surfactant during the completion stage of the well. Through numerous published laboratory studies, it can be concluded that this process possesses a promising potential in improving overall well productivity. Several field-scale results gathered from public data sources also confirmed the laboratory-scale study by correlating the effect of surfactants to the improvement of the estimated ultimate recovery (EUR). However, the absence of independency on those field-scale results often casts doubt on the actual efficacy of the method. The lack of field-scale information in the realm of scientific publications contributes to the limited understanding of surfactant application. This study is to fulfill the obvious need of field-scale studies on the application of surfactant by surfactant-assisted spontaneous imbibition (SASI) during completion of wells in the ULR. Numerical-based upscaling through modification of capillary pressure and relative permeability of the laboratory-scale experimental results provides a view on the effectiveness of this method on the field scale. Comparison is performed between the initial oil production rate, cumulative oil, and cumulative water production. A complete set of the laboratory-scale experimental studies is also included and consists of interfacial tension, contact angle, zeta potential, adsorption isotherm, and CT-assisted spontaneous imbibition. CT-scan technology is incorporated as well in the construction of a core-scale numerical grid model to model the heterogeneity of the shale core plug sample. In the end, sensitivity analysis is also executed to analyze the effect of different reservoir properties and SASI-related completion parameters on the efficiency of the method. There are four main takeaways of this comprehensive study. First, a complete and robust workflow on investigating SASI performance is compiled and tested. This workflow consists of a laboratory-scale experimental study as well as a numerical-based field-scale investigation and can be applied to different shale reservoirs as well as different surfactants. Second, three different surfactants are tested in this study with significant well production improvement observed, thus confirming the increment of production observed in the laboratory-scale study. These results are also compared to other lab-scale experiments conducted with different ULR samples to verify and strengthen the effectiveness of SASI. Third, sensitivity analysis shows that SASI improves well productivity for a variety of fracture and matrix properties. We observed a range of matrix and fracture properties where SASI performs optimally, and last, an independent field data study is provided. This actual case study is done carefully to isolate the effect of SASI on the well production. An agreement on the range of production improvement by SASI between the field data analysis and the numerical field-scale model is also observed.Saralov, A.I., 2019. Adaptivity of archaeal and bacterial extremophiles. Microbiology 88, 379-401. prokaryotes, inhabitants of hot, cold, acidic, alkaline, saline, and deep-sea ecosystems, are classified as mono- and polyextremophilic or extreme-tolerant. Under conditions of heating, acidification, or salinization, thermophilic saprotrophic archaea are capable of maintaining endogenous homeostasis and high growth rates by biosynthesis of heat shock enzymes (proteins ofgeneral stress response), C40C40 membrane tetraesters with different numbers of cyclopentane rings, trehalose, and other hyperosmolytes. Small size of reduced genomes (0.5–3.0 Mb) of archaeal thermoacidophiles and hyperthermophiles was shown to reflect their adaptability mainly due to phenotypic changes and probably to have a reduced potential for speciation. In contrast, psychrophilic heterotrophic bacteria respond to sublethal temperature decrease by increased conformational flexibility of the macromolecules and elevated content of unsaturated fatty acids in the composition of their membrane lipids, synthesize membrane-associated glycoproteins, anti-freeze proteins, a group of general stress response proteins, specific and inducible cold shock proteins, which increase the growth rate. When slowing down and stopping the growth, psychrophiles switch on the processes of secondary metabolism and sharply increasing the biosynthesis of adaptogenic exopolysaccharides. Thus, they ameliorate the direct effects of salinity and hydrostatic pressure on viable cells, block the viral attack, and affect the microstructure and physicochemical properties of ice. Marine psychrophilic and piezopsychrophilic bacteria havelarger genomes of 2.6–6.4 Mb, which reflects their adaptability due to genotypic changes and an increased potential for speciation.Savage, H.M., Polissar, P.J., 2019. Biomarker thermal maturity reveals localized temperature rise from paleoseismic slip along the Punchbowl Fault, CA, USA. Geochemistry, Geophysics, Geosystems 20, 3201-3215.: The Punchbowl Fault, California, USA, is an example of a simple fault zone that has a relatively narrow fault core with further slip localization to principal slip zones. We sampled the principal slip zone, fault core, and wall rocks and conducted hydrous pyrolysis experiments to analyze biomarker thermal maturity within the Punchbowl Fault. Using biomarker maturity as a proxy for temperature rise, we show that the existing principal slip zone experienced greater temperature rise than the surrounding fault core and wall rock, and therefore, we infer that earthquake slip localized along this layer. Furthermore, evidence of slight thermal maturity within the ultracataclasite suggests that the fault core is made up at least in part of reworked former principal slip zones. Using a wide range of possible layer thicknesses, we find that the maximum temperature range during a single earthquake could have varied from ~460 to 1,060 °C at 1‐m/s slip velocity. However, not all samples from within the principal slip zone show a temperature rise, indicating that layer thickness, slip, or shear stress varied during slip. Our temperature estimate also allows us to constrain the frictional energy dissipated during the earthquake to 2.2–25 MJ/m2. Our study demonstrates that localized slip structures can be directly linked to seismicity and that small changes in earthquake or fault parameters can lead to changes in temperature (and likely fault strength) at small scales.Plain Language Summary: Faults are complicated structures, and it would be useful to be able to map which parts of faults have slipped during earthquakes rather than at slower rates. It has been hypothesized that earthquakes occur along narrow structures within fault zones, but lab experiments at slower slip rates can also occur along narrow structures. Because faults heat up during earthquakes, we can look for geologic evidence of high temperatures within a fault to map where within the fault earthquake slip occurred. Here we map past earthquakes in the Punchbowl Fault, CA, USA, an ancient strand of the San Andreas Fault. We show that earthquakes occurred along small structures within the fault zone as had been previously hypothesized and that parts of the fault zone are made up of older, recycled small structures. Furthermore, we estimate how hot the fault might have gotten during an earthquake, which helps constrain the physics and chemistry of fault zone rocks during earthquake slip.Savareear, B., Escobar-Arnanz, J., Brokl, M., Saxton, M.J., Wright, C., Liu, C., Focant, J.-F., 2019. Non-targeted analysis of the particulate phase of heated tobacco product aerosol and cigarette mainstream tobacco smoke by thermal desorption comprehensive two-dimensional gas chromatography with dual flame ionisation and mass spectrometric detection. Journal of Chromatography A 1603, 327-337. analytical methodology based on thermal desorption and comprehensive two-dimensional gas chromatography with dual time-of-flight mass spectrometry and flame ionization detection (TD-GC?×?GC-TOFMS/FID) has been developed for non-target analysis of volatile organic compounds (VOCs). The technique was optimised for the measurement of the VOC content of the particulate phase (PP) fraction of aerosols produced by a tobacco heating product (THP1.0) and 3R4F mainstream tobacco smoke (MTS). The method involves sampling the PP fraction on quartz wool packed in a sorbent tube directly connected to machine-puffing, followed by a dilution through a TD recollection procedure over Tenax/Sulficarb sorbent before TD-GC?×?GC-TOFMS/FID analysis. The comparison of the VOC content of the PP fraction of aerosols produced by THP1.0 and MTS highlighted the compositional difference between tobacco combustion (592 peaks) and tobacco heating process (160 peaks). Mass spectrometric signals were used for qualitative analyses based on linear retention indices, mass spectral matches, and GC?×?GC structured chromatograms, which collectively identified up to 90% of analytes detected in PP samples. FID signals were used for semi-quantitative analyses based on a chemical class external calibration method. The global chemical composition of PP samples showed that hydrocarbons, oxygenated, and nitrogen-containing compounds were fewer in number and much less abundant in THP1.0?PP. Overall, 93 compounds were common to the two sample types. Excepted for a few highly volatile compounds (mainly furan family) as well as glycerine and its acetate, analyte concentrations were higher in MTS PP.Schaack, S., Ranieri, U., Depondt, P., Gaal, R., Kuhs, W.F., Gillet, P., Finocchi, F., Bove, L.E., 2019. Observation of methane filled hexagonal ice stable up to 150 GPa. Proceedings of the National Academy of Sciences 116, 16204-16209.: Gas clathrates in which water cages enclose the guest gas molecules naturally form on our planet, for instance on ocean floors. Related methane hydrates are also expected to be present under very high pressures (10 to 200 GPa) in giant planetary interiors such as Uranus or Neptune. However, the stability of such structures at these pressures is currently debated. Joint Raman spectroscopy and ab initio simulations show the stability of a high-pressure methane hydrate phase up to at least 150 GPa, the highest pressure explored to date for such compounds. The structure of this phase and the complex transition mechanism from the known MH-III phase are detailed and shown to be in accordance with all known experimental observations.Abstract: Gas hydrates consist of hydrogen-bonded water frameworks enclosing guest gas molecules and have been the focus of intense research for almost 40 y, both for their fundamental role in the understanding of hydrophobic interactions and for gas storage and energy-related applications. The stable structure of methane hydrate above 2 GPa, where CH4 molecules are located within H2O or D2O channels, is referred to as methane hydrate III (MH-III). The stability limit of MH-III and the existence of a new high-pressure phase above 40 to 50 GPa, although recently conjectured, remain unsolved to date. We report evidence for a further high-pressure, room-temperature phase of the CH4–D2O hydrate, based on Raman spectroscopy in diamond anvil cell and ab initio molecular dynamics simulations including nuclear quantum effects. Our results reveal that a methane hydrate IV (MH-IV) structure, where the D2O network is isomorphic with ice Ih, forms at ～40 GPa and remains stable up to 150 GPa at least. Our proposed MH-IV structure is fully consistent with previous unresolved X-ray diffraction patterns at 55 GPa [T. Tanaka et al., J. Chem. Phys. 139, 104701 (2013)]. The MH-III → MH-IV transition mechanism, as suggested by the simulations, is complex. The MH-IV structure, where methane molecules intercalate the tetrahedral network of hexagonal ice, represents the highest-pressure gas hydrate known up to now. Repulsive interactions between methane and water dominate at the very high pressure probed here and the tetrahedral topology outperforms other possible arrangements in terms of space filling.Schaeffer, P., Bailly, L., Motsch, E., Adam, P., 2019. The effects of diagenetic aromatization on the carbon and hydrogen isotopic composition of higher plant di- and triterpenoids: Evidence from buried wood. Organic Geochemistry 136, 103889. widely distributed aromatic di- and triterpenoids from higher plants occurring in sediments are formed by diagenetic microbial processes affecting their precursor plant lipids. These compounds and their stable isotopic composition (δ13C and δ2H) have the potential to be used for palaeoenvironmental and palaeoclimatic studies. In the present study, the isotopic composition of di- and triterpenoids aromatized to different extents has been measured to specifically examine the isotopic effects associated with the aromatization reaction. To overcome the possibility of multiple higher plant sources, as is generally the case with sedimentary lipids, the δ13C and δ2H values of aromatized di- and triterpenoids from lipid extracts recovered from conifer and angiosperm buried wood have been determined, allowing an unambiguous substrate/product relationship along the aromatization pathway to be assured. The results show that the δ13C compositions of both di- and triterpenes do not seem to be significantly affected by progressive aromatization, whereas the situation is different for δ2H values. In the case of diterpenoids related to abietic acid, a significant increase of the δ2H values by up to 86‰ with ongoing aromatization was measured. This is in contrast to what is expected for dehydrogenated compounds which should be globally more 2H-depleted than their precursor molecules (e.g., biosynthesized unsaturated fatty acids vs. their saturated precursors). This 2H enrichment of aromatized diterpenoids could indicate that they represent only minor residual intermediates, the majority having been further degraded by processes favoring the degradation of the 1H-containing substrates and having a moderately pronounced 12C/13C selectivity. With triterpenoids, preservation of the δ2H values was observed whatever the nature and extent of the aromatization process considered, which may be related to enzymatic reactions showing a limited influence on the hydrogen stable isotopic composition of the aromatized compounds.Schwartz, B., Huffman, K., Thornton, D., Elsworth, D., 2019. The effects of mineral distribution, pore geometry, and pore density on permeability evolution in gas shales. Fuel 257, 116005. explored the ensemble effects of pore density, pore geometry, and pore stiffness on the permeability evolution of an ellipsoidal pore under both applied uniaxial stress and relative pore pressure change. We found that rocks undergoing identical compressional strain and pore pressure can undergo significantly different magnitudes of pore closure or dilation based on the concomitant influence of these three variables. This is especially important in gas shales, where nano-porosity is challenging to characterize and heterogeneity at all scales has led to disparate permeability responses in both the field and laboratory. Simulations were carried out using a finite element solver, a method that allowed each variable to be studied in isolation and concomitantly. We found that the aspect ratio is the most sensitive parameter influencing pore compressibility. The pore density becomes important when external stress is applied, but it has no significant effect when pore pressure is varied in the absence of external stress. To capture the effects of mineral precipitation and transformation in pore walls, we simulated mismatches between the mineral stiffness of the pore and the surrounding matrix. We determined that for a given strain, mineralogically soft pores (soft relative to the bulk material) experience higher increase in permeability than pores that are mineralogically stiff relative to the surrounding matrix. While soft pores experience greater closure than stiff pores for a given applied stress, they also experience a greater amount of dilation when pore pressure increases.Schweitzer, M.H., Schroeter, E.R., Cleland, T.P., Zheng, W., 2019. Paleoproteomics of Mesozoic dinosaurs and other Mesozoic fossils. PROTEOMICS 19, 1800251. studies have contributed greatly to our understanding of evolutionary processes that act upon virtually every aspect of living organisms. However, these studies are limited with regard to extinct organisms, particularly those from the Mesozoic because fossils pose unique challenges to molecular workflows, and because prevailing wisdom suggests no endogenous molecular components can persist into deep time. Here, the power and potential of a molecular approach to Mesozoic fossils is discussed. Molecular methods that have been applied to Mesozoic fossils?including iconic, non-avian dinosaurs? and the challenges inherent in such analyses, are compared and evaluated. Taphonomic processes resulting in the transition of living organisms from the biosphere into the fossil record are reviewed, and the possible effects of taphonomic alteration on downstream analyses that can be problematic for very old material (e.g., molecular modifications, limitations of on comparative databases) are addressed. Molecular studies applied to ancient remains are placed in historical context, and past and current studies are evaluated with respect to producing phylogenetically and/or evolutionarily significant data. Finally, some criteria for assessing the presence of endogenous biomolecules in very ancient fossil remains are suggested as a starting framework for such studies.Scribano, V., Simakov, S.K., Finocchiaro, C., Correale, A., Scirè, S., 2019. Pyrite and organic compounds coexisting in intrusive mafic xenoliths (Hyblean Plateau, Sicily): Implications for subsurface abiogenesis. Origins of Life and Evolution of Biospheres 49, 19-47. and organic matter closely coexist in some hydrothermally-altered gabbroic xenoliths from the Hyblean Plateau, Sicily. The representative sample consists of plagioclase, Fe-oxides, clinopyroxene, pyrite and minor amounts of many other minerals. Plagioclase displays incipient albitization, clinopyroxene is deeply corroded. Pyrite grains are widely replaced by spongy-textured magnetite, which locally hosts Ca-(and Fe-)sulfate micrograins and blebs of condensed organic matter. Whole-rock trace element distribution evidences that incompatible elements, particularly the fluid-mobile Ba, U and Pb, are significantly enriched with respect to N-MORB values. The mineralogical and geochemical characteristics of the sample, and its U-Pb zircon age of 216.9?±?6.7 MA, conform to the xenolith-based viewpoint that the unexposed Hyblean basement is a relict of the Ionian Tethys lithospheric domain, mostly consisting of abyssal-type serpentinized peridotites with small gabbroic intrusions. Circulating hydrothermal fluids there favored the formation of hydrocarbons trough Fischer-Tropsch-type organic synthesis, giving also rise to sulfidization episodes. Subsequent variations in temperature and redox conditions of the system induced partial de-sulfidization, Fe-oxides precipitation and sulfate-forming reactions, also promoting poly-condensation and aromatization of the already-formed hydrocarbons. Here we show organic matter adhering to a crystal face of a microscopic pyrite grain. Pyrite surfaces, as abiotic analogues of enzymes, can adsorb and concentrate organic molecules, also acting as catalysts for a broad range of proto-biochemical reactions. The present data therefore may support established abiogenesis models suggesting that pyrite surfaces carried out primitive metabolic cycles in suitable environments of the early Earth, such as endolithic recesses in mafic rocks permeated by hydrothermal fluids.Sempéré, R., Va?tilingom, M., Charrière, B., Kawamura, K., Panagiotopoulos, C., 2019. Dicarboxylic and oxocarboxylic acids in the Arctic coastal ocean (Beaufort Sea-Mackenzie margin). Global Biogeochemical Cycles 33, 927-940. distribution of bifunctional carboxylic acids (BCAs) is largely reported as primary or secondary organic aerosols. However, sparse studies describe the distribution of these organic compounds in fluvial and marine environments. In the context of a global warming, we present the first results of a study of the distribution of BCAs in a surface Arctic coastal area near the mouth of the Mackenzie River. These results showed that the Beaufort Sea is an area with elevated BCA content among which glyoxylic acid is predominant, in contrast to low concentrations and predominance of oxalic acid in aerosols reported elsewhere. The carbon fraction of BCAs represents 1.8% to 4.5% of dissolved organic carbon pool in Arctic Ocean. This study reinforces the hypothesis that aquatic biological processes govern the molecular distribution of BCA in marine/river waters, whereas photochemical oxidation reactions regulate their molecular distribution in rain and aerosols. Our results indicate that the Mackenzie River is an important source of BCAs in the Arctic Ocean during July–October period, with a first estimate of 35 × 103 tons of BCAs including 12 × 103 tons of diacids and 23 × 103 tons of oxoacids.Sepúlveda, J., Alegret, L., Thomas, E., Haddad, E., Cao, C., Summons, R.E., 2019. Stable isotope constraints on marine productivity across the Cretaceous-Paleogene mass extinction. Paleoceanography and Paleoclimatology 34, 1195-1217.: The effects of the Cretaceous‐Paleogene (K/Pg) mass extinction (~66 Ma) on marine primary and export productivity remain debated. We studied changes in carbon and nitrogen cycling in eight neritic and upper bathyal sections with expanded K/Pg boundary clay layers in the western Tethys and northeastern Atlantic Ocean, by measuring stable carbon isotopes of bulk carbonate (δ13Ccarb) and organic matter (δ13Corg), nitrogen isotopes in bulk organic matter (δ15N), and selected compound‐specific carbon isotopic records (δ13Clipid). Negative carbon isotope excursions (CIEs) in δ13Ccarb, δ13Corg, and δ13Clipid are temporally and spatially heterogeneous as well as decoupled from each other, suggesting that factors affecting the δ13C of dissolved inorganic carbon, as well as isotopic fractionation during carbon fixation across the K/Pg, are more complex than commonly assumed. The negative CIEs in δ13Corg and δ13Clipid at each site are smaller in amplitude and shorter in duration than those in δ13Ccarb, but in most sections both carbon pools recovered to preboundary conditions within the time of deposition of the boundary clay layer (<103–104 Kyr) or shortly thereafter. This rapid recovery is supported by limited δ15N data, which mostly suggests moderate or minor changes in redox conditions (except in Denmark), marine productivity, and phytoplanktonic nitrate utilization in the earliest Danian. Our results indicate that carbon cycling and primary productivity in neritic and upper bathyal regions recovered to preboundary levels faster (<104Kyr) than in oceanic regions (105–106 years), likely sustained by resilient noncalcifying phytoplankton with resting stages, consistent with modeling and proxy studies.Plain Language Summary: Sixty‐six million years ago, at the boundary between the Cretaceous and Paleogene Periods (K/Pg boundary), a meteorite impacted the Earth during a time of active volcanism causing the mass extinction of marine and terrestrial species. Despite decades of research, the consequences of the mass extinction to marine photosynthesis and the cycling of carbon in the ocean remain contentious. We investigated the light and heavy stable isotopes of carbon preserved in rocks of ancient seafloor along continental margins of the western Tethys and northeastern Atlantic Oceans to establish for how long the cycling of carbon may have been disrupted. Our results indicate that the response of marine productivity and carbon cycling following the impact was heterogenous for thousands and tens of thousands of years but that it recovered to pre‐K/Pg boundary levels hundreds of thousands of years earlier than open ocean regions. We suggest that resilient phytoplankton without carbonate skeletons living along continental margins may have recolonized surface waters relatively quickly after this mass extinction event.Shan, J., Ju, J., Zhang, W., Han, H., Zhou, T., Wang, Y., Yang, S., Cao, Y., 2019. Hydrocarbon accumulation patterns of salt crust covered biogenic gas reservoirs in the Sanhu Depression, Qaidam Basin. Natural Gas Industry 38, 25-32. biogenic gas reservoirs are extensively developed in the Sanhu Depression of the Qaidam Basin, where the largest domestic biogenic gas production base has been built up. In recent years, however, the exploration of biogenic gas there encounters a variety of difficulties, such as the identification of true and false seismic abnormality, the determination of micro-relief structure and the identification and description of lithologic traps, which are the bottlenecks restricting its exploration breakthrough. In this paper, hydrocarbon accumulation patterns of biogenic gas were studied. Then, based on fine structure interpretation results, combined with laboratory experiments, the sealing ability, distribution range, formation time and genesis of salt crust were discussed, and the salt crust covered hydrocarbon accumulation pattern of biogenic gas was put forward. Finally, combined with the conditions of source rocks and reservoirs, the exploration prospect of salt crust covered biogenic gas reservoirs was predicted. And the following research results were obtained. First, the Quaternary in the Sanhu Depression is composed of sandstone–mudstone interbeds of shore-shallow lake facies, with superior conditions of source rocks and reservoirs. Many source–reservoir–caprock assemblages are vertically formed. The biogenic gas has the characteristics of dynamic hydrocarbon accumulation, i.e., continuous migration, accumulation, diffusion and re-accumulation. Second, under the effect of Himalayan movement, the climate changes frequently and the salinity of the ancient lake is zoned in the Sanhu Depression. A freshwater area is formed at the inlet of the river in the south and a brine area is formed in the north. Under the influence of evaporation, the phreatic water in the north is salinized continuously, and a set of extensively distributed salt crust with steady thickness and a strong sealing ability is formed at the eastern part of Lingjian fault. Third, the biogenic gas generated by dark mudstone of lacustrine facies in the depression center migrates laterally and vertically to Lingjian fault zone and gets accumulated under the sealing of salt crust. In conclusion, high-quality source rocks and reservoirs and the salt crust with a strong sealing ability in the Sanhu Depression constitute a good spatial–temporal configuration relationship of source rocks, reservoirs and cap rocks, so salt crust covered biogenic gas reservoirs can be formed to provide abundant natural gas resources with a broad exploration prospect.Sharma, D.K., Dhawan, H., Morgan, T., Crocker, M., 2019. Py-GCMS studies of Indian coals and their solvent extracted products. Fuel 256, 115981. Indian coals having different characteristics, i.e., coking, rank, grade, and carbon and volatile matter (VM) content, were subjected to solvent extraction under mild, ambient pressure conditions to obtain almost ash-free coals. N-methyl pyrrolidone (NMP) containing a small amount of ethylenediamine (EDA) was used as the solvent, the resulting super clean coal (SCC) products being characterised by means of ultimate analysis, solid-state 13C NMR spectroscopy, thermogravimetric analysis (TGA) and pyrolysis-GCMS. The super clean products were found to have increased volatile matter content because of the removal of disassociations and entanglements and the disruption of intermolecular forces. Based on comparison of the pyrolysis-GCMS data for the original (raw) coals (OCs) and SCCs, the extraction led to the segregation of the coal samples into easily volatilized components and strongly cross-linked networks of polycyclic fused ring aromatic components. The polycondensed aromatic components were present in higher concentration in the super clean coals, demonstrating the selectivity of the solvents to act upon the condensed aromatic components and long chain alkanes and extract them selectively, thereby resulting in a more aromatic product.Shen, J., Algeo, T.J., Planavsky, N.J., Yu, J., Feng, Q., Song, H., Song, H., Rowe, H., Zhou, L., Chen, J., 2019. Mercury enrichments provide evidence of Early Triassic volcanism following the end-Permian mass extinction. Earth-Science Reviews 195, 191-212. environments and biotas were in a state of near-continuous perturbation during the Early Triassic, the ~5-million-year interval following the latest Permian mass extinction (LPME), but the underlying cause(s) remain uncertain. The role of episodic volcanic or intrusive magmatic activity in triggering global-scale perturbations during this interval is suspected but has not been strongly evidenced to date. Here, we investigate the record of volcanism through the Early Triassic (with a focus on the Smithian-Spathian Boundary, or SSB) using mercury (Hg) concentrations in marine sediments as a proxy. This study examines five marine sections from three paleo-oceans (Paleo-Tethys, Neo-Tethys, and Panthalassa) representing a range of depositional settings from shallow platform to deep slope. Our results suggest that volcanic and magmatic activity of the Siberian Traps Large Igneous Province (STLIP) was most intense during the first ~1.3 million years following the LPME, and that termination of its most active stage was responsible for a sharp cooling event at the SSB. Variations in the intensity of STLIP activity are thus likely to account for the large (>8‰) fluctuations of δ13Ccarb and related changes in oceanic redox and environmental conditions that characterized the Griesbachian to Smithian substages of the Early Triassic in marine sections globally. We hypothesize that a strong reduction or cessation of STLIP activity at the SSB set the stage for the recovery of marine biodiversity and ecosystems in the Spathian and later.Shen, J., Qin, Y., Zhao, J., 2019. Maceral contribution to pore size distribution in anthracite in the South Qinshui Basin. Energy & Fuels 33, 7234-7243. about the full range of pore sizes in a coal seam is important to investigate the gas storage capacity and pore connectivity for the exploration and development of coalbed methane. To better understand the pores in coal, this study integrated the experimental approaches, such as the separation of coal macerals, petrological analysis, low-temperature nitrogen adsorption, CO2 adsorption, and mercury intrusion porosimetry, to quantitatively characterize the pore geometry of anthracite collected from the southern Qinshui Basin, China. The full spectrum of pore size distribution (PSD) was compiled based on measurements obtained by the adsorption and porosimetry techniques. The results show that vitrinite in anthracite exhibits a unimodal PSD dominated by micropores, under the condition that the interparticle void influence was excluded. The absence of meso- and macropores indicates a lack of connectivity between micropores and fractures. Micropores in vitrinite have a specific surface area of more than 350 m2/g, accounting for >98% of their total specific surface area and providing significant spaces for coalbed methane storage. A numerical fitting model was proposed to quantitatively predict the PSD, which can be further used to estimate the diffusion coefficient or permeability of coalbed methane. It was also found that if the sample size decreased from 40 to 120 mesh, there was no obvious increase in pore volume, suggesting that vitrinite mainly contains no closed pores. Furthermore, pore analyses using the samples with different maceral compositions showed that vitrinite content has a positive correlation with PSD, especially for micropores. Along with minerals, inertinite largely contributes to the volume of mesopores. With an increase in inertinite and mineral matter contents, the specific surface area decreases, which may affect the coalbed methane adsorption capacity and in situ gas content of coal seams.Shen, Z., Song, J., Servais, T., Gong, Y., 2019. Late Devonian palaeobiogeography of marine organic-walled phytoplankton. Palaeogeography, Palaeoclimatology, Palaeoecology 531, 108706. and prasinophytes have generally been considered as organic-walled phytoplankton, and their distribution patterns play a significant role in palaeogeographical and palaeoclimatical reconstructions. In this paper the palaeobiogeography of Late Devonian phytoplankton (mainly Famennian) is quantitatively analyzed based on a global database consisting of 95 genera from 15 geographical units. The data are analyzed using cluster analysis, nonmetric multidimensional scaling, and minimum spanning tree analysis using the Jaccard, Ochiai, Kulczynski, and Yule's Y similarity coefficients. The results show that there was provincialism in the Late Devonian and three phytoplankton palaeobiogeographical realms could be identified: the West Gondwana, East Gondwana, and Boreal realms. There is a high degree of similarity between phytoplankton assemblages in East Gondwana (especially those in Australia and Iran) and Euramerica. Portugal (of the Iberian-Armorican block) was situated to the north of Algeria and probably acted as a stepping stone between Euramerica and West Gondwana. The closed oceanic surface circulation pattern in the Proto-Tethys Ocean between Euramerica and East Gondwana might have hindered the exchange of phytoplankton between East and West Gondwana. The phytoplankton province that had been typically confined to the higher latitudes was still present, while its characteristic genera gradually dispersed into the lower latitudes in the Late Devonian. There is a high similarity between phytoplankton assemblages from the western Junggar of Xinjiang, NW China and Euramerica. Latitude- and current-influenced palaeotemperature and oceanic circulation patterns are considered to have been the major determinants of the geographical distribution and evolution of marine phytoplankton in the Late Devonian.Shillito, L.-M., 2019. Building Stonehenge? An alternative interpretation of lipid residues in Neolithic Grooved Ware from Durrington Walls. Antiquity 93, 1052-1060. residues identified in Grooved Ware pottery from Durrington Walls have been interpreted as evidence for large-scale feasting associated with the construction of Stonehenge, around 2500 BC. While a function related to food consumption is possible, other explanations may be equally plausible. An alternative interpretation not previously considered is that these residues may be related to a non-food use of animal resources, such as in the production of tallow. Such an interpretation would support the ‘greased sled’ theory for the transport of the megaliths for StonehengeShrestha, P., Meisterjahn, B., Hughes, C.B., Mayer, P., Birch, H., Hennecke, D., 2020. Biodegradation testing of volatile hydrophobic chemicals in water-sediment systems – Experimental developments and challenges. Chemosphere 238, 124516. data are crucial for the persistence assessment of chemicals and they are generated using standard OECD guidelines. The OECD 308 describes a simulation biodegradation test of chemicals in water-sediment systems. This guideline is not applicable for testing highly volatile chemicals and recommends a closed biometer test setup for testing slightly volatile chemicals. However, proper details on system geometries, construction and monitoring of aerobic conditions are not provided. The choice of system geometry and sediment:water ratio influences the partitioning of test chemicals between different compartments (water, sediment and headspace) and can therefore affect their degradation. The guideline recommends the addition of test chemical via aqueous solutions, which however is not possible for hydrophobic volatile chemicals due to their volatilization losses and low solubility. Thus, the use of a co-solvent is necessary for the application of such chemicals but its effects in a closed setup has not been studied. We recently developed an improved closed test setup for testing volatile chemicals in soil. The objective was to adapt this improved test setup to conduct OECD 308 tests using 14C labelled chemicals with different volatilities. Using the adapted test setup it was possible to obtain a complete mass balance even for n-decane and tetralin having the highest Henry's constants of the tested chemicals. However, the use of co-solvent affected the oxygen levels, which in turn affected microbial activity and likely also the degradation of test chemicals. Therefore, the adapted test setup needs further developments for the testing of volatile hydrophobic chemicals.Shtyrlin, V.G., Borissenok, V.A., Serov, N.Y., Simakov, V.G., Bragunets, V.A., Trunin, I.R., Tereshkina, I.A., Koshkin, S.A., Bukharov, M.S., Gilyazetdinov, E.M., Shestakov, E.E., Sirotkina, A.G., Zakharov, A.V., 2019. Prebiotic syntheses under shock in the water – formamide – potassium bicarbonate – sodium hydroxide system. Origins of Life and Evolution of Biospheres 49, 1-18. under shock in nitrogen bubbled samples of the water – formamide – bicarbonate – sodium hydroxide system at pH 8.63, 9.46 and 10.44 were performed in the stainless steel preservation capsules. The maximum temperature and pressure in the capsules reached 545 K and 12.5 GPa respectively. Using the LC-MS-MS analysis, the 21 synthesis products have been identified, including amines and polyamines, carboxamide, acetamide and urea derivatives, compounds containing aniline, pyrrolidine, pyrrole, imidazole, as well as alcohol groups. It was found that the Fischer-Tropsch-type syntheses with catalysis on the surface of the stainless steel of the conservation capsule associated with the adsorbed hydrogen cyanide reactions and transamidation processes play the main role in the shock syntheses. Formation reactions of all the above-mentioned compounds have been suggested. It was proposed that hydrogen cyanide, ammonia, isocyanic acid, aminonitrile, aminoacetonitrile, as well as adsorbed species H(a), CH(a), CH2(a), CHOH(a), NH2(a) and H2CNH(a) are especially important for the formation of the products. A reduction reaction of adsorbed bicarbonate with hydrogen to formaldehyde has been first postulated. In the studied system also classical reactions take place – W?hler’s synthesis of urea and Butlerov’s synthesis of methenamine. It was suggest that material of meteorites may be an effective catalyst in the Fischer-Tropsch-type syntheses at falling of the iron-nickel meteorites in the water – formamide regions on the early Earth. It was concluded that life could have originated due to the impact of meteorites on alkaline water-formamide lakes located near volcanoes on the early Earth.Singh, K., 2019. How hydraulic properties of organic matter control effective liquid permeability of mudrocks. Transport in Porous Media 129, 761-777. organic-rich Mudrocks, porous organic matter embedded within mineral matrix along with inorganic pores forms a dual porosity–permeability (?–k) system. How hydraulic properties of organic matter embedded in the mineral matrix contribute to bulk liquid flow however is not well understood. Using computational methods, Navier–Stokes equations are coupled with Brinkman equations for dual (?–k) mineral matrix–organic matter domains obtained from a focused ion beam–scanning electron microscope (FIB-SEM) image set of an organic-rich Murdock and a series of idealized two-dimensional (2D) pore–organic matrix domains. Results of sensitivity analysis show that variations in organic matter permeability cause variations in effective permeability, which follow ‘S-shaped’ characteristics curve on log–log scale. Hydraulic coupling between the dual (?–k) domains shows magnification of the coupled flow behavior when permeability of organic matter is on the same order as the permeability of the connected inorganic pores. The effect of coupled flow becomes negligible when the permeability of organic matter is 102 higher or lower than the permeability of the connected inorganic pores. The fraction of maximum change in magnitude of effective permeability (Im) is found to be exponentially dependent on organic matter–pore channel fraction (f), i.e., Im ∝ e0.77f, for 0?<?f?<?5. The maximum contribution of organic matter on bulk liquid flow and a large variation in fluid flow velocities are found to be dependent on both the proportion of organic matter and length scale of investigation, indicating that the ?m-scale FIB-SEM domains are far from the scale of representative elementary volume (REV). This study, however, describes how the hydrodynamic coupling of dual ?–k porous media contributes to emergent bulk liquid flow in organic-rich Mudrocks, and likely in similar dual ?–k porous media encountered within engineered systems to the ones found in nature.Siriviboon, P., Tungkaburee, C., Weerawongphrom, N., Kulsing, C., 2019. Direct equations to retention time calculation and fast simulation approach for simultaneous material selection and experimental design in comprehensive two dimensional gas chromatography. Journal of Chromatography A 1602, 425-431. selection and experimental design are recognized to be wear-and-tear processes to obtain a good fingerprinting result with comprehensive two dimensional gas chromatography (GC?×?GC). The processes involve a large number of experiments for analysis of each sample due to the optimized conditions depending on the selected column sets. In this study, the analytical solutions of time summation model combined with temperature dependent linear solvation energy relationship (LSER) were derived for constant flow separation in GC?×?GC. The derived equations allow calculation of analyte retention time in first and second dimensional separation (1tR and 2tR), under temperature program separation employing any column combination with known LSER database. As a result, optimization software was developed enabling simulation of several hundred thousand GC?×?GC results (fingerprints) for separation of each sample. Good correlations between our predicted results and the results obtained with the previously established numerical approach, were obtained with the R2 of 1.000 and 0.998 for simulation of 1tR and 2tR, respectively. The developed approaches were further applied to simulation of 96,000 individual fingerprints in temperature programmed GC?×?GC, with the focus on application of 16 column sets including non-ionic liquid and ionic liquid (IL) stationary phases for separation of 678 model compounds. These approaches resulted in the computational time of 1 day compared with 1?year provided by the numerical method. Best column sets and experimental conditions (secondary column lengths and temperature programs) could then be extracted according to maximizing number of separated peaks in separation, which represents the quality of each fingerprinting.Sivaramakrishnan, K., de Klerk, A., Prasad, V., 2019. Viscosity of Canadian oilsands bitumen and its modification by thermal conversion, in: Rahimi, P., Ovalles, C., Zhang, Y., Adams, J.J. (Eds.), Chemistry Solutions to Challenges in the Petroleum Industry. American Chemical Society, Washington DC, pp. 115-199. dependence of the viscosity of Canadian oilsands-derived bitumen on different factors such as the microstructure, chemical composition, compatibility, and interactions among the different constituent components has been documented in the literature, but a comprehensive review is lacking. The goal of this chapter is to explore, in depth, the sensitivity of the viscosity of bitumen to some of these parameters and to provide a scientific explanation for the observed changes. Noncatalytic thermal conversion is used as a tool for realizing this objective. Previous studies on the thermal treatment of bitumen reported contrasting trends in viscosity with reaction time, but a substantial explanation was not provided; this served as a motivation for the experimental investigations in this chapter. Specifically, details of the postreaction procedures, including the nature of the solvent used to extract the products from the reactor and the rheological conditions, such as shear rate, used for viscosity measurements, had a significant impact on viscosity. Because some solvent remained after evaporation, methylene chloride introduced hydrogen-bonding interactions, which plausibly increased the viscosity of the thermally converted bitumen significantly. This effect was not observed with toluene as the extraction solvent. The tracking of changes in other properties, such as free-radical content, boiling-point distribution, and aromatic and aliphatic contents, during thermal conversion and before and after solvent addition and removal assisted in explaining the viscosity changes. The chemical composition of the feed and its geological origin also seems to have an effect on its viscosity. Assuming a colloidal representation for bitumen, we propose a theory on the effect of the nature of asphaltene aggregation on viscosity in terms of changes in the effective volume of the aggregate clusters during thermal conversion.Skvortsov, V.A., 2019. The sedimentary–migration–igneous hypothesis of oil formation. Doklady Earth Sciences 486, 692-694.–chemical simulation of the conditions of hydrocarbon formation at the Erema–Chona oil accumulation (Lena–Tunguska petroleum province) revealed that methane and organic matter accumulates at the basin bottom at the stage of sedimentogenesis (T = 35°C, P = 0.1 MPa). At the stage of diagenesis (T = 60°C, P = 5–10 MPa) (60–100 m depth), during the formation of oil-source rocks, films and drops of oil appear and pentane C5H12 forms. At the stage of catagenesis, at 250 m depth, hexene C6H14 forms; at 2000 m, heptene C7H16; at 3100 m, octane C8H12; and at 3800 m (T = 90°C, P = 110 MPa), nonane C9H20. In the period of apocatagenesis and metamorphism at 13–15 km depth (T = 105°C, P = 450 MPa), dodecane C10H22 forms, whereas at T = 200°C undecane C11Н24 appears. With temperature and pressure increased up to 250°C and 490 MPa, respectively, at about 15 km depth, a large group of hydrocarbons forms: liquid ones include the range from dodecane C12H26 to pentadecane C15H32, while solid ones range from hexadecane C16H34 to octadecane C18H38. Finally, when the pressure reaches 850 MPa, at 25 km depth, isoprenoids ranging from nonadecane C19H40 to tetracosane C24H50 appear, as well as other hydrocarbons. Proceeding from the modeling results, it is obvious that hydrocarbon formation at depths down to 25 km cannot be explained solely by any hypothesis of organic or inorganic oil generation. A new sedimentary–migration–igneous hypothesis of oil formation is proposed. Its basic idea is that methane from the bottom of water basins and organic matter act as sources of hydrocarbons down to 3800–4000 m depth, replaced by deep mantle methane at 13–15 and 25 km depth.Smit, N.T., Rush, D., Sahonero-Canavesi, D.X., Verweij, M., Rasigraf, O., Guerrero Cruz, S., Jetten, M.S.M., Sinninghe Damsté, J.S., Schouten, S., 2019. Demethylated hopanoids in ‘Ca. Methylomirabilis oxyfera’ as biomarkers for environmental nitrite-dependent methane oxidation. Organic Geochemistry 137, 103899. are lipids that are widespread in the bacterial domain and well established molecular biomarkers in modern and paleo environments. In particular, the occurrence of 13C-depleted 3-methylated hopanoids are characteristic of aerobic bacteria involved in methane oxidation. Previously the intra-aerobic methanotroph ‘Candidatus Methylomirabilis oxyfera’ (‘Ca. M. oxyfera’), which performs nitrite-dependent methane oxidation in anoxic environments, has been shown to synthesize bacteriohopanepolyols (BHPs) and their 3-methylated counterparts. However, since ‘Ca. M. oxyfera’ does not utilize methane as a carbon source, its biomass and lipids do not show the characteristic 13C-depletion. Therefore, the detection of ‘Ca. M. oxyfera’ in various environments is challenging, and still underexplored. Here, we re-investigated the hopanoid content of ‘Ca. M. oxyfera’ bacteria using enrichment cultures. We found the GC-amenable hopanoids of ‘Ca. M. oxyfera’ to be dominated by four demethylated hopanoids of which only one, 22,29,30-trisnorhopan-21-one, had been identified previously. The three novel hopanoids were tentatively identified as 22,29,30-trisnorhopan-21-ol, 3-methyl-22,29,30-trisnorhopan-21-one and 3-methyl-22,29,30-trisnorhopan-21-ol. These unique demethylated hopanoids are most likely biosynthesized directly by ‘Ca. M. oxyfera’ bacteria. Bioinformatical analysis of the ‘Ca. M. oxyfera’ genome revealed potential candidate genes responsible for the demethylation of hopanoids. For the sensitive detection of the four trisnorhopanoid biomarkers in environmental samples, a multiple reaction monitoring (MRM) method was developed and used to successfully detect the trisnorhopanoids in a peatland where the presence of ‘Ca. M. oxyfera’ had been confirmed previously by DNA-based analyses. These new biomarkers may be a novel tool to trace nitrite-dependent methane oxidation in various (past) environments.So, P.-K., Yang, B.-C., Li, W., Wu, L., Hu, B., 2019. Simple fabrication of solid-phase microextraction with surface-coated aluminum foil for enhanced detection of analytes in biological and clinical samples by mass spectrometry. Analytical Chemistry 91, 9430-9434. detection of analytes in biological and clinical samples is highly desirable, and significant progress has been made with direct mass spectrometric (MS) analysis. Rapid and sensitive detection, however, remains a major challenge in direct analysis of raw samples. In this study, we described a simple, rapid, and efficient method for enhanced detection of analytes in complex samples, using surface-coated aluminum (Al) foil that was simply made with conductive resin for physical adhesion of functional particles. The surface-coated Al foils were used as a solid-phase microextraction (SPME) tip for rapid sampling of target analytes from raw samples and then applied as an electrospray ionization (ESI) tip to couple MS for sensitive detection. Our results show that surface-coated Al foil is highly effective for enhanced detection of analytes in complex samples with excellent analytical performances, including sensitivity, reproducibility, and linear ranges. Overall, this development enabled an extremely simplified protocol to integrate SPME and ESI that is expected to have a significant impact on rapid screening of raw samples.Sokol, J., 2019. Fossils show large predator prowled Cambrian sediments. Science 365, 417. the summer of 2018, paleontologists hammering away at rocks high in the Canadian Rockies turned up hundreds of specimens of an unknown, but evidently hyperabundant creature. With a hand-size carapace that looks like it was sketched out in science fiction concept art, the diggers nicknamed it “the spaceship” (Science, 23 November 2018, p. 880). Now, they've given the creature its first scientific description and a name: Cambroraster falcatus—after the famed Millennium Falcon starship from Star Wars.“It's just such a bizarre-looking animal” says Joseph Moysiuk, a graduate student at the University of Toronto in Canada and first author of the study published this week in the Proceedings of the Royal Society B. “We thought we'd have a little fun.”The ship was one of the largest known animals of its day to churn up the sea floor. It sailed in fleets over muddy ocean sediment, plying its unusual claws in the hunt for small prey.Most fossils of the animal showed only hard parts. But one specimen preserved the entire creature: a carapace with two eyes peeking out from either side, trailed by soft, undulating flaps for swimming. “You so rarely get the whole body,” says paleontologist Allison Daley of the University of Lausanne in Switzerland, who did not participate in the research. “I was really excited when I saw this.”The fossils come from the Burgess Shale, a formation that for more than a century has yielded a strange and world-famous menagerie living roughly 507 million years ago, during the first bloom of animal life on Earth. During this period, burrowing organisms and their would-be predators like trilobites began an evolutionary arms race that may have helped spur the explosion of new forms. But most creatures were small, and no digging carnivores of this size had come to light.Cambroraster had a round mouth lined with toothlike plates, fronted with comblike claws it could hold out like a basket. Its eyes sat in deep notches that give the carapace its signature “spaceship” look. Expedition leader Jean-Bernard Caron of the Royal Ontario Museum (ROM) in Toronto and Moysiuk place it in the radiodontans, a long-enigmatic group of extinct arthropods.Radiodonts offer a glimpse of how today's arthropods evolved their now-standardized body plan from stranger beginnings. The most famous radiodont is the free-swimming Anomalocaris, the Cambrian's iconic meter-long apex predator. Others in the group were filter feeders, and now Cambroraster shows that some scrounged the sea floor like modern-day horseshoe crabs. Given that radiodonts filled so many ecological niches, it's “surprising they got outcompeted,” says Harvard University paleontologist Joanna Wolfe.In 2018, the ROM team unearthed dozens of separated carapaces and claws in single layers of shale, suggesting C. falcatus individuals had congregated and then molted their exoskeletons, huddling together for safety or to reproduce, like some arthropods do today.Back at the museum, the team found unrecognized or mislabeled “spaceships” in drawers and realized that C. falcatus lived at other Burgess Shale sites, too. Last year, a Chinese team published a fossil carapace with a similar shape from the 518-million-year-old Chengjiang biota. And paleontologist Liu Yu of Yunnan University in Kunming, China, is studying yet another Cambrian creature that he intends to assign to the genus Cambroraster. “I think this animal was widespread worldwide,” Liu says.Song, H., Du, Y., Algeo, T.J., Tong, J., Owens, J.D., Song, H., Tian, L., Qiu, H., Zhu, Y., Lyons, T.W., 2019. Cooling-driven oceanic anoxia across the Smithian/Spathian boundary (mid-Early Triassic). Earth-Science Reviews 195, 133-146. Smithian/Spathian boundary (SSB) represents a major climatic-oceanic-biotic event within the ~5-Myr-long recovery interval of the Early Triassic following the end-Permian mass extinction. The SSB was associated with pronounced cooling following the middle Smithian hyper-greenhouse, a ~?+2 to +8‰ positive carbon isotope excursion, and a second-order mass extinction, yet its underlying cause(s) remain poorly understood. Here, we review oceanic environmental changes during the middle Smithian to early Spathian interval and their potential mechanisms. In addition, we undertook an analysis of the carbon?sulfur?iron (C-S-Fe) systematics of the South Majiashan section, which was located on the paleo-western margin of the South China Craton during the Early Triassic, to better understand the causation of these environmental changes. This analysis revealed low δ13Ccarb (i.e., the N3 minimum) in the middle Smithian but rapidly rising δ13Ccarb (i.e., to the P3 maximum) and δ34SCAS within the SSB interval (i.e., late Smithian-earliest Spathian). Both the middle Smithian and SSB intervals are marked by development of marine euxinia, which we hypothesize had fundamentally different causes. The middle Smithian was associated with hyperwarming (the “Smithian Thermal Maximum”), which was probably triggered by a peak in magmatic activity of the Siberian Traps LIP. In contrast, the SSB interval was associated with global climatic cooling, which may have stimulated oceanic overturning circulation and upwelling on continental margins, leading to transient local increases in marine productivity and expansion of oceanic oxygen-minimum zones (OMZs). The concurrent positive excursions in δ13Ccarb and δ34SCAS at South Majiashan and other sections worldwide are evidence of enhanced burial of organic carbon and pyrite on a regional or global scale, as well as of a concurrent decline in atmospheric pCO2 that may have positively re-enforced the SSB cooling event.S?rensen, L., McCormack, P., Altin, D., Robson, W.J., Booth, A.M., Faksness, L.-G., Rowland, S.J., St?rseth, T.R., 2019. Establishing a link between composition and toxicity of offshore produced waters using comprehensive analysis techniques – A way forward for discharge monitoring? Science of The Total Environment 694, 133682. of produced waters from five mature Norwegian Sea oil fields were examined as total organic extracts (TOEs) and after fractionation into operationally-defined ‘polar’ and ‘apolar’ fractions. The TOEs and fractions were examined by gas chromatography (GC), GC-mass spectrometry (GC–MS), two dimensional GC–MS (GC?×?GC–MS) and liquid chromatography with high-resolution spectrometry (LC-HRMS) techniques.Low molecular weight aromatics, phenols and other common petroleum-derived hydrocarbons were characterized and quantified in the TOEs and fractions. In addition, a range of more uncommon polar and apolar constituents, including those likely derived from production chemicals, such as trithiolane, imidazolines and quaternary amine compounds (so-called ‘quats’), were tentatively identified, using GC?×?GC–MS and LC-HRMS.The acute toxicity of the TOEs and subfractions was investigated using early life stages of the marine copepod Acartia tonsa. Toxicity varied significantly for different PW TOEs and subfractions. For some PWs, the toxicity was attributed mainly to the ‘polar’ components, while that of other PWs was associated mainly with the ‘apolar’ components. Importantly, the observed toxicity could not be explained by the presence of the commonly reported compounds only.Although, due to the vast chemical complexity even of the sub-fractions of the PW extracts, specific compounds driving the observed toxicity could be not be elucidated in this study, the proposed approach may suggest a way forward for future revisions of monitoring regimes for PW discharges.Sotos, J.G., 2019. Biotechnology and the lifetime of technical civilizations. International Journal of Astrobiology 18, 445-454. number of people able to end Earth's technical civilization has heretofore been small. Emerging dual-use technologies, such as biotechnology, may give similar power to thousands or millions of individuals. To quantitatively investigate the ramifications of such a marked shift on the survival of both terrestrial and extraterrestrial technical civilizations, this paper presents a two-parameter model for civilizational lifespans, i.e. the quantity L in Drake's equation for the number of communicating extraterrestrial civilizations. One parameter characterizes the population lethality of a civilization's biotechnology and the other characterizes the civilization's psychosociology. L is demonstrated to be less than the inverse of the product of these two parameters. Using empiric data from PubMed to inform the biotechnology parameter, the model predicts human civilization's median survival time as decades to centuries, even with optimistic psychosociological parameter values, thereby positioning biotechnology as a proximate threat to human civilization. For an ensemble of civilizations having some median calculated survival time, the model predicts that, after 80 times that duration, only one in 1024 civilizations will survive – a tempo and degree of winnowing compatible with Hanson's ‘Great Filter.’ Thus, assuming that civilizations universally develop advanced biotechnology, before they become vigorous interstellar colonizers, the model provides a resolution to the Fermi paradox.Sova, V., Kerimov, A.-G., 2019. Large undiscovered oil resources are predicted south of Russia. Journal of Petroleum Exploration and Production Technology 9, 1659-1676. Region is one of the oldest petroleum provinces on South of Russian Federation. Today, most of its fields are depleted and prospects for the discovery of new large hydrocarbon deposits considered exhausted. However, our studies allow us to talk about the possibility of the existence of previously undiscovered oil reservoirs, clamped in the source rocks associated with North-Stavropol tectonic element. In the middle of the last century, similar deposits have been identified within Prikumsk-Tyulenevskiy (Praskoveyskoe, Achikulakskoye, Ozek-Suat and a number of other fields) and Chernolesskiy (Zhuravskoye, Vorobyevskoye) tectonic elements. However, these findings were largely spontaneous due to lack of approved and unified approach to the petrophysical evaluation of dedicated reservoirs from well logs. At the same time the experience of shale reservoirs studies, as well as the results of its implementation to evaluation of deposits of Zhuravsky-Vorobyevsky petroleum accumulation zone, allows to revise existing well log materials for deep wells of explorational and depleted structures, and to identify promising intervals for further re-exploration and testing. In this work, Paleocene sediments of Blagodarnenskaya explorational structure of the Stavropol Region were studied. Despite the approval of the oil bearing of these deposits within the Prikumsk-Tyulenevskiy tectonic element and the positive signs of hydrocarbon saturation from initial well logs data, its evaluation and testing within Blagodarnenskaya structure associated with North-Stavropol tectonic element, were not conducted. However, the results of well logs analysis performed by us with the use of interpretation technique approved on reservoirs of Zhuravsky-Vorobyevsky petroleum accumulation zone, as well as the core tests indicate the presence of oil-saturated reservoirs in the Paleocene sediments of Blagodarnenskaya structure.Stalport, F., Rouquette, L., Poch, O., Dequaire, T., Chaouche-Mechidal, N., Payart, S., Szopa, C., Coll, P., Chaput, D., Jaber, M., Raulin, F., Cottin, H., 2019. The photochemistry on Space Station (PSS) experiment: Organic matter under Mars-like surface UV radiation conditions in low Earth orbit. Astrobiology 19, 1037-1052. search for organic molecules at the surface of Mars is a top priority of the Mars Science Laboratory (NASA) and ExoMars 2020 (ESA) space missions. Their main goal is to search for past and/or present molecular compounds related to a potential prebiotic chemistry and/or a biological activity on the Red Planet. A key step to interpret their data is to characterize the preservation or the evolution of organic matter in the martian environmental conditions. Several laboratory experiments have been developed especially concerning the influence of ultraviolet (UV) radiation. However, the experimental UV sources do not perfectly reproduce the solar UV radiation reaching the surface of Mars. For this reason, the International Space Station (ISS) can be advantageously used to expose the same samples studied in the laboratory to UV radiation representative of martian conditions. Those laboratory simulations can be completed by experiments in low Earth orbit (LEO) outside the ISS. Our study was part of the Photochemistry on the Space Station experiment on board the EXPOSE-R2 facility that was kept outside the ISS from October 2014 to February 2016. Chrysene, adenine, and glycine, pure or deposited on an iron-rich amorphous mineral phase, were exposed to solar UV. The total duration of exposure to UV radiation is estimated to be in the 1250–1420?h range. Each sample was characterized prior to and after the flight by Fourier transform infrared (FTIR) spectroscopy. These measurements showed that all exposed samples were partially degraded. Their quantum efficiencies of photodecomposition were calculated in the 200–250?nm wavelength range. They range from 10?4 to 10?6 molecules·photon?1 for pure organic samples and from 10?2 to 10?5 molecules·photon?1 for organic samples shielded by the mineral phase. These results highlight that none of the tested organics are stable under LEO solar UV radiation conditions. The presence of an iron-rich mineral phase increases their degradation.Staniszewska, A., Kunicka-Styczyńska, A., Otlewska, A., Gawor, J., Gromadka, R., ?uchniewicz, K., Ziemiński, K., 2019. High-throughput sequencing approach in analysis of microbial communities colonizing natural gas pipelines. MicrobiologyOpen 8, e00806. study provides a deep modern insight into the phylogenetic diversity among bacterial consortia found in working and nonworking high‐methane natural gas pipelines located in Poland. The working pipeline was characterized by lower biodiversity (140–154 bacterial genera from 22 to 23 classes, depending on the source of the debris) in comparison to the off‐gas pipeline (169 bacterial genera from 23 classes). The sediment recovered from the working pipeline contained mostly DNA identified as belonging to the phylum Firmicutes (66.4%–45.9% operational taxonomic units [OTUs]), predominantly Bacillus (41.4%–31.1% OTUs) followed by Lysinibacillus (2.6%–1.5% OTUs) and Clostridium (2.4%–1.8% OTUs). In the nonworking pipeline, Proteobacteria (46.8% OTUs) and Cyanobacteria (27.8% OTUs) were dominant. Over 30% of the Proteobacteria sequences showed homologies to Gammaproteobacteria, with Pseudomonas (7.1%), Enhydrobacter (2.1%), Stenotrophomonas (0.5%), and Haempohilus (0.4%) among the others. Differences were noted in terms of the chemical compositions of deposits originating from the working and nonworking gas pipelines. The deposits from the nonworking gas pipeline contained iron, as well as carbon (42.58%), sulphur (15.27%), and oxygen (15.32%). This composition can be linked to both the quantity and type of the resident microorganisms. The presence of a considerable amount of silicon (17.42%), and of aluminum, potassium, calcium, and magnesium at detectable levels, may likewise affect the metabolic activity of the resident consortia in the working gas pipeline. All the analyzed sediments included both bacteria known for causing and intensifying corrosion (e.g., Pseudomonas, Desulfovibrio, Shewanella, Serratia) and bacteria that can protect the surface of pipelines against deterioration (e.g., Bacillus). Biocorrosion is not related to a single mechanism or one species of microorganism, but results from the multidirectional activity of multiple microbial communities. The analysis presented here of the state of the microbiome in a gas pipeline during the real gas transport is a particularly valuable element of this work.Stanley, K.M., Heppell, C.M., Belyea, L.R., Baird, A.J., Field, R.H., 2019. The importance of CH4 ebullition in floodplain fens. Journal of Geophysical Research: Biogeosciences 124, 1750-1763. in estimates of CH4 emissions from peatlands arise, in part, due to difficulties in quantifying the importance of ebullition. This is a particular concern in temperate lowland floodplain fens in which total CH4 emissions to the atmosphere (often measured as the sum of diffusive and plant‐mediated fluxes) are known to be high, but few direct measurements of CH4 ebullition fluxes have been made. Our study quantified CH4 fluxes (diffusion, plant‐mediated, and ebullition) from two temperate floodplain fens under conservation management (Norfolk, UK) over 176 days using funnels and static chambers. CH4 ebullition was a major component (>38%) of total CH4 emissions over spring and summer. Seasonal variations in quantifiable CH4 ebullition fluxes were marked, covering six orders of magnitude (5 × 10?5 to 62 mg·CH4·m?2·hr?1). This seasonal variability in CH4 ebullition fluxes arose from changes in both bubble volume flux and bubble CH4 concentration, highlighting the importance of regular measurements of the latter for accurate assessment of CH4 ebullition using funnels. Soil temperature was the primary control on CH4 ebullition fluxes. Elevated water level was also associated with increased CH4 ebullition fluxes, with a distinct increase in CH4 ebullition flux when water level rose to within 10 cm of the peat surface. In contrast, CH4 ebullition flux decreased steadily with increasing plant cover (measured as vascular green area). Ebullition was both steady and episodic in nature, and drops in air pressure during the two‐day funnel deployments were associated with higher fluxes.Staps, M., van Gestel, J., Tarnita, C.E., 2019. Emergence of diverse life cycles and life histories at the origin of multicellularity. Nature Ecology & Evolution 3, 1197-1205. evolution of multicellularity has given rise to a remarkable diversity of multicellular life cycles and life histories. Whereas some multicellular organisms are long-lived, grow through cell division, and repeatedly release single-celled propagules (for example, animals), others are short-lived, form by aggregation, and propagate only once, by generating large numbers of solitary cells (for example, cellular slime moulds). There are no systematic studies that explore how diverse multicellular life cycles can come about. Here, we focus on the origin of multicellularity and develop a mechanistic model to examine the primitive life cycles that emerge from a unicellular ancestor when an ancestral gene is co-opted for cell adhesion. Diverse life cycles readily emerge, depending on ecological conditions, group-forming mechanism, and ancestral constraints. Among these life cycles, we recapitulate both extremes of long-lived groups that propagate continuously and short-lived groups that propagate only once, with the latter type of life cycle being particularly favoured when groups can form by aggregation. Our results show how diverse life cycles and life histories can easily emerge at the origin of multicellularity, shaped by ancestral constraints and ecological conditions. Beyond multicellularity, this finding has similar implications for other major transitions, such as the evolution of sociality.Stebbins, A., Algeo, T.J., Krystyn, L., Rowe, H., Brookfield, M., Williams, J., Nye Jr, S.W., Hannigan, R., 2019. Marine sulfur cycle evidence for upwelling and eutrophic stresses during Early Triassic cooling events. Earth-Science Reviews 195, 68-82. to the global carbon and sulfur cycles recurred episodically throughout the ~5-Myr-long Early Triassic, in the aftermath of the end-Permian mass extinction, the largest biocrisis in Earth's history. In this study, analyses of carbonate-associated sulfate (CAS) sulfur, CAS oxygen, and pyrite sulfur-isotope ratios in a continental shelf section from the southern Neo-Tethys Ocean (Spiti Valley, India) provide new insights into the Early Triassic marine sulfur cycle. Secular variation in CAS sulfur-isotope values at Spiti is similar to that in South China, suggesting that CAS was a robust recorder of a global seawater sulfate signal. The Spiti CAS and pyrite δ34S profiles show that the highest rates of pyrite burial coincided with cooler sea-surface temperatures. We infer that climatic cooling steepened equator-to-pole temperature gradients, invigorating thermohaline overturning circulation, and enhancing upwelling of nutrients that stimulated marine productivity and organic carbon sinking fluxes. Enhanced productivity fueled and sustained microbial respiration, increased oxygen demand, and, within the southern Neo-Tethys, caused the zone of microbial sulfate reduction to migrate upwards and become more connected to the water column. Microbial sulfate reduction, under these conditions, was no longer limited by organic matter or sulfate availability, leading to burial of more 34S-depleted pyrite and 34S- and 18O-enrichment of the oceanic sulfate pool. This environmental scenario suggests possible environmental stresses related to eutrophication during positive carbon-isotope excursions around the Griesbachian-Dienerian, Dienerian-Smithian, and Smithian-Spathian boundaries. Additionally, the difference between CAS and pyrite sulfur-isotope values, Δ34SCAS-pyr, slowly rose through the Early Triassic, reflecting a slow increase in seawater sulfate concentrations following a minimum close to the Permian-Triassic boundary.Stelmach, K.B., Yarnall, Y.Y., Cooper, P.D., 2019. Nitrogen sublimation as a driver of chemistry in Pluto-analog laboratory ices: Formation of carbon suboxide (C3O2) and various salts. ACS Earth and Space Chemistry 3, 1640-1655. number of planetary bodies, including Triton and Pluto, and a number of Kuiper Belt objects contain nitrogen ices on their surfaces. Nitrogen ices were also used in laboratory experiments as a matrix isolation material before noble gases could be condensed. Planetary bodies with nitrogen ices then may act as giant matrix isolation experiments, trapping reactive species onto the surface and concentrating them. Upon sublimation, these reactive species are much more likely to encounter each other or another molecule to react with. A pilot study was conducted to test the feasibility of testing the chemistry occurring during the sublimation of nitrogen ices. A high vacuum laboratory setup was used to create ices at ～6 K (±0.5 K). Ices were deposited under microwave radiation to create radicals to simulate what might be present in the tenuous atmospheres of these planetary bodies. The ices consisted of a mixture of 1:1:100 carbon source + H2O + N2, where the carbon source was either CO or CH4. Reagents and products were primarily identified using FTIR and UV–vis transmission spectroscopy. Once the predominantly N2 ice was characterized with the spectroscopic techniques, the N2 was sublimated to create a H2O ice, and then this ice was characterized using the aforementioned techniques. One completely new product was observed, namely, carbon suboxide (C3O2), and a couple products identified in the nitrogen ice formed various salts. Future work could make use of multiple sublimation steps and other astrochemically relevant matrices and introduce more astrophysically relevant sources of radiation like electron beams or UV irradiation.Stromberg, J.M., Parkinson, A., Morison, M., Cloutis, E., Casson, N., Applin, D., Poitras, J., Marti, A.M., Maggiori, C., Cousins, C., Whyte, L., Kruzelecky, R., Das, D., Leveille, R., Berlo, K., Sharma, S.K., Acosta-Maeda, T., Daly, M., Lalla, E., 2019. Biosignature detection by Mars rover equivalent instruments in samples from the CanMars Mars Sample Return Analogue Deployment. Planetary and Space Science 176, 104683. work details the laboratory analysis of a suite of 10 samples collected from an inverted fluvial channel near Hanksville, Utah, USA as a part of the CanMars Mars Sample Return Analogue Deployment (MSRAD). The samples were acquired along the rover traverse for detailed off-site analysis to evaluate the TOC and astrobiological significance of the samples selected based on site observations, and to address one of the science goals of the CanMars mission: to evaluate the ability of different analytical techniques being employed by the Mars2020 mission to detect and characterize any present biosignatures. Analytical techniques analogous to those on the ExoMars, MSL and the MER rovers were also applied to the samples. The total organic carbon content of the samples was <0.02% for all but 4 samples, and organic biosignatures were detected in multiple samples by UV–Vis–NIR reflectance spectroscopy and Raman spectroscopy (532?nm, time-resolved, and UV), which was the most effective of the techniques. The total carbon content of the samples is?<?0.3?wt% for all but one calcite rich sample, and organic C was not detectable by FTIR. Carotene and chlorophyll were detected in two samples which also contained gypsum and mineral phases of astrobiological importance for paleoenvironment/habitability and biomarker preservation (clays, gypsum, calcite) were detected and characterized by multiple techniques, of which passive reflectance was most effective. The sample selected in the field (S2) as having the highest potential for TOC did not have the highest TOC values, however, when considering the sample mineralogy in conjunction with the detection of organic carbon, it is the most astrobiologically relevant. These results highlight importance of applying multiple techniques for sample characterization and provide insights into their strengths and limitations.Su, Y., Ma, X., Page, J., Shi, R., Xia, Y., Ouyang, Z., 2019. Mapping lipid C=C location isomers in organ tissues by coupling photochemical derivatization and rapid extractive mass spectrometry. International Journal of Mass Spectrometry 445, 116206. desaturation plays important roles in biological processes and the disease states. Here, we report a simple but efficient method for mapping unsaturated phospholipids including the spatial distribution of lipid C=C location isomers in animal organs by coupling the C=C specific derivatization with direct analysis mass spectrometry (MS). Lipids are sampled directly by a stainless-steel wire from rat brain or kidney, extracted, and derivatized via the Paternò–Büchi reaction in a glass emitter of the nanoelectrospray ionization (nanoESI) source. Subsequent analysis by nanoESI-tandem mass spectrometry reveals C=C locations and relative quantities of lipid C=C location isomers. Unsaturated lipids, such as phospholipids and free fatty acids, have been identified with ion intensities spanning two orders of magnitude in rat brain. Typical sample consumption is less than 10 μg/measurement and the time for each analysis is about 3?min. This method should serve as a complementary method to high spatial resolution mass spectrometry imaging techniques, because it offers a streamlined experimental workflow for rapid profiling of lipids with C=C specificity to enable such applications as point-of-care disease diagnostics.Su, Y., Zha, M., Ding, X., Qu, J., Gao, C., Jin, J., Iglauer, S., 2019. Petrographic, palynologic and geochemical characteristics of source rocks of the Permian Lucaogou Formation in Jimsar Sag, Junggar Basin, NW China: Origin of organic matter input and depositional environments. Journal of Petroleum Science and Engineering 183, 106364. Lucaogou Formation contains significant amount of shale oil and tight oil resources in China, and the target strata studied here is located in the Jimsar Sag, Junggar Basin. A combination of mudstone, silty mudstone, dolomite mudstone and limy mudstone from this formation was investigated for the organic petrology and organic geochemistry and thus organic matter origin, thermal maturity and depositional condition were evaluated. Source rocks indicate good potential in hydrocarbon generation, which were featured by high TOC, S2 and HI. Tmax and biomarker ratios reveal that source rocks are mature and have enter oil generation window. Microscopical analyses reveal that liptinitic organic matter are dominant components, especially the amorphous components, which are commonly accompanied with advanced plant fragments. Organic matter assemblages indicate organic materials originated from aquatic organisms and terrestrial plants, which is evidenced from the discrimination diagrams of Pr/nC17-Ph/nC18 and C27–C29 regular steranes. Vertical variations in the abundance of organic matter from the bottom up reflect the changes of the depositional conditions, which are consistent with the indications of organic geochemical parameters. In the lower Lucaogou (LLF), the depositional conditions varied from the relatively shallow water, moderate-energy, proximal suboxic/dysoxic-anoxic condition to the deeper, low-energy, distal suboxic-anoxic condition, as endorsed by the enhanced OM degradation and the preservation of palynomorphs. In the upper Lucaogou (ULF), the conditions changed gradually from a brackish, stratified, suboxic-anoxic condition to fresh, aerobic condition, followed by a stratified oxygen-depleted setting with a relatively higher saline upwards, as supported by the variation in the organic components. Overall, the conditions of LLF are more reducing than that of ULF, which is demonstrated by Pr/Ph ratios, gammacerane index and ETR. The understanding of the redox conditions and their evolution of the Lucaogou Formation is crucial to expound the formation of source rocks and evaluate the hydrocarbon-generating potential.Su, Y., Zhang, Z., Wu, D., Zhan, L., Shi, H., Xie, B., 2019. Occurrence of microplastics in landfill systems and their fate with landfill age. Water Research 164, 114968. (MPs) are emerging pollutants that have been extensively detected in marine and terrestrial environments. Landfills are receptacles for cumulative loading of plastic waste derived from industry and households, but data on MPs occurrences in landfill systems are lacking. In the current study, the occurrence, characteristics and distribution patterns of MPs in landfills (including leachate and refuse) of the megacity Shanghai were investigated in accordance with different landfill ages (3–20 years). The results revealed that the average abundances of MPs in leachate and refuse were 8 (±3) items/L and 62 (±23) items/g, respectively. The predominant shapes and polymer types of the detected MPs were fibers and cellophane in leachate, whereas they were fragments and polyethylene in refuse. The patterns of abundance and size distribution of MPs in refuse varied from different landfill age, and different polymer MPs exhibited various occurrence patterns with increasing landfill age. Further spectra analysis suggested the presence of oxidative degradation of polyethylene MPs in the landfill process, especially for the landfill time of more than 20 years, so the fates of MPs in landfills were determined by the increase consumptions of plastics products and the degradation process of MPs in landfills. This study firstly provided a systematic overview of MPs pollution characteristics in landfill systems, and the results will foster the understanding of MPs fates over a long time scale in the environments.Sudol, P.E., Gough, D.V., Prebihalo, S.E., Synovec, R.E., 2020. Impact of data bin size on the classification of diesel fuels using comprehensive two-dimensional gas chromatography with principal component analysis. Talanta 206, 120239. component analysis (PCA) is a widely applied chemometric tool for classifying samples using comprehensive two-dimensional (2D) gas chromatography (GC?×?GC) separation data. Classification via PCA can be improved by 2D binning of the data. A “standard operating procedure (SOP) bin size” is often applied to improve the S/N and to mitigate potential retention time misalignment issues. The SOP bin size is generally selected to be slightly larger than the typical 2D peak dimensions. In this study we examine to what extent a single SOP bin size is optimal for all of the class comparisons that can be made in a single PCA scores plot. For this purpose, a GC?×?GC-FID dataset comprised of 5 different diesel fuels (i.e., 5 sample classes), each run with 4 replicates using a reverse column configuration (polar 1D column and non-polar 2D column) was utilized. The dataset was collected within about one day, which minimized retention time misalignment in order to allow the study to focus on S/N enhancement concurrent with maintaining the chemical selectivity provided by the GC?×?GC separations. A total of 110 bin sizes were evaluated. Degree-of-class separation (DCS) was utilized as a quantitative metric to assess the impact of binning in improving separation in the scores plot. The DCS was calculated pair-wise between nearest neighbor sample classes for each of the 5 sample classes in the scores plot (5 sample class pairs). Results indicated the SOP bin size did not provide the highest DCS for any of the 5 fuel pairs. Each fuel pair is found to have its own optimal bin size, suggesting the binning finds the balance between S/N optimization concurrent with leveraging the chemical selectivity information differences in the samples as manifested in their GC?×?GC separation “patterns”. Robustness of the findings in this study were supported by leaving out one fuel at a time and re-running the PCA models.Sun, F., Yao, Y., Li, G., 2019. Slight insights and perspectives of future heavy oil recovery. Journal of Petroleum Exploration and Production Technology 9, 2145-2147. this paper, we put forward critical future prospects based on the paper that was published on International Journal of Heat and Mass Transfer. At present, engineers are familiar with the advantages and disadvantages of different working fluids in thermal recovery of heavy oil. For all the oil displacement mechanism, they can be summarized into only three aspects: (a) physical heat conduction, (b) chemical reactions, and (c) the differences in hydrodynamic properties between fluids. This is already well known in the existing body of knowledge. However, how much will each of these three mechanisms contribute to the total oil recovery efficiency is quite interesting and important to the industry. Based on the commented paper and some related references, we pointed out the future research directions in this area.Sun, H., Liu, L., Jiang, X., Huang, S., Geng, M., Chen, S., Li, N., Shen, P., 2019. Distribution characteristics and its controlling factor of lacustrine high-quality source rocks in the Bozhong sag, Bohai Bay Basin. Petroleum Research 4, 227-237. of Paleogene lacustrine high-quality source rocks in the Bozhong sag in Bohai Bay Basin is analyzed through data of geochemistry, geology and well logging, and its differences under the control of climate and tectonics is also well discussed. Distribution characteristics of the high-quality source rocks developed in the saline environment controlled by the climate are quite different from that developed in the rapid subsidence environment controlled by tectonics. The high-quality source rocks in Member 1 of Shahejie Formation developed in the saline environment account for 81.9% of total subsag area, and are distributed widely and extensively. The high-quality source rocks in Member 3 of Shahejie Formation and Member 3 of Dongying Formation is developed in the tectonic subsidence environment, and horizontally, the subsag subsidence rates has a positive correlation with the area proportion of the high-quality source rocks in the sag; vertically, the reduction-oxidation interface of the lake controls the enrichment of high-quality source rocks. Controlled by the saline environment and rapid subsidence environment, the high-quality source rocks in the Bozhong sag and adjacent areas have three types of development condition: the saline water, the tectonic subsidence, and joint control of the saline water and the tectonic subsidence. The humid climate and low subsidence rate are not favorable for development of high-quality source rocks.Sun, Q., Xiao, F., Gao, X., Zong, W., Li, Y., Zhang, J., Sun, S., Chen, S., 2019. A new discovery of Mesoproterozoic erathem oil, and oil–source correlation in the Niuyingzi area of western Liaoning Province, NE China. Marine and Petroleum Geology 110, 606-620. Yanliao Fault–Depression Belt is an important area for Precambrian oil and gas exploration in China. Through drilling of the Niu D1 well in the Niuyingzi area, located in western Liaoning Province (NE China), oil shows were discovered in the Mesoproterozoic Gaoyuzhuang carbonate reservoirs. In this study, we discuss the geochemical characteristics of the potential source rocks and oil-bearing rocks, as well as the relationship between the crude oil in the Niu D1 well and these source rocks, on the basis of organic geochemical analyses including biomarker compounds and stable carbon isotopes. The crude oil hosted in the limestone at depths of 341.65–362.00?m in the Niu D1 well underwent moderate biodegradation and shows three characteristic features: (i) the presence of the complete C18–C23 13α(n-alkyl)-tricyclic terpane series; (ii) high abundances of the drimane series, C19–C21 tricyclic terpanes, C24 tetracyclic terpane, and diahopanes, and low abundance of gammacerane; and (iii) depleted stable carbon isotopes of saturated and aromatic hydrocarbons (less than ?30‰). All of these features suggest that the crude oil in the limestones of the Niu D1 well originated mainly from the organic-rich Hongshuizhuang Formation shale. Considering the lack of effective Neoproterozoic source rock, the detection of diversified steranes implies a degree of contamination from Phanerozoic sources with eukaryotic biological input. This is the first time that primary crude oil of Mesoproterozoic age has been discovered from wells drilled in the Yanliao Fault–Depression Belt, and demonstrates that Mesoproterozoic carbonates in this area have good hydrocarbon exploration potential.Sun, X., Miao, L., Chen, R., 2019. Effects of different clay’s percentages on improvement of sand-clay mixtures with microbially induced calcite precipitation. Geomicrobiology Journal 36, 810-818. induced calcite precipitation (MICP) is currently appraised for the improvement of sandy soils, but only few studies use it to improve sand-clay mixtures. The effect of contents of kaolin clay and the effect of ions in kaolin clay on bacterial urease activity and productive rates for calcium carbonate were studied. Moreover, sand solidification tests were conducted and the solidifying effects of MICP for sand-clay mixtures were evaluated. The results show that adding kaolin clay has an inhibitory effect on the urease activity of bacteria, and adding too many kaolin clays also decrease the productive rates for calcium carbonate. With adding Al2O3 or FeCl3, urease activity both decreases and it becomes lower with adding more Al2O3 or FeCl3. The permeability of sand columns all decreased gradually with MICP curing. With more kaolin clay, the increasing range of bacterial utilization rates of those with larger particle sizes is bigger. The maximum productive rate for calcium carbonate of samples with smaller particle sizes exists in sample with 5% of kaolin clay while other samples with 7.5% of clay have more calcium carbonate. Sand columns with different sand particle sizes have different suitable amounts of added kaolin clays for MICP solidification.Sutherland, D.L., Ralph, P.J., 2019. Microalgal bioremediation of emerging contaminants - Opportunities and challenges. Water Research 164, 114921. contaminants (ECs) are primarily synthetic organic chemicals that have a focus of increasing attention due to either increased awareness of their potential risks to humans and aquatic biota, or only recently been detected in the aquatic environment or drinking water supplies, through improved analytical techniques. . Many ECs have no regulatory standards due to the lack of information on the effects of chronic exposure. Pharmaceuticals, personal care products, pesticides and flame retardants are some of the most frequently detected ECs in aquatic environments, with over 200 individual compounds identified, to date. Current wastewater treatment is ineffective at removing ECs and there is a vital need for the development of efficient, cost-effective EC treatment systems that can be applied to a range of scales and wastewater types. Microalgae have demonstrated potential for detoxifying organic and inorganic pollutants, with a number of large-scale wastewater treatment microalgal technologies already developed. There are three main pathways that microalgae can bioremediate ECs; bioadsorption, bio-uptake and biodegradation. Microalgal bioadsorption occurs when ECs are either adsorbed to cell wall components, or onto organic substances excreted by the cells, while bio-uptake involves the active transport of the contaminant into the cell, where it binds to intracellular proteins and other compounds. Microalgal biodegradation of ECs involves the transformation of complex compounds into simpler breakdown molecules through catalytic metabolic degradation. Biodegradation provides one of the most promising technologies for the remediation of contaminants of concern as it can transform the contaminant to less toxic compounds rather than act as a biofilter. Further research is needed to exploit microalgal species for EC bioremediation properties, such as increased bioadsorption, enhanced biodegrading enzymes and optimised growth conditions. When coupled with nutrient removal, microalgal treatment of EC can be a cost-effective viable option for the reduction of contaminant pollution in waterways.Sydney, E.B., Neto, C.J.D., de Carvalho, J.C., Vandenberghe, L.P.d.S., Sydney, A.C.N., Letti, L.A.J., Karp, S.G., Soccol, V.T., Woiciechowski, A.L., Medeiros, A.B.P., Soccol, C.R., 2019. Microalgal biorefineries: Integrated use of liquid and gaseous effluents from bioethanol industry for efficient biomass production. Bioresource Technology 292, 121955. new method for CO2 recovery was proposed for cultivation of different microalgae. First, a chemical fixation, where CO2 was injected in alkalinized vinasse to form (bi)carbonate salts, was performed. In addition, biological fixation with CO2-enriched air injection was also accomplished for evaluation of the most promising results. Two bioreactor systems, a stirred-tank reactor and a bubble column reactor, were employed. A higher carbon transfer rate (43.35?g.L?1.h?1) was achieved in the bubble column reactor using NaOH-alkalinized vinasse, along with reductions of the chemical oxygen demand (COD), biological oxygen demand (BOD) and turbidity (TD). This allowed the cultivation of microalgae and cyanobacteria at vinasse concentrations between 70 and 100%, reaching a biomass production of 2.25?g.L?1 in 15?days of culture. The viability of chemical CO2 fixation together with the use of 100% treated vinasse from a bioethanol production unit for microalgae cultivation has been demonstrated in a successfully integrated biorefinery approach.Tamura, K., 2019. Perspectives on the origin of biological homochirality on Earth. Journal of Molecular Evolution 87, 143-146. origin of biological homochirality on Earth has been an important unresolved issue in the field of molecular evolution and many hypotheses have been proposed to explain this. The most prevailing view may be that of astrobiologists, in that a slight enantiomeric excess of l-amino acids in meteorites can account for the origin. However, the view ignores two important factors: amino acid racemization, and the evolution and continuity of biological systems on Earth. Therefore, on the basis of these two standpoints, the plausibility of the hypothesis that chiral-selective tRNA aminoacylation could have led to crucial homochiral protein biosynthesis should be emphasized. Recent molecular dynamic simulations have clearly elucidated the mechanisms of enantiomer-specific aminoacylation. These studies strengthen the possibility that the hypothesized chiral selection of amino acids in biological systems actually occurred at the molecular level. It is significant to raise the points because the topic so far has tended to be expressed unclearly and ambiguously and also handled as such owing to its very nature.Tan, Z., Lu, S., Li, W., Zhang, Y., He, T., Jia, W., Peng, P.a., 2019. Climate-driven variations in the depositional environment and organic matter accumulation of lacustrine mudstones: Evidence from organic and inorganic geochemistry in the Biyang depression, Nanxiang Basin, China. Energy & Fuels 33, 6946-6960. influence of the paleoclimate on the organic matter (OM) accumulation and depositional process in the third member of the Hetaoyuan Formation shales is unclear in the Paleogene lacustrine systems in the Biyang Depression, Nanxiang Basin, Eastern China. Here, inorganic and organic geochemical analyses were performed on samples from a 25 m profile to examine the effects of paleoclimate change on the depositional environment and OM accumulation within this interval. Based on mineralogical and geochemical data from the B1 Well, two major lithofacies assemblages, calcareous mudstone-dominated (LA1) and clay-rich mudstone-dominated (LA2), were identified. Although generally anoxic bottom water was present during sedimentation, subtle differences in depositional environment and OM enrichment were found for the two lithofacies. The mineral composition and multiple geochemical proxies, including detritus index (sum of quartz, clay minerals, and feldspar contents), C-value [∑(Fe + Mn + Cr + Ni + V + Co)/∑(Ca + Mg + Sr + Ba + K + Na)], chemical index of alteration (CIA = 100 × Al2O3/(Al2O3 + CaO* + Na2O + K2O), Rb/Sr, V/(V + Ni), Sr/Ba, Pr/Ph, and gammacerane/C30 hopane ratios all indicated that LA1 was deposited in a stable stratified saline lake with anoxic bottom water in a relatively cool, arid paleoclimate. However, these parameters suggested that LA2 was deposited in a brackish-to-saline lake with anoxic bottom water in a relatively warm, humid paleoclimate. Abundant OM (average total organic carbon (TOC) content 4.24 wt %) was accumulated mainly in LA1, with relatively high primary productivity suggested by high values of P/Ti, Ba/Al, 4-methylsterane/∑C29 steranes index (4-MSI), ααα20RC27/ααα20RC29 sterane (C27/C29), and ααα20RC28/ααα20RC29 (C28/C29) sterane ratios. In contrast, in warmer, more humid conditions, the corresponding sediments in LA2 contained less OM (average TOC 2.29 wt %), consistent with ratios indicating lower primary productivity and higher detritus input. We draw the conclusions that the accumulation of higher OM in LA1 was controlled by the combination of paleoproductivity and preservation in anoxic bottom water, while the formation of the LA2 organic-rich mudstone was mainly related to primary productivity, anoxic conditions, and the dilution by terrigenous detrital matter.Tang, L., Pang, X., Song, Y., Jiang, Z., Jiang, S., Li, Q., Zhang, H., Yang, Y., Li, X., 2019. Lower limit of hydrocarbon generation in source rocks: A case study from the Dongpu Depression, Bohai Bay Basin, East China. Journal of Asian Earth Sciences 182, 103928. the increasing demand for hydrocarbons, exploration tends to be deeper and unconventional resources. However, whether there are the lower limits for exploration depth or thermal maturity (Ro) appears to be particularly essential. It is of considerable significance to determine the lower limit of hydrocarbon generation (LLHG) since this limit can provide guidelines for hydrocarbon potential estimation. According to the mechanisms of hydrocarbon generation and expulsion, five methods are combined to determine and verify the LLHG, whose values can be expressed by LLHG(Ro) and LLHG(H). Source rock samples from the Paleogene Shahejie Formation (Es) in the Dongpu Depression were taken as an example to determine the LLHG, and then controlling factors of the LLHG were discussed. LLHG(Ro) values for Es range from 3.23% to 3.97% (average 3.71%) and LLHG(H) values range from 5244?m to 5525?m (average 5433?m). Regionally, LLHG values display obvious differences between the northern and southern of depression. LLHG values in the north are roughly larger than those in the south. In the northern depression, the LLHG(Ro) values are ranging from 3.61% to 3.97% (average 3.81%) and LLHG(H) values are ranging from 5415?m to 5545?m (average 5488?m). However, in the southern part, the LLHG(Ro) values range from 3.20% to 3.74% (average 3.48%) and the LLHG(H) values range from 5265?m to 5375?m (average 5278?m). The main controlling factors for LLHG diversity between the north and the south of depression are organic matter (OM) type and abundance, formation temperature and pressure.Tannous, J.H., de Klerk, A., 2019. Quantification of the free radical content of oilsands bitumen fractions. Energy & Fuels 33, 7083-7093. spin resonance (ESR) spectroscopy was employed to perform quantitative analysis of the free radical content of oilsands bitumen, asphaltenes, deasphalted oil, vacuum residue, and vacuum gas oil fractions, as well as thermally converted product fractions. Calibration standards for ESR were compared, and 2,2-diphenyl-1-picrylhydrazyl was selected. The heaviest fractions, including asphaltenes, had free radical concentrations in the range 1017–1018 spins/g, whereas lighter fractions such as the lighter gas oil fractions had free radical concentrations in the range 1016–1017 spins/g. It was found that the bulk liquid properties affected the measured free radical concentration even after compensating for effects that could affect the spectroscopy. These differences were not analytical artifacts and could be explained with reference to the literature in terms of the “equilibrium” composition resulting from dimerization and decomposition of free radical pairs. Reported free radical concentrations must consequently be interpreted by considering the nature of the bulk liquid that was analyzed. Practically, the results have implications for thermal conversion of bitumen. It appears that the free radical concentration and availability of reactive free radicals can be independently manipulated through temperature and the bulk liquid properties.Tao, H., Zhang, L., Liu, Q., Zhao, Y., Feng, Q., 2019. Competitive adsorption and selective diffusion of CH4 and the intruding gases in coal vitrinite. Energy & Fuels 33, 6971-6982., the adsorption and diffusion of CH4 and the intruding gases in coal were systematically simulated via Monte Carlo. The adsorption selectivity of carbon dioxide over methane (SCO2/CH4, >1) decreases significantly at P < 6 MPa and is kept stable when P > 6 MPa. However, SN2/CH4 (<1) monotonously increases with the increasing pressure, temperature, and bulk mole fraction (BMF) of N2. Both the cross exchange (Di,j) and diagonal diffusion (Di,i) coefficients in the nCO2 + mCH4 and nN2 + mCH4 systems gradually increase with the increasing temperature. Di,j is far higher than Di,i for these two systems, indicating the weaker coupling strength of gas–gas interactions than the gas–coal interactions. D111 (or D112) increases while D221 (or D222) decreases with the increase of CO2 (or N2) BMF. The swelling ratios of nCO2 + mCH4 and nN2 + mCH4 increase slightly at temperatures lower than 338 K and significantly at temperatures higher than 338 K, and both of them are positively related to BMFs of CO2 and CH4, respectively. Both SCO2/CH4d and SN2/CH4d increase with the increasing BMF of carbon dioxide and methane, respectively, indicating that the replacement effects of CO2 and N2 engineering are weightily related to the mole fractions of the invading gases. SCO2/CH4d first increases (≤398 K) and then decreases (398 < T < 438 K). Concerning the geological conditions, the optimization injection depths were 800–1100 m (7.94–10.88 MPa) and 600–900 m (5.98–8.92 MPa) for carbon dioxide and nitrogen, respectively.Tewari, A., D'Rozario, A., Bhattacharya, S., Barua, A., Bera, M., Bera, S., Dutta, S., 2019. Biomarker signatures of the iconic Glossopteris plant. Palaeogeography, Palaeoclimatology, Palaeoecology 531, 108887. is the quintessential marker plant that dominated the forests of the Southern Hemisphere continents during the Permian before their abrupt extinction at the close of the Palaeozoic. Fossilized leaf and stem remains of Glossopteris plants, collected from the Permian succession of eastern India, were analysed to recognize the molecular signatures of solvent-extractable and non-extractable organic matter. Lipid-derived aliphatic and aromatic biomarkers were studied using GC–MS and GC?×?GC-TOFMS, while tetramethylammonium hydroxide (TMAH) thermochemolysis with GC–MS and GC?×?GC-TOFMS was used to reveal lignin precursors. The thermal maturity indices indicate low thermal rank for both samples. The presence of aromatic diterpanes in the leaf extract suggests that the Glossopteris plant was able to biosynthesize abietic acid and related plant terpenoids. The thermochemolysis products (thermochemolysates) of the samples contain monomethoxy-, and dimethoxybenzene derivatives produced from p?hydroxyphenyl and guaiacyl units of lignin, respectively, which are the main constituents of extant gymnosperm lignin. The thermochemolysates indicate that lignin biosynthesis had evolved in Glossopteris.Thakur, N., Wahab, M.F., Khanal, D.D., Armstrong, D.W., 2019. Synthetic aluminosilicate based geopolymers – Second generation geopolymer HPLC stationary phases. Analytica Chimica Acta 1081, 209-217. survey of existing stationary phases classified by the United States Pharmacopeia reveals that 120 groups of chromatographic supports mostly utilize silica-silane chemistry, polymeric materials along with some niche metal oxides. In this work, the synthesis and characterization of transition-metal free geopolymers as a new class of stationary phases for hydrophilic interaction liquid chromatography and normal phase separations is reported. The geopolymers were synthesized by reaction of synthetic aluminosilicate with potassium silicate (fumed silica dissolved in KOH) in a water-in-oil emulsion. For comparative purposes of peak shapes, a geopolymer from natural metakaolin was also synthesized. The geopolymers were examined by X-ray diffraction, energy dispersive spectroscopy, laser diffraction, and N2-adsorption isotherms. This two-step approach gives spherical microparticles with surface area and pore size comparable to silica phases (150?m2/g and 120?? respectively). Both synthetic aluminosilicates based and natural metakaolin based geopolymers occupy a unique “spot” in the HILIC selectivity chart when compared to 35 HILIC phases. An additional promising feature of geopolymers is high pH and temperature stability which are used to tune selectivity for small polar analytes. High pH separations are shown with carboxylic acids. Geopolymers also show mixed mode behavior in retention with ion-exchange properties in purely aqueous mobile phases. The separation of derivatized sugars is demonstrated and compared with porous graphitic carbon (Hypercarb?) as another pH-stable stationary phase.Thatje, S., Brown, A., Hillenbrand, C.-D., 2019. Prospects for metazoan life in sub-glacial Antarctic lakes: the most extreme life on Earth? International Journal of Astrobiology 18, 416-419. 400 subglacial lakes are known from Antarctica. The question of whether life unique of subglacial lakes exists has been paramount since their discovery. Despite frequent evidence of microbial life mostly from accretion ice, subglacial lakes are characterized by physiologically hostile conditions to metazoan life, as we know it. Pure water (salinity ≤0.4–1.2%), extreme cold (?3°C), high hydrostatic pressure, areas of limited or no oxygen availability and permanent darkness altogether require physiological adaptations to these harsh conditions. The record of gene sequences including some associated with hydrothermal vents does foster the idea of metazoan life in Lake Vostok. Here, we synthesize the physico-chemical environment surrounding sub-glacial lakes and potential sites of hydrothermal activity and advocate that the physico-chemical stability found at these sites may be the most likely sites for metazoan life to exist. The unique conditions presented by Lake Vostok may also offer an outlook on life to be expected in extra-terrestrial subglacial environments, such as on Jupiter's moon Europa or Saturn's moon Enceladus.Thi?ner, J.B., Nett, L., Zhou, S., Preibisch, Y., Hollert, H., Achten, C., 2019. Identification of 7–9 ring polycyclic aromatic hydrocarbons in coals and petrol coke using High performance liquid chromatography – Diode array detection coupled to Atmospheric pressure laser ionization – Mass spectrometry (HPLC-DAD-APLI-MS). Environmental Pollution 252, 723-732. aromatic hydrocarbons containing at least 24 carbon atoms (≥C24-PAH) are often associated with pyrogenic processes such as combustion of fuel, wood or coal, and occur in the environment in diesel particulate matter, black carbon and coal tar. Some of the ≥C24-PAH, particularly the group of dibenzopyrenes (five isomers, six aromatic rings) are known to show high mutagenic and carcinogenic activita.Gas chromatography – mass spectrometry is a well-established method for the analysis of lower molecular weight PAH but is not optimally suited for the analysis of ≥C24-PAH due to their low vapor pressures. Also, hundreds of ≥C24-PAH isomers are possible but only a few compounds are commercially available as reference standards. Therefore, in this study, a combination of multidimensional liquid chromatography, UV–Vis diode array detection, PAH selective and highly sensitive atmospheric pressure laser ionization – mass spectrometry is used to detect and unequivocally identify PAH. For identification of PAH in two bituminous coals and one petrol coke sample, unique and compound specific UV–Vis spectra were acquired. It was possible to identify ten compounds (naphtho[1,2,3,4-ghi]perylene, dibenzo[b,ghi]perylene, dibenzo[e,ghi]perylene, dibenzo[cd,lm]perylene, benzo[a]coronene, phenanthrol[5,4,3,2-abcde]perylene, benzo[ghi]naphtho[8,1,2-bcd]perylene, benzo[pqr]naphtho[8,1,2-bcd]perylene, naphtho[8,1,2-abc]coronene and tribenzo[e,ghi,k]perylene) by comparison of acquired spectra with spectra from literature. Additionally, it was possible to detect similar distribution patterns in different samples and signals related to alkylated naphthopyrenes, naphthofluoranthenes or dibenzopyrenes. Subsequent effect-directed analysis of a bituminous coal sample using the microEROD (ethoxyresorufin-O-deethylase) bioassay showed high suitability and revealed lower EROD induction for the ≥C24-PAH (TEQ range 0.67–10.07?ng/g) than for the allover?<?C24-PAH containing fraction (TEQ 84.00?ng/g). Nevertheless, the toxicity of ≥C24-PAH has a significant impact compared with <C24-PAH and must be considered for risk assessment. The LC-DAD-APLI-MS method, presented in this study, is a powerful tool for the unequivocal identification of these?≥?C24-PAH.Thomazo, C., Brayard, A., Elmeknassi, S., Vennin, E., Olivier, N., Caravaca, G., Escarguel, G., Fara, E., Bylund, K.G., Jenks, J.F., Stephen, D.A., Killingsworth, B., Sansjofre, P., Cartigny, P., 2019. Multiple sulfur isotope signals associated with the late Smithian event and the Smithian/Spathian boundary. Earth-Science Reviews 195, 96-113. Early Triassic is generally portrayed as a time of various, high ecological stresses leading to a delayed biotic recovery after the devastating end-Permian mass extinction. This interval is notably characterized by repeated biotic crises (e.g., during the late Smithian), large-scale fluctuations of the global carbon, nitrogen and sulfur cycles as well as harsh marine conditions including a combination of ocean acidification, anoxia, extreme seawater temperatures and shifting productivity. Observations from different paleolatitudes suggest that sulfidic (H2S-rich) conditions may have developed widely during the Early Triassic, possibly reaching up to ultra-shallow environments in some places. However, the existence and the spatio-temporal extent of such redox swings remain poorly constrained. In order to explore Early Triassic paleoceanographic redox changes and their potential influences on the biotic recovery, we analyzed multiple sulfur isotopes (32S, 33S, 34S, and 36S) of sedimentary pyrite and carbonate associated sulfate (δ34SCAS) from the Mineral Mountains section, Utah. Sediments from this section were mainly deposited in shallow waters and span the Smithian and lower Spathian. We report a 68‰ range of variations in δ34Spy associated with Δ33Spy varying from ?0.01‰ to +0.12‰, whereas the δ34SCAS varies between +19.5‰ and?+?34.8‰. We interpret the observed signal of multiple sulfur isotopes as reflecting the operation of pore-water synsedimentary microbial sulfate reduction in open system with respect to sulfates before the late Smithian, evolving to a closed system, sulfate limited, Rayleigh-type distillation across the Smithian/Spathian boundary (SSB) and immediately after the SSB. We argue that this marked change is driven by the effectiveness of the connection between the sedimentary pore waters and the overlying water column, which is, in this case, controlled by the local sedimentological conditions such as the bioturbation intensity and the sedimentation rate. Therefore, our results suggest that changes in the sulfur cycle before and across the SSB at Mineral Mountains is probably a local consequence of the loss of the mixed sedimentary layer during the late Smithian extinction event, as opposed to reflecting the development of a lethal anoxic ocean at the global scale.Tomkins, A.G., Genge, M.J., Tait, A.W., Alkemade, S.L., Langendam, A.D., Perry, P.P., Wilson, S.A., 2019. High survivability of micrometeorites on Mars: Sites with enhanced availability of limiting nutrients. Journal of Geophysical Research: Planets 124, 1802-1818.: NASA's strategy in exploring Mars has been to follow the water, because water is essential for life, and it has been found that there are many locations where there was once liquid water on the surface. Now perhaps, to narrow down the search for life on a barren basalt‐dominated surface, there needs to be a refocusing to a strategy of “follow the nutrients.” Here we model the entry of metallic micrometeoroids through the Martian atmosphere, and investigate variations in micrometeorite abundance at an analogue site on the Nullarbor Plain in Australia, to determine where the common limiting nutrients available in these (e.g., P, S, Fe) become concentrated on the surface of Mars. We find that dense micrometeorites are abundant in a range of desert environments, becoming concentrated by aeolian processes into specific sites that would be easily investigated by a robotic rover. Our modeling suggests that micrometeorites are currently far more abundant on the surface of Mars than on Earth, and given the far greater abundance of water and warmer conditions on Earth and thus much more active weather system, this was likely true throughout the history of Mars. Because micrometeorites contain a variety of redox sensitive minerals including FeNi alloys, sulfide and phosphide minerals, and organic compounds, the sites where these become concentrated are far more nutrient rich, and thus more compatible with chemolithotrophic life than most of the Martian surface.Plain Language Summary: NASA's exploration program has allowed the scientific community to demonstrate clearly that Mars had a watery past, so the search for life needs to move on to identifying the places where water and nutrients coincided. We have investigated the relative abundance of micrometeorites on Mars compared to the Earth because these contain key nutrients that the earliest life forms on Earth used, and because their contained minerals can be used to investigate past atmospheric chemistry. We suggest that micrometeorites should be far more abundant on the Martian surface than on Earth's, and that wind‐driven modification of sediments is expected to concentrate micrometeorites, and their contained nutrients, in gravel beds and cracks in exposed bedrock.Torres-Farradá, G., Manzano-León, A.M., Rineau, F., Ramos Leal, M., Thijs, S., Jambon, I., Put, J., Czech, J., Guerra Rivera, G., Carleer, R., Vangronsveld, J., 2019. Biodegradation of polycyclic aromatic hydrocarbons by native Ganoderma sp. strains: identification of metabolites and proposed degradation pathways. Applied Microbiology and Biotechnology 103, 7203-7215. polycyclic aromatic hydrocarbons (PAHs) are mutagenic, teratogenic, and carcinogenic, they are of considerable environmental concern. A biotechnological approach to remove such compounds from polluted ecosystems could be based on the use of white-rot fungi (WRF). The potential of well-adapted indigenous Ganoderma strains to degrade PAHs remains underexplored. Seven native Ganoderma sp. strains with capacity to produce high levels of laccase enzymes and to degrade synthetic dyes were investigated for their degradation potential of PAHs. The crude enzymatic extracts produced by Ganoderma strains differentially degraded the PAHs assayed (naphthalene 34—73%, phenanthrene 9—67%, fluorene 11—64%). Ganoderma sp. UH-M was the most promising strain for the degradation of PAHs without the addition of redox mediators. The PAH oxidation performed by the extracellular enzymes produced more polar and soluble metabolites such as benzoic acid, catechol, phthalic and protocatechuic acids, allowing us to propose degradation pathways of these PAHs. This is the first study in which breakdown intermediates and degradation pathways of PAHs by a native strain of Ganoderma genus were determined. The treatment of PAHs with the biomass of this fungal strain enhanced the degradation of the three PAHs. The laccase enzymes played an important role in the degradation of these compounds; however, the role of peroxidases cannot be excluded. Ganoderma sp. UH-M is a promising candidate for the bioremediation of ecosystems polluted with PAHs.Trembath-Reichert, E., Butterfield, D.A., Huber, J.A., 2019. Active subseafloor microbial communities from Mariana back-arc venting fluids share metabolic strategies across different thermal niches and taxa. The ISME Journal 13, 2264-2279. are many unknowns regarding the distribution, activity, community composition, and metabolic repertoire of microbial communities in the subseafloor of deep-sea hydrothermal vents. Here we provide the first characterization of subseafloor microbial communities from venting fluids along the central Mariana back-arc basin (15.5–18°N), where the slow-spreading rate, depth, and variable geochemistry along the back-arc distinguish it from other spreading centers. Results indicated that diverse Epsilonbacteraeota were abundant across all sites, with a population of high temperature Aquificae restricted to the northern segment. This suggests that differences in subseafloor populations along the back-arc are associated with local geologic setting and resultant geochemistry. Metatranscriptomics coupled to stable isotope probing revealed bacterial carbon fixation linked to hydrogen oxidation, denitrification, and sulfide or thiosulfate oxidation at all sites, regardless of community composition. NanoSIMS (nanoscale secondary ion mass spectrometry) incubations at 80?°C show only a small portion of the microbial community took up bicarbonate, but those autotrophs had the highest overall rates of activity detected across all experiments. By comparison, acetate was more universally utilized to sustain growth, but within a?smaller range of activity. Together, results indicate that microbial communities in venting fluids from the Mariana back-arc contain active subseafloor communities reflective of their local conditions with metabolisms commonly shared across geologically disparate spreading centers throughout the ocean.Tsybin, Y.O., Nagornov, K.O., Kozhinov, A.N., 2019. Chapter 5 - Advanced fundamentals in Fourier transform mass spectrometry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 113-132. transform mass spectrometry (FTMS) is an enabling technique to many challenging applications in molecular sciences. In this chapter we revisit FTMS fundamentals to further rationalize the selection of data acquisition and data processing approaches for the everyday FTMS practice. Whereas the FT-ICR MS fundamentals have been investigated and extensively reported for more than 40 years, the same level of understanding and description is not available for the teenager and rapidly evolving Orbitrap FTMS. Despite the widespread presence of the Orbitrap technology and its exponential development over the past decade, the associated data processing procedures are not always comprehensively described in the scientific literature. With this Chapter, we thus attempt to better inform the general user about the basics in mass spectra summation (averaging) and noise characteristics, as well as the benefits and consequences of using the data reduction approaches. For the latter, we describe the principles and compare the outcome of the full profile and the reduced profile mass spectra representation. To further bridge the knowledge gap, we compared ICR and Orbitrap FTMS techniques in regard to their resolution performance reflected through the theoretical didactic examples.Tucker, L.H., Hamm, G.R., Sargeant, R.J.E., Goodwin, R.J.A., Mackay, C.L., Campbell, C.J., Clarke, D.J., 2019. Untargeted metabolite mapping in 3D cell culture models using high spectral resolution FT-ICR mass spectrometry imaging. Analytical Chemistry 91, 9522-9529. tumor spheroids (MTS) are a well-established model system for drug development and are a valuable in vitro research tool for use prior to employing animal models. These 3D-cell cultures are thought to display chemical gradients of oxygen and nutrients throughout their structure, giving rise to distinct microenvironments in radial layers, thus, mimicking the pathophysiological environment of a tumor. Little is known about the localized distributions of metabolites within these microenvironments. To address this, here we utilize high spectral resolution Fourier-transform ion cyclotron resonance (FT-ICR), MALDI mass spectrometry imaging (MSI) to image the distribution of endogenous metabolites in breast cancer MCF-7 spheroids. We show that known specific metabolite markers (adenosine phosphates and glutathione) indicate that the central region of these cell culture models experiences increased hypoxic and oxidative stress. By using discriminatory analysis, we have identified which m/z values localize toward the outer proliferative or central hypoxic regions of an MTS. Elemental formulae were assigned with sub-ppm mass accuracy, allowing metabolite assignment. Using this information, we have mapped these metabolites back to distinct pathways to improve our understanding of the molecular environment and biochemistry of these tumor models.Tuite, M.L., Williford, K.H., Macko, S.A., 2019. From greenhouse to icehouse: Nitrogen biogeochemistry of an epeiric sea in the context of the oxygenation of the Late Devonian atmosphere/ocean system. Palaeogeography, Palaeoclimatology, Palaeoecology 531. Late Devonian emergence of extensive arborescent terrestrial ecosystems produced changes in the Earth's atmosphere and climate that resulted in substantial changes to the biogeochemistry of marine ecosystems. The biogeochemistry of nitrogen in epeiric seas was particularly susceptible to alteration because of its dependence upon the series of redox-mediated reactions that comprise the marine N cycle. In order to explore the impact of climate change on N biogeochemistry in a Late Devonian epeiric sea, we sampled a core from the Appalachian Basin that spans the interval from the greenhouse climate at the base of the Famennian period to glacial conditions near its conclusion. Based upon stable isotope analysis of N, C, and S as well as elemental analysis of N, C, P, S, and Fe, we contend that two distinct biogeochemical regimes obtained during the contrasting climates. The greenhouse regime featured low seawater O2 and pH that served to significantly curtail the oxidation of ammonia – i.e. nitrification – resulting in an ammonium-dominated water column and low sediment δ15N values. The greenhouse also featured more extensive recycling of C, N, and P. In contrast, the higher seawater O2 and pH of the icehouse regime permitted nitrification in the water column resulting in a nitrate-dominated system and higher sediment δ15N values. We conclude that nitrification was the key component of the N cycle that differentiated the two climate/biogeochemical regimes.Turkovskaya, O., Muratova, A., 2019. Plant–bacterial degradation of polyaromatic hydrocarbons in the rhizosphere. Trends in Biotechnology 37, 926-930. of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria and plant root exudate enzymes from contaminated rhizospheres suggest that pollutant rhizodegradation involves the joint work of bacteria and plants. Plant–microbial associations with coupled metabolic capabilities that completely degrade PAHs while avoiding the formation of dangerous intermediates are biotechnologically promising.Uveges, B.T., Junium, C.K., Boyer, D.L., Cohen, P.A., Day, J.E., 2019. Biogeochemical controls on black shale deposition during the Frasnian-Famennian biotic crisis in the Illinois and Appalachian Basins, USA, inferred from stable isotopes of nitrogen and carbon. Palaeogeography, Palaeoclimatology, Palaeoecology 531, 108787. Frasnian-Famennian biotic crisis is marked by two distinct intervals known as the Lower and Upper Kellwasser Events (KWEs) that in many locations are associated with deposition of organic-rich shales. Sedimentary nitrogen and carbon isotopes offer insight into the biogeochemical processing of nutrients, production of organic matter, and palaeoceanographic conditions during the KWEs. Here we present new bulk nitrogen (δ15Nbulk) and organic carbon (δ13Corg) isotope data from the Late Devonian Appalachian and Illinois Basins (AB and IB), with a focus on intervals encompassing the KWEs. Black shales from the IB and AB, including the KWEs, are 15N-depleted (?1.0–+2.0‰) and have significantly lower δ15Nbulk than interbedded grey shales (+0.5–+4.0‰), a trend consistent with many instances of black shale deposition in the Phanerozoic. Organic carbon isotopes exhibit the broad, positive excursions (~+3.5‰ from background) that are typical of the KWEs globally. Superimposed over these positive excursions in δ13Corg are sharp decreases of up to ~3.0‰ within the black shale beds, to as low as ?30.5‰. The pattern of δ15Nbulk and δ13Corg values suggests that the depth of the chemocline and the degree of water-column stratification exert a primary control on both δ15Nbulk and δ13Corg during black shale deposition. In the context of the Frasnian-Famennian biotic crisis, the oscillating redox state and changing temperatures would have likely placed extreme stress on organisms within the marine environment of the AB and IB and may potentially have been a contributing factor to diversity loss over this time period.Vallalar, B., Meyer-Dombard, D.A.R., Cardace, D., Arcilla, C.A., 2019. Multimetal resistant, alkalitolerant bacteria isolated from serpentinizing fluid-associated sediments and acid mine drainage in the Zambales ophiolite, the Philippines. Geomicrobiology Journal 36, 792-809. in ophiolitic exposure settings often produces fluids and sediments that have elevated concentrations of various toxic heavy metals such as chromium, nickel, cobalt, copper, and zinc. Microorganisms inhabiting these environments (e.g., serpentinite soils or sediments) are likely adapted to tolerate these metals along with other physicochemical extremes. The purpose of this study is to isolate bacteria capable of tolerating extremely high concentrations of multiple metals and to assess the various tolerance mechanisms exhibited by different organisms. Sediment samples for microbial culturing were collected from Manleluag Spring National Park and Barlo Mine located on the island of Luzon, the Philippines. Luria-Bertani (LB) agar medium was supplemented with increasing concentrations of five trace elements – Cu, Cr, Co, Ni, and Zn. Over 20 isolates were obtained from media with concentrations ranging from 25?mg/L to 400?mg/L of each metal. Most isolates were identified as belonging to the genus Bacillus. Adaptation mechanisms, including potential biomineralization, were considered for select strains using inductively coupled plasma optical emission spectroscopy (ICP-OES), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and X-ray diffraction (XRD). ICP-OES analysis suggests that the primary resistance mechanism used by most isolates is cellular efflux, although it was determined that some organisms were able to reduce aqueous Cu concentration by up to 40%. Most strains exhibited growth at pH 12, demonstrating that alkalitolerant, highly metal resistant organisms are found in these ophiolite-associated environments. These organisms may be exploited for bioremediation, secondary metabolite production, and other industrial applications.van Acken, D., Tütken, T., Daly, J.S., Schmid-R?hl, A., Orr, P.J., 2019. Rhenium?osmium geochronology of the Toarcian Posidonia Shale, SW Germany. Palaeogeography, Palaeoclimatology, Palaeoecology 534, 109294. shale samples from sedimentary layers below and between the Unterer Stein, Oberer Stein, Inoceramus Bank, and Nagelkalk horizons from the Dormettingen quarry, SW Germany were analysed for their Re and Os isotope composition and content. The ~12-m-thick sedimentary sequence of the Posidonia Shale Formation, composed of multiple layers of black shale and intercalated limestone beds, was deposited during the Early Jurassic (Toarcian), a time during which black shale sedimentation was ubiquitous in Western Europe during a widespread oceanic anoxic event. Both the marl and shale layers beneath the black shales and adjacent to the Oberer Stein limestone layer show signs of bioturbation. The excellent biostratigraphic constraints and the high Re and Os contents (24–290?ppb and 290–1050?ppt, respectively) of the Dormettingen shales thus make these samples ideal for testing the influence of bioturbation on the Re-Os isotope system, as well as refining age constraints for the Toarcian OAE and potential triggers for this event. The calculated isochron age for the Dormettingen shales is 183.0?±?2.0?Ma, with a low initial 187Os/188Osi of 0.377?±?0.065, indicating a Pliensbachian to Toarcian age. This age is in agreement with published U-Pb and Re-Os ages for other Lower Jurassic sites, astronomical constraints, and biostratigraphic correlations, suggesting limited disturbance of the isotope system by minor degrees of biological activity. The low 187Os/188Osi is consistent with significant influx of mantle-derived material into the Toarcian ocean, likely from weathering of Karoo-Ferrar Large Igneous Province basalts.Vellekoop, J., Woelders, L., Sluijs, A., Miller, K.G., Speijer, R.P., 2019. Phytoplankton community disruption caused by latest Cretaceous global warming. Biogeosciences Discussions 2019, 1-19. responses to a ~?350 kiloyear long phase of gradual late Maastrichtian (latest-Cretaceous) global warming starting at ~?66.4?Ma can provide valuable insights into the long-term influences of global change on marine ecosystems. Here we perform micropaleontological analyses on three cores from the New Jersey paleoshelf, to assess the response of phytoplankton using cyst-forming dinoflagellates and benthic ecosystems using benthic foraminifera. Our records show that this Latest Maastrichtian Warming Event (LMWE), characterized by a 4.0?±?1.3??C warming of sea-surface waters on the New Jersey paleoshelf, resulted in a succession of nearly monospecific dinoflagellate cyst assemblages, dominated by the species Palynodinium grallator. This response, likely triggered by the combination of warmer and seasonally thermally-stratified seas, appears to have been more intense at offshore sites than at nearshore sites. The LMWE, and related dinoflagellate response, is associated with an impoverished benthic ecosystem. A wider geographic survey of literature data reveals that the dominance of P. grallator is a marker for the LMWE throughout the northern mid-latitudes. While the dinocyst assemblage returned to a stable, normal marine community in the last tens of thousands of years of the Maastrichtian, benthic foraminiferal diversity remained slightly suppressed. Increased ecosystem stress during the latest Maastrichtian potentially primed global ecosystems for the subsequent mass extinction following the K-Pg boundary Chicxulub impact.Vigderovich, H., Liang, L., Herut, B., Wang, F., Wurgaft, E., Rubin-Blum, M., Sivan, O., 2019. Evidence for microbial iron reduction in the methanic sediments of the oligotrophic southeastern Mediterranean continental shelf. Biogeosciences 16, 3165-3181. iron reduction is probably one of the oldest types of metabolisms that still participates in important biogeochemical cycles, such as those of carbon and sulfur. It is one of the more energetically favorable anaerobic microbial respiration processes and is usually coupled to the oxidation of organic matter. Traditionally this process is thought to be limited to the shallow part of the sedimentary column in most aquatic systems. However, iron reduction has also been observed in the methanic zone of many marine and freshwater sediments, well below its expected zone and occasionally accompanied by decreases in methane, suggesting a link between the iron and the methane cycles. Nevertheless, the mechanistic nature of this link (competition, redox or other) has yet to be established and has not been studied in oligotrophic shallow marine sediments. In this study we present combined geochemical and molecular evidences for microbial iron reduction in the methanic zone of the oligotrophic southeastern (SE) Mediterranean continental shelf. Geochemical porewater profiles indicate iron reduction in two zones, the uppermost part of the sediment, and the deeper zone, in the layer of high methane concentration. Results from a slurry incubation experiment indicate that the deep methanic iron reduction is microbially mediated. The sedimentary profiles of microbial abundance and quantitative PCR (qPCR) of the mcrA gene, together with Spearman correlation between the microbial data and Fe(II) concentrations in the porewater, suggest types of potential microorganisms that may be involved in the iron reduction via several potential pathways: H2 or organic matter oxidation, an active sulfur cycle, or iron-driven anaerobic oxidation of methane. We suggest that significant upward migration of methane in the sedimentary column and its oxidation by sulfate may fuel the microbial activity in the sulfate methane transition zone (SMTZ). The biomass created by this microbial activity can be used by the iron reducers below, in the methanic zone of the sediments of the SE Mediterranean.Vinh, J., 2019. Chapter 17 - Proteomics and proteoforms: Bottom-up or top-down, how to use high-resolution mass spectrometry to reach the Grail, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 529-567. consists of the dynamic characterization of functional proteins within a biological model in a given environment at a given time. It relies on the use of biological mass spectrometry with upstream purification/fractionation strategies. The study of proteoforms can be done by considering either these intact entities (top-down approach) or the proteolytic peptides (bottom-up approach). A partial proteolysis allows to address more specific longer peptides, for an easier study (middle-down approach). High accuracy/high resolution improves the robustness of the study of complex samples. Metadata is processed using signal processing and deconvolution algorithms for protein inference, and sequences database searching and statistical analysis. Here, we will discuss the various proteomics strategies by referring to the latest and most recent review articles at the time of writing of this text. Despite the complementarity of discussed approaches, none of which seems to allow for exhaustive coverage of the proteome.Vitas, M., Dobovi?ek, A., 2019. Towards?a general definition of life. Origins of Life and Evolution of Biospheres 49, 77-88. new definition of life is proposed and discussed in the present article. It is formulated by modifying and extending NASA’s working definition of life, which postulates that life is a “self-sustaining chemical system capable of Darwinian evolution”. The new definition includes a thermodynamical aspect of life as a far from equilibrium system and considers the flow of information from the environment to the living system. In our derivation of the definition of life we have assumed the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems that only subsequently acquired the capacity of genetic heredity. The new proposed definition of life is independent of the mode of evolution, regardless of whether Lamarckian or Darwinian evolution operated at the origins of life and throughout evolutionary history. The new definition of life presented herein is formulated in a minimal manner and it is general enough that it does not distinguish between individual (metabolic) network and the collective (ecological) one. The newly proposed definition of life may be of interest for astrobiology, research into the origins of life or for efforts to produce synthetic or artificial life, and it furthermore may also have implications in the cognitive and computer sciences.Vorrath, M.-E., Müller, J., Esper, O., Mollenhauer, G., Haas, C., Schefu?, E., Fahl, K., 2019. Highly branched isoprenoids for Southern Ocean sea ice reconstructions: a pilot study from the Western Antarctic Peninsula. Biogeosciences 16, 2961-2981. geochemical and micropaleontological analyses of surface sediments collected in the southern Drake Passage and the Bransfield Strait, Western Antarctic Peninsula, enable a proxy-based reconstruction of recent sea ice conditions in this climate-sensitive area. We study the distribution of the sea ice biomarker IPSO25, and biomarkers of open marine environments such as more unsaturated highly branched isoprenoid alkenes and phytosterols. Comparison of the sedimentary distribution of these biomarker lipids with sea ice data obtained from satellite observations and diatom-based sea ice estimates provide for an evaluation of the suitability of these biomarkers to reflect recent sea surface conditions. The distribution of IPSO25 supports earlier suggestions that the source diatom seems to be common in near-coastal environments characterized by annually recurring sea ice cover, while the distribution of the other biomarkers is highly variable. Offsets between sea ice estimates deduced from the abundance of biomarkers and satellite-based sea ice data are attributed to the different time intervals recorded within the sediments and the instrumental records from the study area, which experienced rapid environmental changes during the past 100 years. To distinguish areas characterized by permanently ice-free conditions, seasonal sea ice cover and extended sea ice cover, we apply the concept of the PIP25 index from the Arctic Ocean to our data and introduce the term PIPSO25 as a potential sea ice proxy. While the trends in PIPSO25 are generally consistent with satellite sea ice data and winter sea ice concentrations in the study area estimated by diatom transfer functions, more studies on the environmental significance of IPSO25 as a Southern Ocean sea ice proxy are needed before this biomarker can be applied for semi-quantitative sea ice reconstructions.Wadham, J.L., Hawkings, J.R., Tarasov, L., Gregoire, L.J., Spencer, R.G.M., Gutjahr, M., Ridgwell, A., Kohfeld, K.E., 2019. Ice sheets matter for the global carbon cycle. Nature Communications 10, 3567. cycling of carbon on Earth exerts a fundamental influence upon the greenhouse gas content of the atmosphere, and hence global climate over millennia. Until recently, ice sheets were viewed as inert components of this cycle and largely disregarded in global models. Research in the past decade has transformed this view, demonstrating the existence of uniquely adapted microbial communities, high rates of biogeochemical/physical weathering in ice sheets and storage and cycling of organic carbon (>104 Pg C) and nutrients. Here we assess the active role of ice sheets in the global carbon cycle and potential ramifications of enhanced melt and ice discharge in a warming world.Wadsworth, J., Rettberg, P., Cockell, C.S., 2019. Aggregated cell masses provide protection against space extremes and a microhabitat for hitchhiking co-inhabitants. Astrobiology 19, 995-1007. European Space Agency's EXPOSE facility, located on the outside of the International Space Station, was used to investigate the survival of cell aggregates of a cyanobacterium, Gloeocapsa sp., in space and simulated martian conditions for 531 days in low Earth orbit as part of the “Biofilm Organisms Surfing Space” (BOSS) experiments.Postflight analysis showed that the cell aggregates of the organism conferred protection against space conditions compared to planktonic cells. These cell aggregates, which consisted of groups of metabolically inactive cells that do not form structured layered biofilms, demonstrated that disordered “primitive” aggregates of sheathed cells can provide protection against environmental stress such as UV radiation. Furthermore, the experiment demonstrated that the cyanobacterial cell aggregates provided a microhabitat for a smaller bacterial co-cultured species that also survived in space. This observation shows that viable cells can “hitchhike” through space within the confines of larger protecting cells or cell aggregates, with implications for planetary protection, human health, and other space microbiology applications.Walker, X.J., Baltzer, J.L., Cumming, S.G., Day, N.J., Ebert, C., Goetz, S., Johnstone, J.F., Potter, S., Rogers, B.M., Schuur, E.A.G., Turetsky, M.R., Mack, M.C., 2019. Increasing wildfires threaten historic carbon sink of boreal forest soils. Nature 572, 520-523. forest fires emit large amounts of carbon into the atmosphere primarily through the combustion of soil organic matter. During each fire, a portion of this soil beneath the burned layer can escape combustion, leading to a net accumulation of carbon in forests over multiple fire events. Climate warming and drying has led to more severe and frequent forest fires, which threaten to shift the carbon balance of the boreal ecosystem from net accumulation to net loss1, resulting in a positive climate feedback8. This feedback will occur if organic-soil carbon that escaped burning in previous fires, termed ‘legacy carbon’, combusts. Here we use soil radiocarbon dating to quantitatively assess legacy carbon loss in the 2014 wildfires in the Northwest Territories of Canada. We found no evidence for the combustion of legacy carbon in forests that were older than the historic fire-return interval of northwestern boreal forests. In forests that were in dry landscapes and less than 60 years old at the time of the fire, legacy carbon that had escaped burning in the previous fire cycle was combusted. We estimate that 0.34 million hectares of young forests (<60 years)?that burned in the 2014 fires could have experienced legacy carbon combustion. This implies a shift to a domain of carbon cycling in which these forests become a net source—instead of a sink—of carbon to the atmosphere over consecutive fires. As boreal wildfires continue to increase in size, frequency and intensity7, the area of young forests that experience legacy carbon combustion will probably increase and have a key role in shifting the boreal carbon balance.Wallace, M.A.G., Pleil, J.D., Whitaker, D.A., Oliver, K.D., 2019. Recovery and reactivity of polycyclic aromatic hydrocarbons collected on selected sorbent tubes and analyzed by thermal desorption-gas chromatography/mass spectrometry. Journal of Chromatography A 1602, 19-29. article describes the optimization of methodology for extending the measurement of volatile organic compounds (VOCs) to increasingly heavier polycyclic aromatic hydrocarbons (PAHs) with a detailed focus on recent sorbent tube technology. Although PAHs have lower volatility than compounds such as benzene, toluene, ethylbenzene and xylenes, these semi-volatile compounds can be detected in air and breath samples. For this work, PAHs were captured on sorbent tubes and subsequently analyzed using automated thermal desorption gas chromatography – mass spectrometry (ATD-GC/MS). While many different sorbent tubes are commercially available, optimization for airborne PAH sampling using sorbent tubes has not been previously considered. Herein, several commercially available sorbent tubes, including Carbograph 2?TD/1TD, Tenax TA, XRO-440, and inert-coated PAH tubes are compared to determine the relative recovery for eight PAHs commonly found in the environment. Certain types of sorbent materials were found to be better suited for PAH recovery during thermal desorption, and PAH reaction products were observed on several types of sorbent tubes, including graphitized carbon black sorbents with stainless steel tube materials. As such, selection of sorbent tube media should be carefully considered prior to embarking on a PAH study.Wallace, R., 2019. Do aliens dream of offworld sheep? International Journal of Astrobiology 18, 396-404. Stanley Miller experiment suggests that amino acid-based life is ubiquitous in our universe, although its varieties will not have followed the particular, highly contingent and path-dependent, evolutionary trajectory found on Earth. Are many alien organisms likely to be individually conscious in ways we would recognize? Almost certainly. Will alien consciousness require a ‘sleep cycle’? A strong argument suggests it will. Can some species develop analogs to culture and high-order technology? Less likely, but still fairly probable. If so, will we be able to communicate with them? Only on a basic level, and only with profound difficulty. The reasoning is fairly direct and involves convolution of a learned heritage system with individual and collective consciousness.Wan, Z., Algeo, T.J., Gensel, P.G., Scheckler, S.E., Stein, W.E., Cressler, W.L., Berry, C.M., Xu, H., Rowe, H.D., Sauer, P.E., 2019. Environmental influences on the stable carbon isotopic composition of Devonian and Early Carboniferous land plants. Palaeogeography, Palaeoclimatology, Palaeoecology 531, 109100. analysis of the stable carbon isotopic composition of fossil land plants (δ13Cp) has the potential to offer new insights regarding paleoclimate variation and plant-environment interactions in early terrestrial ecosystems. δ13Cp was measured for 190 fossil plant specimens belonging to 10 genera of Early to Late Devonian age (Archaeopteris, Drepanophycus, Haskinsia, Leclercqia, Pertica, Psilophyton, Rhacophyton, Sawdonia, Tetraxylopteris, and Wattieza) and 2 genera of Early Carboniferous age (Genselia and Rhodeopteridium) collected from sites located mainly in the Appalachian Basin (22–30°S paleolatitude). For the full carbon-isotopic dataset (n?=?309), δ13Cp ranges from ?20.3‰ to ?30.5‰ with a mean of ?25.5‰, similar to values for modern C3 land plants. In addition to a secular trend, δ13Cp exhibits both intra- and intergeneric variation. Intrageneric variation is expressed as a small (mean 0.45‰) 13C-enrichment of leaves and spines relative to stems that may reflect differential compound-specific compositions. Intergeneric variation is expressed as a much larger (to ~5‰) spread in the mean δ13Cp values of coeval plant genera that was probably controlled by taxon-specific habitat preferences and local environmental humidity. Among Early Devonian taxa, Sawdonia yielded the most 13C-depleted values (?27.1?±?1.7‰), reflecting lower water-use efficiency that was probably related to growth in wetter habitats, and Leclercqia, Haskinsia, and Psilophyton yielded the most 13C-enriched values (?23.0?±?1.6‰, ?22.3?±?1.3‰, and ?24.8?±?1.6‰, respectively), reflecting higher water-use efficiency probably related to growth in drier habitats.Wanczek, K.P., Kanawati, B., 2019. Chapter 1 - Historical developments in Fourier transform ion cyclotron resonance mass spectrometry, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 3-33. this review, the technical developments of the Fourier transform ion cyclotron resonance (FT ICR) mass spectrometry as well as the developments of the ICR before the implementation of Fourier transform into this technique are described in historical order. Instrumentation, theory and applications are covered in ion chemistry, ion physics, and structural analysis of a very broad variety of compounds, from atoms and small molecules to biological and petrochemical analytes. For investigation, the ions can be generated inside or outside the ICR cell. They are trapped in the ICR cell, reacted with neutral molecules, photons, or ions. Finally, mass spectra of primary ions and ionic reaction products are produced with ultrahigh resolution and precision. From the many thousand publications in the field, the authors selected 221 publications for this review. The criterion was that a new development, a new aspect, a new extension, or a new application of the method was presented for the first time. In the first decades, many fundamental discoveries took place. However, the FT ICR technique has not reduced its dynamical development until today and will continue its success with many extended applications and instrumental developments in the future.Wanczek, K.P., Kanawati, B., 2019. Chapter 18 - Gas phase ion-molecule reactions of inorganic compounds in FT-ICR-MS, in: Kanawati, B., Schmitt-Kopplin, P. (Eds.), Fundamentals and Applications of Fourier Transform Mass Spectrometry. Elsevier, pp. 569-591. between ions and reactive neutrals in the gas phase at near thermal energy conditions are feasible, provided that means exist to trap ions for a couple of seconds for collisions between ions and reactive neutrals to occur. The ion cyclotron resonance (ICR) technique provides an excellent environment for such gas phase ion-molecule reactions to take place, giving also the opportunity to correlate both reactant and product ions and to determine sum formulae with ultra-high resolution. Moreover, ICR can also enable structure elucidation by several techniques like collision induced dissociation (CID) experiments. Acceleration of some reactive ions can also induce endothermic ion-molecule reactions to occur. The authors give a systematic overview of gas phase ion chemistry of non-metal main group elements, covering a wide spectrum of reactions, as well as their rate constant determinations and thermodynamic ion energetics.Wang, A., Wang, Z., Li, L., Fan, C., Zhang, K., Xiang, B., Zhou, N., Wang, Y., 2019. Hydrocarbon migration in the multiple-sourced petroleum system in the northwestern Junggar Basin (northwestern China): Constraint from geochemical and phase fractionation analysis. American Association of Petroleum Geologists Bulletin 103, 2247-2284. mixing and absence of source-rock samples make it difficult to identify the hydrocarbon migration routes in a petroleum system. We provide a case study in the northwestern Junggar Basin to show that combined geochemical and phase fractionation analyses are robust tools to unravel the complex hydrocarbon migration processes. The study rebuilds a migration history that multiple-sourced hydrocarbons migrated, mixed, accumulated, and fractionated along the evolution of regional tectonics. In detail, the Shawan and Mahu sags expelled the early-stage hydrocarbons during the Late Triassic and Late Jurassic, respectively, because of their variable subsidence. These hydrocarbons charged the entire area based on the evidence from bitumen and oil inclusions. During the Early Cretaceous, both sags subsided rapidly and expelled their late-stage hydrocarbons. These hydrocarbons first mixed along unconformities in the sags, which generated mixed-source oils and induced gas washing. Subsequently, they further mixed with or displaced the encountered early-stage oils during migration along the basal unconformity of the upper Permian into the area, causing a horizontal distribution of oil maturity zones. In addition, gases flowing through the early-stage oils induced gas washing again, creating heavy oils, condensate oils, and mixed gases. After the late-stage oils finally accumulated in fractured volcanics, migration fractionation caused the remigration of light-end compositions. This study also shows the strong control of structures on hydrocarbon migration: the unconformity network provided opportunities for long-distance migration and widespread mixing of multiple-sourced hydrocarbons, whereas the paleoridge line of the Zhongguai high defined the boundary of regional migration.Wang, B., 2019. The RNA i-motif in the primordial RNA world. Origins of Life and Evolution of Biospheres 49, 105-109. primordial RNA world is a hypothetical era prior to the appearance of protein and DNA, when RNA molecules were the sole building blocks for early forms of life on Earth. A critical concern with the RNA-world hypothesis is the instability of the cytosine nucleobase compared to the other three bases (adenine, guanine, and uracil). The author proposes that cytosine residues could have stably existed in the primordial world in the RNA i-motif, a four-stranded quadruplex structure formed by base-pairing of protonated and unprotonated cytosine residues under acidic conditions. The i-motif structure not only increases the lifetime of cytosine residues by slowing their deamination rate, but could also allow RNA polymers to bind to certain ligands (e.g., anions) to perform critical functions. Future studies focused on determining the rate of cytosine deamination in RNA i-motifs over a range of pH, temperature, and pressure conditions, and on interrogating the interactions between ligands and RNA i-motifs, could uncover new evidence of the origin of life on Earth.Wang, C.-T., Jiang, B., Zhou, Y.-W., Jiang, T.-W., Liu, J.-H., Zhu, G.-D., Cai, W.-B., 2019. Exploiting the surface-enhanced IR absorption effect in the photothermally induced resonance AFM-IR technique toward nanoscale chemical analysis. Analytical Chemistry 91, 10541-10548. photothermally induced resonance AFM-IR technique (denoted as PTIR) is a promising and still developing analytical method that can provide nanoscale chemical and topographical information. Herein, by taking advantage of a customized PTIR system with either top-down or bottom-up incidence mode for a quantum cascade laser (QCL), we explore how the surface-enhanced IR absorption (SEIRA) effect due to the Au-coated AFM tip and/or substrate may affect the PTIR signals from 25 to 580 nm thick p-nitrobenzoic acid (PNBA) samples, as a function of sample thickness, incidence mode, laser polarization, and Au film morphology. By analysis of the νas(NO2) band intensity, it is revealed that the SEIRA effect may increase the PTIR signals by 1.5–8.3 times, with that from the Au-coated substrate being greater than that from the Au-coated tip. Nevertheless, the overall PTIR signal goes up monotonically over the entire thickness range for the top-down incidence mode, while it increases and then decreases with the sample thickness for the bottom-up incidence mode. The p-polarized laser enhances the PTIR signal more than does the s-polarized laser, especially on the Au-coated substrate. The significant loss of the PTIR signal of a PNBA sample corroborates the substantial loss of the SEIRA effect of an annealed Au film. The present work may promote the application of the SEIRA effect to the PTIR technique and provides hints for developing the PTIR technique into a more versatile analytical tool.Wang, G., Qin, X., Shen, J., Zhang, Z., Han, D., Jiang, C., 2019. Quantitative analysis of microscopic structure and gas seepage characteristics of low-rank coal based on CT three-dimensional reconstruction of CT images and fractal theory. Fuel 256, 115900. pores/fractures are places for gas migration and storage in coal. Their structure complexity will directly influence the pore structure parameters and gas seepage properties of coal. Therefore, we selected 6 low-rank coal samples and quantitatively studied these influences utilizing the high-resolution micro computed tomography (μCT) and fractal theory. The total pore structure and connected pore structure parameters of 6 samples were acquired from three-dimensional (3D) reconstruction of CT images. The fractal dimensions of total pore structures (Df), solid structures (Ds) and connected pore structures (Dc) were calculated using 3D box-counting method. The relationship between Df and porosity was analyzed through the 3D total pore model, and the relationships between Dc and connectivity as well as permeability were analyzed through the 3D connected pore model. The results show that Df, which is between 2.10 and 2.43, could accurately describe the fractal characteristics of coal and the solid structure of coal is not fractal. The porosities of the 6 samples are between 3.33% and 12.18% and their relationship with Df can be defined by a monotonically increasing power function. The larger the Df is, the larger the porosity of the tested coal sample. Dc is between 2.28 and 2.32, the connectivity is between 0.54 and 0.83, and the permeability is in the range of 1.76–11.63?×?10?8?m2 (except samples 1 and 6). Dc is negatively correlated with connectivity and permeability and its relationship with connectivity and permeability can be represented by the quadratic function and monotone decreasing power function, respectively.Wang, H., Lu, L., Chen, X., Bian, Y., Ren, Z.J., 2019. Geochemical and microbial characterizations of flowback and produced water in three shale oil and gas plays in the central and western United States. Water Research 164, 114942. understanding of wastewater streams produced from shale oil and gas wells impedes best practices of wastewater treatment and reuse. This study provides a comprehensive and comparative analysis of flowback and produced water from three major and newly developed shale plays (the Bakken shale, North Dakota; the Barnett shale, Texas; and the Denver-Julesburg (DJ) basin, Colorado) in central and western United States. Geochemical features that included more than 10 water quality parameters, dissolved organic matter, as well as microbial community structures were characterized and compared. Results showed that wastewater from Bakken and Barnett shales has extremely high salinity (～295?g/L total dissolved solids (TDS)) and low organic concentration (80–252?mg/L dissolved organic carbon (DOC)). In contrast, DJ basin showed an opposite trend with low TDS (～30?g/L) and high organic content (644?mg/L DOC). Excitation-emission matrix (EEM) fluorescence spectra demonstrated that more humic acid and fluvic acid-like organics with higher aromaticity existed in Bakken wastewater than that in Barnett and DJ basin. Microbial communities of Bakken samples were dominated by Fe (III)-reducing bacteria Geobacter, lactic acid bacteria Lactococcus and Enterococcus, and Bradyrhizobium, while DJ basin water showed higher abundance of Rhodococcus, Thermovirga, and sulfate reducing bacteria Thermotoga and Petrotoga. All these bacteria are capable of hydrocarbon degradation. Hydrogenotrophic methanogens dominated the archaeal communities in all samples.Wang, J., Jacobson, A.D., Zhang, H., Ramezani, J., Sageman, B.B., Hurtgen, M.T., Bowring, S.A., Shen, S.-Z., 2019. Coupled δ44/40Ca, δ88/86Sr, and 87Sr/86Sr geochemistry across the end-Permian mass extinction event. Geochimica et Cosmochimica Acta 262, 143-165. report high-resolution, high-precision δ44/40Ca, δ88/86Sr, and 87Sr/86Sr records spanning the Permian-Triassic boundary (PTB) from the Meishan and Dajiang carbonate successions in south China. The goal of the study was to understand the behavior of Ca and Sr isotopes during a time period in Earth history characterized by severe biological and environmental perturbations, including a major mass extinction, flood basalt volcanism, ocean acidification, and sea level fluctuations. Dajiang displays negative δ44/40Ca and δ88/86Sr excursions and invariant 87Sr/86Sr ratios in the <60 kyr timeframe between the main extinction horizon and the PTB. The Meishan δ44/40Ca and δ88/86Sr records are generally shifted to higher values and display both synchronous and asynchronous trends relative to Dajiang. In addition, 87Sr/86Sr ratios at Meishan are significantly elevated and do not define a clear secular pattern. We reconcile diverse conceptual models for the dataset with the aid of supporting elemental and isotope measurements (e.g., Sr/Ca, δ13C, and δ18O), as well as sequential leaching experiments. The combined body of evidence indicates that Dajiang sediments experienced recrystallization and neomorphism under rock-buffered conditions that preserved primary signals. In contrast, the Meishan records display influences from both primary and secondary processes, including local differences in fractionation, fluid-buffered early marine diagenesis, and late stage diagenetic overprinting. The three isotopic records for Dajiang, and to some extent, the δ44/40Ca and δ88/86Sr records for Meishan, preserve information about the geochemistry of end-Permian seawater. We find that enhanced weathering of shelf carbonates during sea level fall provides the best explanation for rapidly decreasing seawater δ44/40Ca and δ88/86Sr values without affecting 87Sr/86Sr ratios.Wang, J., Liu, G., Xu, Y., Zhu, B., Wang, Z., 2019. Separation and characterization of new components and impurities in leucomycin by multiple heart-cutting two-dimensional liquid chromatography combined with ion trap/time-of-flight mass spectrometry. Chromatographia 82, 1333-1344. this study, nine new components and six impurities in leucomycin were discovered. A method was developed for the separation and characterization of new components and impurities in leucomycin by multiple heart-cutting two-dimensional liquid chromatography combined with ion trap/time-of-flight mass spectrometry in both positive and negative electrospray ionization modes. With this method, a non-volatile buffer solution was used as mobile phase in the first-dimensional system for good separation. Eluent of each peak from the first-dimensional system was trapped by a switching valve and sent to the liquid chromatography-mass spectrometry system using a volatile mobile phase. The complete fragmentation patterns of the new components and degradation impurities were deduced based on MSn data. The structures of nine new components in leucomycin were deduced as unsaturated ketone in the 16-membered ring of leucomycin. The structures of six impurities were characterized for the first time, four of which were acid degradation products, and the other two were process impurities. The correlation between impurities and the purification process of leucomycin was also studied. The degradation impurities were produced during purification of leucomycin fermentation broth, which requires a low-pH environment. Based on the characterization of impurities, this study not only revealed the mechanism of impurity production, thus providing guidance to pharmaceutical companies for manufacturing process improvement and impurity reduction, but also provided a scientific basis for further improvement of official monographs in pharmacopoeias.Wang, M., Ma, R., Li, J., Lu, S., Li, C., Guo, Z., Li, Z., 2019. Occurrence mechanism of lacustrine shale oil in the Paleogene Shahejie Formation of Jiyang Depression, Bohai Bay Basin, China. Petroleum Exploration and Development 46, 833-846. determine the occurrence mechanism and mobility of shale oil in the Shahejie Formation in the Jiyang Depression, organic geochemistry analysis, thin-section petrological observation, low-temperature nitrogen adsorption, high-pressure mercury intrusion porosimetry, field emission scanning electron microscopy experiments were conducted on shale samples to reveal its storage mechanism, including pore size, ratio of adsorbed oil to free oil, mobility and its influencing factors, and mode of storage. Residual shale oil is mainly present in pores less than 100 nm in diameter under the atmospheric temperature and pressure. The lower limit of pore size for free oil is 5 nm, and the lower limit of pore size for movable oil occurrence is about 30 nm. The light components, low TOC and high porosity are the main factors contributing to the high proportion of movable oil. Each type of pore can contain residual shale oil, but not all pores have shale oil. Pore connectivity and surface wettability are the determinants of shale oil enrichment degree and enrichment state.Wang, Q., Huang, H., Chen, H., Zhao, Y., 2020. Secondary alteration of ancient Shuntuoguole oil reservoirs, Tarim Basin, NW China. Marine and Petroleum Geology 111, 202-218. tectonic movements and charge episodes have occurred in the Tazhong Uplift of the Tarim Basin, NW China, contributing to widespread solid bitumen, heavy oil, normal oil, condensate and gas in the Shuntuoguole High, especially in the Lower Silurian Kepingtage Formation. A detailed investigation of cores and fluid inclusions from different intervals, i.e. S1k3?3, S1k3?1, S1k1, has been carried out using petrographic analysis, gas chromatograph–mass spectrometry and micro–Fourier transform infrared spectroscopy. Three hydrocarbon charge events in the Kepingtage Formation have been recognized associated with the late Caledonian, late Hercynian and Himalayan orogenies. In the late Caledonian, oils were charged into the S1k3?3, S1k3?1 and S1k1 intervals, but evolved to solid bitumen due to biodegradation and water washing, as the Silurian strata have experienced both strong uplift and erosion during the early Hercynian Orogeny, and the influence of igneous intrusions during the Permian. Hydrocarbons associated with the Caledonian contain no regular steranes, diasteranes, hopanes or extended tricyclic terpanes due to in-reservoir thermal cracking. The second charge period occurred in the late Hercynian, which has experienced severe biodegradation and water washing. Hydrocarbons of this period are characterized by an obvious chromatographic hump of the unresolved complex mixture (UCM) coupled with petroleum inclusions that fluoresce light-blue and yellow, possibly indicating variable maturity. Whether or not high maturity oil charged during this period into the S1k1 interval has commercial production value needs further investigation. The third change occurred during the Himalayan Orogeny. Highly mature hydrocarbons were emplaced into the S1k3?3, S1k3?1 and S1k1 intervals with the S1k1 interval as being the most significant. Biodegradation, water washing, and igneous intrusion had no impact on hydrocarbons charged during this period, resulting in higher potential for economic production.Wang, W., Fan, D., Sheng, G., Chen, Z., Su, Y., 2019. A review of analytical and semi-analytical fluid flow models for ultra-tight hydrocarbon reservoirs. Fuel 256, 115737. the last decade, numerous approaches, e.g., analytical and semi-analytical pressure solutions, production decline curve, reservoir-scale numerical models, have been used to increase our understanding of fluid transport in hydraulically fractured ultra-tight reservoirs and to improve predictions of well production. Among these approaches, analytical and semi-analytical methods have proved useful to petroleum engineers, because of the balance between the reliability of theoretical model outputs and the computational cost. Analytical or semi-analytical solutions can be used to analyze pressure-transient responses, to estimate hydraulic and induced fracture properties, to forecast production, and to optimize well spacing and multi-stage hydraulic fracking.This work reviews the development of analytical/semi-analytical multi-linear and radial flow models for hydraulically-fractured horizontal wells over the past decade. In particular, the review summarizes and compares the fundamental physics and mathematics of the gas transport mechanisms that are important in unconventional reservoirs. We highlight the analytical approaches that have successfully coupled 1) reservoir spatial heterogeneity, e.g., subdivision of the stimulated reservoir volume (SRV) and fractal SRV, 2) non-continuum flow mechanisms, e.g., Knudsen diffusion, surface diffusion, and gas slip, into diffusivity equations, and 3) the impact of pressure depletion on gas desorption, and pore size change in propped and unpropped fractures. We also discuss the gas permeability models that have been proposed in the past decade and the challenges that remain to the development of oil flow models. Our knowledge of fluid transport, especially for confined fluid at multiple reservoir scales, remains incomplete, and our understanding of flow contributions from different flow regions, and mass transfer between them remains limited.Wang, Y.-F., Dick, R.P., Lorenz, N., Lee, N., 2019. Interactions and responses of n-damo archaea, n-damo bacteria and anammox bacteria to various electron acceptors in natural and constructed wetland sediments. International Biodeterioration & Biodegradation 144, 104749. methane oxidizing organisms, including sulfate dependent archaea (SAMO), nitrite dependent bacteria (n-damo), and nitrate archaea (n-damo), may collaborate with anaerobic ammonia oxidizers (anammox) bacteria in wetlands to remove inorganic nitrogen. The objective was to examine the structure and abundance of these organisms and their response to substrate inputs (sulfate, nitrate, or nitrite) in two wetlands of contrasting properties: a natural wetland and a constructed wetland to treat swine manure. No SAMO archaea were detected in either wetland. For n-damo bacteria, Ca. Methylomirabilis oxyfera dominated the natural wetland, while Clade 2 dominated the constructed wetland. For n-damo archaea, Clade 1 dominated the constructed wetland, while Clade 3 dominated the natural wetland. For anammox bacteria, Ca. Brocadia dominated both the natural wetland and the constructed wetland. Generally, the natural wetland contained higher gene abundance and more diversity of these three microorganisms than the constructed wetland, which could be due to high ammonium concentrations in the constructed wetland, forcing selections of genotypes to a narrow range of microorganisms. A slurry incubation experiment showed that both n-damo archaea and anammox bacteria increased over time in the constructed wetland sediment, indicating these two microorganisms might cooperate to complete the denitrification process from nitrate to dinitrogen gas.Wang, Z., Li, J., Wei, G., Deng, W., Chen, X., Zeng, T., Wang, X., Ma, J., Zhang, L., Tu, X., Wang, Q., McCulloch, M., 2019. Biologically controlled Mo isotope fractionation in coral reef systems. Geochimica et Cosmochimica Acta 262, 128-142. we investigate the fractionation of Mo isotopes (δ98MoNIST) in biogenic carbonates and assess its viability as an environmental and biological proxy in coral skeletons. An annually resolved 40-year record of δ98MoNIST values is reported for a Porites coral from the Great Barrier Reef (GBR), Australia. This, together with a four-day time-series of δ98MoNIST measurements of seawater and samples from a range of coral species from Luhuitou Reef in Sanya Bay, northern South China Sea is used to investigate the relative fractionation of Mo isotopes between coral and seawater and assess the potential of δ98MoNIST as a proxy for tracing biological activity.δ98MoNIST values in the GBR coral skeleton are lighter than those of seawater (2.05‰, relative to NIST SRM 3134) and display large variations from 0.63‰ to 1.73‰, with a mean of 1.29‰. A significant relationship was found between coral δ98MoNIST and sea surface temperature (SSTcal) in the GBR coral. These observations and the Luhuitou Reef seawater data indicate that temperature-mediated biological activity in coral polyps potentially modulate coral δ98MoNIST. A biological fractionation model is proposed to explain how symbiotic zooxanthellae produce the considerable variations in Mo isotopic composition measured in the GBR coral. This fractionation suggests that Mo isotopes could potentially be used as a proxy for biological processes in corals.Wang, Z., Li;, S., Wu, F., Hou, J., 2019. Experimental study on methane hydrate formation and evaluation in porous medium. International Journal of Oil, Gas and Coal Technology 21, 482-494. hydrate (MH) is considered as a potential energy resource and its laboratory research is very significant. Although many patterns about MH formation have been proposed by many researchers, the formation rate and formation efficiency of MH have rarely been reported. In this work, two patterns of gas injection (intermittent gas injection and continuous gas injection) have been conducted to simulate the hydrate reservoir formation process. It is shown that the continuous gas injection pattern can result in higher hydrate saturation in a relatively short time, while in the intermittent pattern, the early formation of MH near the gas inlet valve will prevent the later injected CH4. The continuous gas injection pattern can keep higher pressure in the reactor, which is beneficial to the MH formation. Moreover, two evaluation indicators, hydrate formation efficiency (Es) and formation rate (Ve), have been proposed to compare the performance of the two patterns. The continuous gas injection pattern has higher Es of 0.837 and Ve of 9.03E-04 min?1, while in intermittent gas injection, Es is 0.754 and average Ve is 7.41E-05 min?1. It is recommended that continuous gas injection pattern is used in the laboratory.Wanner, P., Aravena, R., Fernandes, J., BenIsrael, M., Haack, E.A., Tsao, D.T., Dunfield, K.E., Parker, B.L., 2019. Assessing toluene biodegradation under temporally varying redox conditions in a fractured bedrock aquifer using stable isotope methods. Water Research 165, 114986. complex hydrogeological settings little is known about the extent of temporally varying redox conditions and their effect on aromatic hydrocarbon biodegradation. This study aims to assess the impact of changing redox conditions over time on aromatic hydrocarbon biodegradation in a fractured bedrock aquifer using stable isotope methods. To that end, four snapshots of highly spatio-temporally resolved contaminant and redox sensitive species concentrations, as well as stable isotope ratio profiles, were determined over a two-years time period in summer 2016, spring 2017, fall 2017 and summer 2018 in a toluene contaminated fractured bedrock aquifer. The concentration profiles of redox sensitive species and stable isotope ratio profiles for dissolved inorganic carbon (DIC) and sulfate (δ13CDIC, δ34SSO4, δ18OSO4) revealed that the aquifer alternates between oxidising (spring 2017/summer 2018) and reducing conditions (summer 2016/fall 2017). This alternation was attributed to a stronger aquifer recharge with oxygen-rich meltwater in spring 2017/summer 2018 compared to summer 2016/fall 2017. The temporally varying redox conditions coincided with various extents of toluene biodegradation revealed by the different magnitude of heavy carbon (13C) and hydrogen (2H) isotope enrichment in toluene. This indicated that the extent of toluene biodegradation and its contribution to plume attenuation was controlled by the temporally changing redox conditions. The highest toluene biodegradation was observed in summer 2016, followed by spring 2017 and fall 2017, whereby these temporal changes in biodegradation occurred throughout the whole plume. Thus, under temporally varying recharge conditions both the core and the fringe of a contaminant plume can be replenished with terminal electron acceptors causing biodegradation in the whole plume and not only at its distal end as previously suggested by the plume fringe concept. Overall, this study highlights the importance of highly temporally resolved groundwater monitoring to capture temporally varying biodegradation rates and to accurately predict biodegradation-induced contaminant attenuation in fractured bedrock aquifers.Wei, M., Zhang, L., Xiong, Y., Peng, P.a., 2019. Main factors influencing the development of nanopores in over-mature, organic-rich shales. International Journal of Coal Geology 212, 103233. cores of the Lower Silurian Longmaxi Formation from wells in the Fuling and Changning-Weiyuan shale gas demonstration zones and the Wuxi shale exploration block of the Sichuan Basin were investigated to determine the key factors controlling nanopore development in over-mature, organic-rich shales. These samples were studied using organic, geochemical, and petrological analyses, as well as low pressure nitrogen and carbon dioxide adsorption, and broad ion-beam-field emission scanning electron microscopy (BIB-FESEM). The results show that organic-rich shales of the Lower Silurian Longmaxi Formation have complex pore structures, in which the surface areas of micropores and fine mesopores (diameter?<?10?nm), along with the total mesopore volume, are the most important parameters controlling nanopore development. The samples have micropore and fine mesopore surface areas of 10.03–46.47?m2/g (mean 22.65?m2/g), accounting for a significant portion (up to 99%) of the total surface areas. Mesopore volumes of 6.28?×?10?3 to38.35?×?10?3?cm3/g (mean 18.36?×?10?3?cm3/g) also account for a significant portion (up to 77%) of the total pore volume. The development of differently sized pores depends on various factors. For example, pores with a diameter?<?10?nm exhibit a significant positive linear correlation with organic matter content and thermal maturity. Total organic carbon (TOC), quartz, clays, and pyrite contents are the main controlling factors in the formation of medium mesopores (10–25?nm). The generation and distribution of coarse mesopores(25–50?nm) are dominantly controlled by clay contents, especially those of illite and mixed-layer minerals of illite and smectite (I/S). Macropores are typically mineral-associated pores (e.g., pores associated with the dissolution of calcite and albite). For organic-rich shales, the development of organic pores can be evaluated using the micropore surface area per unit mass of TOC, such that the results show an increase with increasing maturity from the early mature to the over-mature stage for type I and type IIa kerogen shales, but an obvious inversion or decrease when the vitrinite reflectance (Ro)?>?2.5%. For shale samples with type IIb and type III kerogens, the micropore surface area per unit mass of TOC first rises from early mature to the mature stage, and then declines from the mature to over-mature stages of approximately ~2.0% Ro. Therefore, abundant organic matter, type I and type IIa kerogen, relatively high quartz and clay contents (especially illite), and early stage mineral dissolution are favorable factors for the development of nanopores in over-mature shales in the study areas. These findings will help improve our understanding of the development of nanopores in over-mature organic-rich shales.Wei, W., Hou, J., Yao, C., Bi, Q., Wang, X., Li, Z., Jin, Q., Lei, M., Feng, Z., Wu, W., Guo, D., 2019. A high-efficiency strategy integrating offline two-dimensional separation and data post-processing with dereplication: Characterization of bufadienolides in Venenum Bufonis as a case study. Journal of Chromatography A 1603, 179-189. analysis and identification of chemical components are very important to evaluate the efficacy and safety of traditional Chinese medicine (TCM). Meanwhile, the discovery of new natural compounds is of great significance for drug exploitation and development. Although two-dimensional liquid chromatography (2D LC) systems expand the peak capacity and improve selectivity and resolution, interpreting the post-processing data is tedious and time-consuming. In this study, an off-line two-dimensional liquid chromatography/ultra-high performance supercritical fluid chromatography tandem quadrupole time-of-flight mass spectrometry (2D LC/UHPSFC-Q-TOF/MS) system was established for systematic chromatographic separation and identification of bufadienolides. Subsequently, the Global Natural Product Social Molecular Networking (GNPS) was applied for dereplication of chemical components of adjacent fractions with high efficiency and accuracy. The key parameters which affected separation and detection with respect to chromatographic conditions and mass spectrometry conditions were optimized. The extract of Venenum Bufonis was fractionated into forty fractions by first-dimensional reversed phase high-performance liquid chromatography (HPLC), which were further analyzed by the second-dimensional UHPSFC-Q-TOF/MS in positive ion mode. The data of forty fractions was imported into GNPS and processed automatically within about five hours. Furthermore, the chemical components with similar featured fragments were classified into the same cluster, which was helpful for components identification. A total of 229 bufadienolides were characterized and two subclasses of compounds (bufogenins conjugated with carboxylic acid and N-heterocyclic bufogenins) were found in Venenum Bufonis for the first time. In addition, UHPSFC exhibited powerful separation ability of isomers in Venenum Bufonis. In this analysis, two new compounds were isolated and fully characterized by NMR verifying the feasibility of this combined analytical strategy. This integrated strategy can improve the efficiency in the detection of new compounds and offer greater observation of isomers from medicinal herbs and other natural sources.Wen, T., Woda, J., Marcon, V., Niu, X., Li, Z., Brantley, S.L., 2019. Exploring how to use groundwater chemistry to identify migration of methane near shale gas wells in the Appalachian Basin. Environmental Science & Technology 53, 9317-9327. (CH4) enters waters in hydrocarbon-rich basins because of natural processes and problems related to oil and gas wells. As a redox-active greenhouse gas, CH4 degrades water or emits to the atmosphere and contributes to climate change. To detect if methane migrated from hydrocarbon wells (i.e., anomalous methane), we examined 20?751 methane-containing groundwaters from the Upper Appalachian Basin (AB). We looked for concentrations (mg/L) that indicated AB brine salts (chloride concentrations ([Cl]) > 30; [Ca]/[Na] < 0.52) to detect natural methane, and we looked for concentrations of redox-active species ([SO4] ≥ 6; [Fe] ≥ 0.3) to detect anomalous methane. These indicators highlight natural contamination by methane-containing brines or recent onset of microbial oxidation of methane coupled to iron- or sulfate-reduction. We hypothesized that only waters recently contaminated by methane still exhibit high iron and sulfate concentrations. Of the AB samples, 17 (0.08%) from 12 sites indicated potential contamination. All were located in areas with high densities of shale-gas or conventional oil/gas wells. In contrast, in southwestern Pennsylvania where brines are shallow and coal, oil, and gas all have been extracted extensively, no sites of recent methane migration were detectable. Such indicators may help screen for contamination in some areas even without predrill measurements.Whitelaw, P., Uguna, C.N., Stevens, L.A., Meredith, W., Snape, C.E., Vane, C.H., Moss-Hayes, V., Carr, A.D., 2019. Shale gas reserve evaluation by laboratory pyrolysis and gas holding capacity consistent with field data. Nature Communications 10, 3659. for shale gas occurs in onshore basins, with two approaches used to predict the maximum gas in place (GIP) in the absence of production data. The first estimates adsorbed plus free gas held within pore space, and the second measures gas yields from laboratory pyrolysis experiments on core samples. Here we show the use of sequential high-pressure water pyrolysis (HPWP) to replicate petroleum generation and expulsion in uplifted onshore basins. Compared to anhydrous pyrolysis where oil expulsion is limited, gas yields are much lower, and the gas at high maturity is dry, consistent with actual shales. Gas yields from HPWP of UK Bowland Shales are comparable with those from degassed cores, with the ca. 1% porosity sufficient to accommodate the gas generated. Extrapolating our findings to the whole Bowland Shale, the maximum GIP equate to potentially economically recoverable reserves of less than 10 years of current UK gas consumption.Wishart, D.S., 2019. NMR metabolomics: A look ahead. Journal of Magnetic Resonance 306, 155-161. has been used to perform metabolic studies, metabolic profiling and metabolomics in biofluids and tissues for more than 40 years. This close connection between metabolic measurements and NMR has flourished because of NMR’s many unique strengths for characterizing the chemical composition of complex mixtures. However, a number of other technologies, including mass spectrometry, have appeared in the past few years that are encroaching on NMR’s dominance in metabolomics and metabolic studies. In this brief review, some of the current strengths and existing limitations of NMR-based metabolomics are highlighted. Additionally, a number of recent advances in NMR hardware, methodology and software are also described and these advancements are used to speculate about where NMR-based metabolomics is going, what needs to be done to make it more popular and how it will evolve in the next 5-10 years.Wu, M., Wu, J., Zhang, X., Ye, X., 2019. Effect of bioaugmentation and biostimulation on hydrocarbon degradation and microbial community composition in petroleum-contaminated loessal soil. Chemosphere 237, 124456. study assessed the benefits of biostimulation with nitrogen and phosphorous (BS) versus bioaugmentation with native petroleum degrading flora (BA) in terms of petroleum hydrocarbon removal and microbial community structure shift in petroleum-polluted loessal soil. After 12 weeks of remediation, the TPH degradation efficiencies were 28.3% and 13.9% in BS and BA treated soils, respectively. Biostimulation was more effective than bioaugmentation for petroleum hydrocarbon degradation. Soil microbial community composition changed while microbial diversity decreased greatly by bioaugmentation treatment. The inoculum could survive, grow up quickly and become the predominant microorganisms after one week of inoculation. In the biostimulation treatment, microbial community composition is more evenness and richness than in the bioaugmented remediation. The strong positive correlations of the nitrogen and phosphorus with the petroleum hydrocarbon suggest the importance of nutrients for petroleum biodegradation in the contaminated loessal soil. The results indicate that the stabilization and variety of the microbial community structure are essential for the petroleum biodegradation performance. Further engineering is suggested to improve the evenness and richness of the soil microbial community since an abundance of nitrogen and phosphorus nutrients ensures the degraders’ activity in the petroleum polluted soil.Xia, L.-W., Cao, J., Wang, M., Mi, J.-L., Wang, T.-T., 2019. A review of carbonates as hydrocarbon source rocks: basic geochemistry and oil–gas generation. Petroleum Science 16, 713-728. have been known to act as hydrocarbon source rocks, but their basic geochemical and associated hydrocarbon generation characteristics remain not well understood as they occur with argillaceous source rocks in most cases, and the hydrocarbon generation from each rock type is difficult to distinguish, forming one of puzzling issues within the field of petroleum geology and geochemistry. To improve the understanding of this critical issue, this paper reviews recent advances in this field and provides a summary of key areas that can be studied in future. Results show that carbonate source rocks are generally associated with high-salinity environments with low amounts of terrestrial inputs and low dissolved oxygen contents. Petrographically, these source rocks are dark gray or black, fine-grained, stratified, and contain bacterial and algal bioprecursors along with some other impurities. They generally have low organic matter contents, although these can vary significantly in different cases (e.g., the total organic carbon contents of marine and lacustrine carbonate source rocks in China are generally 0.1%–1.0% and 0.4%–4.0%, respectively). These rocks contain type I and type II kerogen, meaning there is a lack of vitrinites. This means that assessment of the maturity of the organic matter in these sediments needs to use non-traditional techniques rather than vitrinite reflectance. In terms of molecular geochemistry, carbonate source rocks have typical characteristics indicative of generally reducing and saline environments and lower organism-dominated bioprecursors of organic matter, e.g., high contents of sulfur compounds, low Pr/Ph ratios, and dominance of n-alkanes. Most of the carbonate source rocks are typically dominated by D-type organic facies in an oxidized shallow water mass, although high-quality source rocks generally contain A- and B-type organic facies in saline lacustrine and marine-reducing environments, respectively. The hydrocarbon generation model for the carbonate source rocks can involve early, middle, and late stages, with a diversity of hydrocarbons within these rocks, which can be aggregated, adsorbed, enclosed within minerals, or present as inclusions. This in turn implies that the large-scale hydrocarbon expulsion from these rocks is reliant on brittle deformation caused by external forces. Finally, a number of aspects of these source rocks remain unclear and need further study, including the effectiveness of carbonates as hydrocarbon source rocks, bioprecursors, and hydrocarbon generation models of carbonate source rock, and the differences between marine and lacustrine carbonate source rocks.Xiang, P., Yang, Y., Zhao, Z., Chen, A., Liu, S., 2019. Experimentally validating open tubular liquid chromatography for a peak capacity of 2000 in 3 h. Analytical Chemistry 91, 10518-10523. advancements in life science research mandate effective tools capable of analyzing large numbers of samples with low quantities and high complexities. As an essential analytical tool for this research, liquid chromatography (LC) encounters an ever-increasing demand for enhanced resolving power, accelerated analysis speed, and reduced limit of detection. Although theoretical studies have indicated that open tubular (OT) columns can produce superior resolving power under comparable elution pressures and analysis times, ultrahigh-resolution and ultrahigh-speed open tubular liquid chromatography (OTLC) separations have never been reported. Here we present experimental results to demonstrate the predicted potential of this technique. We use a 2 μm i.d. × 75 cm long OT column coated with trimethoxy(octadecyl)silane for separating pepsin/trypsin digested E. coli lysates and routinely produce exceptionally high peak capacities (e.g., 1900–2000 in 3–5 h). We reduce the column length to 2.7 cm and exhibit the capability of OTLC for ultrafast separations. Under an elution pressure of 227.5 bar, we complete the separation of six amino acids in ～800 ms and resolve these compounds within ～400 ms. In addition, we show that OTLC has low attomole limits of detection (LOD) and each separation requires samples of only a few picoliters. Importantly, no ultrahigh elution pressures are required. With the ultrahigh resolution, ultrahigh speed, low LOD, and low sample volume requirement, OTLC can potentially be a powerful tool for biotech research, especially single cell analysis.Xiang, P., Yang, Y., Zhao, Z., Chen, M., Liu, S., 2019. Ultrafast gradient separation with narrow open tubular liquid chromatography. Analytical Chemistry 91, 10738-10743. speed and resolution are two important figures of merit in chromatography. Often, one gains the speed at the cost of the resolution, and vice versa. Scientists have employed short-packed columns for ultrafast separations but encountered challenges such as limited mobile phase velocity, extra-column effect caused band broadening, and column packing difficulty. We have recently demonstrated ultrahigh resolutions of narrow open tubular liquid chromatography (NOTLC); this allows us to trade some of the resolution for speed. In this work, we explored NOTLC for ultrafast LC separations. We used a 2.7 cm (effective length) narrow open tubular (NOT) column and showed a baseline separation of 6 amino acids in less than 700 ms. Ways to further increase the speed were discussed. Using short narrow open tubular (NOT) columns to perform ultrafast separation we overcame the challenges from using short packed columns. To demonstrate the feasibility of using this ultrafast separation technique for practical applications, we separated complex protein digests; peptides were nicely resolved in ～1 min.Xu, F., Liu, H., Wang, Q., Pan, S., Zhao, D., Liu, Y., 2019. Study of non-isothermal pyrolysis mechanism of lignite using ReaxFF molecular dynamics simulations. Fuel 256, 115884. with the isothermal pyrolysis, non-isothermal pyrolysis is more accurate and efficient, and closer to the actual reaction process. To better understand the pyrolysis mechanism of lignite, a series of ReaxFF molecular dynamics (ReaxFF-MD) simulations were performed within the temperature range of 300–3000?K at different heating rates. The results indicated that the secondary reaction of tar took place when the temperature was above 2400?K at a low heating rate (2?K/ps). In comparison with light tar, more heavy tar was converted to gas or char through further decomposition or condensation reaction. The influence of heating rate on pyrolysis reaction was investigated at the heating rates of 2, 10, 50 and 100?K/ps. In the low heating rate range (below 10?K/ps), the heating rate exhibited a prominent influence on the product distribution. Moreover, more tar and pyrolysis gas were generated at low temperatures (below 2400?K) compared to those at high heating rates. The reaction mechanisms of typical lignite pyrolysis products (C2H4 and phenols) were explored. The formation of C2H4 was attributed to the presence of large amounts of methylene carbon in lignite. Possible formation and transformation pathways of phenols have been proposed, and the simulation results were found to be consistent with the evolution of gases.Xu, J.-X., Li, X.-M., Sun, G.-X., Cui, L., Ding, L.-J., He, C., Li, L.-G., Shi, Q., Smets, B.F., Zhu, Y.-G., 2019. Fate of labile organic carbon in paddy soil is regulated by microbial ferric iron reduction. Environmental Science & Technology 53, 8533-8542. paddy soil is the primary source of methane, a potent greenhouse gas. It is therefore highly important to understand the carbon cycling in paddy soil. Microbial reduction of iron, which is widely found in paddy soil, is likely coupled with the oxidation of dissolved organic matter (DOM) and suppresses methanogenesis. However, little is known about the biotransformation of small molecular DOM accumulated under flooded conditions and the effect of iron reduction on the biotransformation pathway. Here, we carried out anaerobic incubation experiments using field-collected samples amended with ferrihydrite and different short-chain fatty acids. Our results showed that less than 20% of short-chain fatty acids were mineralized and released to the atmosphere. Using Fourier transform ion cyclotron resonance mass spectrometry, we further found that a large number of recalcitrant molecules were produced during microbial consumption of these short-chain fatty acids. Moreover, the biotransformation efficiency of short-chain fatty acids decreased with the increasing length of carbon chains. Ferrihydrite addition promoted microbial assimilation of short-chain fatty acids as well as enhanced the activation and biotransformation of indigenous stable carbon in the soil replenished with formate. This study demonstrates the significance of ferrihydrite in the biotransformation of labile DOM and promotes a more comprehensive understanding of the coupling of iron reduction and carbon cycling in paddy soils.Xu, J., Zheng, L., Su, G., Sun, B., Zhao, M., 2019. An improved peak clustering algorithm for comprehensive two-dimensional liquid chromatography data analysis. Journal of Chromatography A 1602, 273-283. this work, an improved algorithm was developed for two-dimensional (2D) peak detection in complex two-dimensional liquid chromatography (LC×LC) data sets. In the first step, conventional one-dimensional peak detection was performed. In the second step, retention time, bidirectional overlap and unimodality criteria were applied to decide which of the individual peaks should be merged. To improve the peak detection with LC×LC analysis using shifting second dimension (2D) gradients, the variable thresholds, which permitted different thresholds for candidate peaks at different first dimension (1D) retention times, were employed for examination of the 2D retention time differences. Furthermore, the bidirectional overlap criterion performed at specified height was recommended to improve detection for tailing peaks. The developed algorithm was further tested on data sets from different LC×LC analyses of a complex peptide mixture, and then quantitatively evaluated by comparison between the results by the algorithm and mass analysis. Evidently improved performance with an accuracy rate over 60% was obtained by the algorithm, even for peak detection with LC×LC analysis under relatively low 1D sampling frequency or shifting 2D gradients. This would help to improve LC×LC quantitative analysis and performance assessment.Xu, R., Prodanovi?, M., Landry, C.J., 2019. Study of subcritical and supercritical gas adsorption behavior in different nanopore systems in shale using lattice Boltzmann method. International Journal of Coal Geology 212, 103263. has been studied for decades in either petroleum or chemical industry. However, the detailed adsorption behavior is yet not well understood in nanoporous media with complex pore structures and surface properties, especially for subcritical gases when capillary condensation might occur. Shale (mudrock) has complex pore systems as a result of heterogeneous mineralogy and diagenesis, and interparticle (interP) and intraparticle (intraP) pores are two main components. Understanding gas adsorption and phase transition behavior in different pore systems is essential for petrophysical characterization, reserve estimation and production forecast. In this study, we use lattice Boltzmann method (LBM) to study nitrogen (subcritical) and methane (supercritical) adsorption behavior in reconstructed shale nanopore systems. The model accounts for the van der Walls (vdW) forces between fluid molecules by incorporating a modified pseudopotential model based on Peng-Robinson equation of state (PR-EOS). Rock-fluid interaction is also considered by introducing phenomenological surface forces, which take two different forms for subcritical and supercritical gases respectively. The correlation between parameters defined in LBM and physical properties (i.e. density, pressure, isosteric heat of adsorption) is established systematically. Using the developed model, we observe quantitative agreement between LBM and lattice density functional theory (LDFT)/experimental data in terms of adsorption isotherms and density distributions. We then compare adsorption behavior in two ‘model’ interP and intraP pore systems and a synthesized polyethylene porous medium with more complex pore shapes. We observe three adsorption stages for subcritical gas adsorption: a) early capillary condensation near grain contacts or sharp corners, forming isolated pendular rings or fluid clusters; b) growing, merging, and spreading of the isolated condensed phase, forming circular gas/liquid meniscus; c) the condensed phase becomes fully-connected across the geometry, leaving isolated gas bubbles. We observe a signature behavior for the adsorption isotherm of intraP pore system, where a stepped feature occurs around relative pressure of 0.8, and the adsorption uptake for the polyethylene porous medium is bounded by the upper and lower limits given by the interP and intraP pore systems. On the other hand, we find that supercritical methane adsorption in mesoporous media is less sensitive to pore shape, but rather controlled by the specific surface area. The existence of micropores also affects the adsorption uptake.Xu, S., Yu, K., Fan, T., Jiang, W., Wang, R., Zhang, Y., Yue, Y., Wang, S., 2019. Coral reef carbonate δ13C records from the northern South China Sea: A useful proxy for seawater δ13C and the carbon cycle over the past 1.8?Ma. Global and Planetary Change 182, 103003. reefs are well known for playing an important role in the global carbon cycle, however little research has been done into their potential for documenting carbon cycles of the past. Here we report the δ13C of coral reef carbonate from a 928.75-m-long core (CK2) from the northern South China Sea (SCS). The chronological profile of CK2 has been well established based on Strontium isotopes and magnetostratigraphy. Our aim is to explore the potential for δ13C in coral reef carbonate to act as a proxy for the seawater δ13C in the northern SCS and related regional carbon cycle in the geological time scale. Our results demonstrate that variations in CK2 δ13C values were generally consistent with changes in seawater δ13C levels in the northern SCS (as inferred from planktonic foraminifer in the northern SCS) over the past 1.8?Ma. This indicates that the δ13C in our CK2 coral reef carbonate was influenced by seawater δ13C levels. The δ13C values of CK2 also presented obvious periodic variations corresponding to glacial-interglacial cycles, with values being higher during glacial periods and lower during interglacial periods. We speculate that the higher δ13C values during glacial periods indicate higher seawater productivity, i.e., increased photosynthesis intensity in coral reefs. In addition, we also found a coherent relationship between changes in CK2 δ13C values and changes in the East Asian terrestrial ecosystem, and we suppose that the CK2 δ13C values maybe partially influenced by the East Asian terrestrial ecosystem through its regulation of SCS seawater δ13C levels. Therefore, we suggest that δ13C values of coral reef carbonate from the northern SCS represent a potential proxy for the seawater δ13C in the northern SCS and related carbon cycle changes in the East Asia.Xu, Z., Liu, L., Jiang, S., Wang, T., Wu, K., Feng, Y., Xiao, F., Chen, Y., Chen, Y., Feng, C., 2019. Migration model of hydrocarbons in the slope of the superimposed foreland basin: A study from the South Junggar, NW China. Journal of Petroleum Science and Engineering 182, 106337. superimposed foreland basins mainly develop in central-western China, namely the Himalayan foreland basins superimposed on the Indo-China foreland basins. Previous research on hydrocarbon migration predominantly focused on the typical foreland basins and the fore-deep depression of superimposed foreland basins. As a result of multi-superimposition, large hydrocarbon potentials in the slope zones are evaluated, and the hydrocarbon migration shows significant differences with those in the typical foreland basins. Moreover, the hydrocarbon migration models in the slope zone of superimposed foreland basins are poor analyzed. The Chepaizi High in the South Junggar Basin, a typical slope of superimposed foreland basin, has been taken into consideration. Several points have been ascertained. 1) Multistage charging and readjustment events should be the predominant characters. 2) The combination of multi-type sand-bodies, multistage faults and unconformities have formed step- or “Z”-shaped migration pathways spatially. 3) Hydrocarbons migrated from the areas of high oil potential in the fore-deep depression to those of low oil potential in the slope. 4) The migration models of the J1b, K1q, N1s1, and N1s2 have been established. Hydrocarbon reservoirs in the slope zones show the shallow accumulation from deep/distal sources with multiple reservoirs vertically and multi-charging and -readjustments chronologically. 5) The areas of (Wells SM3, C53-C90, and CF2), (Wells SM5, C80, and CF13), and (Wells K8, HG4, SM4, and CF2) can be the favorable targets for the J1b, K1q, and N1s, respectively.Yadav, M., Shivani, Misra, A., Tandon, P., 2019. Theoretical study of possible reaction mechanisms for the formation of carbodiimide in the interstellar medium (ISM) and polarizabilities of carbodiimide. Origins of Life and Evolution of Biospheres 49, 89-103. Structure of carbodiimide has been studied by using quantum chemical methods. Carbodiimide (HNCNH) has been detected towards Sagittarius B2 (N) in interstellar medium (ISM). Two reaction mechanisms have been proposed to study the formation of interstellar Carbodiimide. The first reaction mechanism is based on molecule-radical and the second one is a radical-radical mechanism, through previously detected interstellar molecules or radicals. Quantum chemical calculations have been performed by using density functional theory (DFT) and Moller-Plesset second order perturbation (MP2) theory, in gas phase as well as in polarizable continuum model (PCM). The proposed reaction paths are exothermic and barrierless which indicates the possibility of carbodiimide formation in ISM. Several basis sets have been used to verify the validity and accuracy of the results. The isotropic and anisotropic polarizabilities of carbodiimide have been calculated from relevant tensor components for both reaction mechanisms with the help of data obtained by DFT/B3LYP and MP2 methods using aug-cc-pVTZ basis sets in gaseous phase as well as in PCM.Yan, J., He, X., Zhang, S., Feng, C., Wang, J., Hu, Q., Cai, J., Wang, M., 2020. Sensitive parameters of NMR T2 spectrum and their application to pore structure characterization and evaluation in logging profile: A case study from Chang 7 in the Yanchang Formation, Heshui area, Ordos Basin, NW China. Marine and Petroleum Geology 111, 230-239. evaluation of the pore structure of tight sandstone reservoirs has a significant influence on the effective exploration and development of tight sandstone oil. Laboratory measurements including scanning electron microscopy (SEM), mercury-injection capillary pressure (MICP), gas adsorption, nuclear magnetic resonance (NMR), and Nano-CT can provide detailed pore structure data. However, only NMR results can be used to evaluate the pore structure in a logging profile due to NMR logging. In this study, the relationships between NMR T2 distribution, pore structure, and pore size of tight sandstone in Chang 7 of the Yanchang Formation, in the Heshui area of the Ordos Basin, are analyzed based on NMR principles. The characteristics of the NMR T2 distribution of different rock samples are analyzed; the sensitive parameters of the NMR T2 spectrum are proposed. These parameters are then used to classify pore structure types in tight sandstone reservoirs and divide the active layers in the logging profile of the study area. The results indicate that different pore size structures have different distributions, and that the NMR T2 spectrum can highlight the difference in the pore structure type and pore size distribution using sensitive parameters such as T2P2 (the value of T2 corresponding to the last peak of the bimodal NMR T2 spectrum) and TDM (the mean value of T2 relaxation time obtained by weighted average method). As the pore structure of the rock samples in the study area worsened, their porosity and permeability worsened, T2P2 and TDM decreased, and the displacement pressure and NMR irreducible water saturation increased. The results of classifying the pore structure types obtained in the logging profile are helpful in evaluating the effectiveness of the reservoir and in the broad application of NMR logging in terms of understanding pore structure.Yang, S., Zhang, K., Chen, J., Qiu, C., Min, C., 2019. Distribution characteristics and hydrocarbon accumulation conditions of biogenic gas reservoirs all over the world. Natural Gas Industry 38, 10-24. order to clarify the future exploration direction of large-scale biogenic gas reservoirs, this paper reviewed the basic information of 18 global major development areas of biogenic gas reservoirs and the petroleum geological conditions of 14 development areas of primary conventional biogenic gas reservoirs of early biogenesis. Then, the distribution characteristics of primary biogenic gas reservoirs and their relationships with the hydrocarbon accumulation conditions were analyzed. Finally, the macroscopic geological conditions for the formation of large-scale primary biogenic gas reservoirs were summarized. And the following research results were obtained. First, the reserve distribution of biogenic gas reservoirs is characterized by young reservoir age, smaller burial depth and deep-water and ultradeep-water remnant ocean basin. Second, over 70% reserves of the primary conventional biogenic gas reservoirs of early biogenesis in the whole world are distributed in the sedimentary environments related to palaeodelta river mouth or submarine fan (especially large-scale deepwater fan) with low surface (sea floor) temperature and low geothermal gradient. Third, the thick sandstone–mudstone strata developed in these areas have a high sedimentation rate and a low sandstone/formation ratio. Therefore, the source rocks dominated by humic organic matter with a certain abundance (TOC>0.5%) are formed, and they can not only provide large space and nutrient for the microbe activity in the long period, but also inhibit the dispersion of biogenic gas. In conclusion, the future exploration direction of large-scale biogenic gas reservoirs focuses on the areas with the following four conditions, including a permafrost region and a deepwater zone with low surface (sea floor) temperatures, a basin with a low geothermal gradient, sedimentary environment related to palaeodelta river mouth–submarine fans and positive structure belts with moderate tectonic activity intensity. Specifically, exploration direction is as follows: (1) The deepwater zones at the outer belt of passive continental margin basin with large provenance, e.g. the deepwater of the Niger Delta Basin, Congo fan, Amazon fan and some palaeodelta development area at both sides of the South Atlantic; (2) The remnant ocean basins with large submarine fan, e.g. Bengal fan and Indus fan; (3) The foredeep zones of foreland basin with the characteristics of deep foredeep, e.g. the eastern foredeep of Papuan Basin; (4) The sags inside the craton basins in those permafrost areas.Yang, X., Wang, C., Shao, H., Zheng, Q., 2019. Non-targeted screening and analysis of volatile organic compounds in drinking water by DLLME with GC–MS. Science of The Total Environment 694, 133494. organic compounds (VOCs) in drinking water may potentially be hazardous. We developed a novel non-targeted analysis method of VOCs in drinking water that uses dispersive liquid-liquid microextraction coupled with gas chromatography–mass spectrometry. Analysis parameters were selected from range-finding tests on the peak number and average area of the extracted compounds. The optimized method was applied to analyze VOCs in tap water samples collected from Wuhan City, China. Twenty-seven compounds with high match degrees and a high prevalence were selected for quantification and evaluation. We used structure-activity relationships to predict the carcinogenicity of these compounds. Although most of the compounds were non-toxic, compounds such as dibutyl phthalate and diacetone alcohol should be investigated further. Untargeted analysis of the tap water samples identified 75–200 VOCs, including 67 highly prevalent compounds. Industrial and pharmaceutical chemicals accounted for approximately 70% of the VOCs in the samples. This method of non-targeted analysis and in silico toxicity prediction is simple and economic, and could be used in screening VOCs in drinking water.Yeap, D., Hichwa, P.T., Rajapakse, M.Y., Peirano, D.J., McCartney, M.M., Kenyon, N.J., Davis, C.E., 2019. Machine vision methods, natural language processing, and machine learning algorithms for automated dispersion plot analysis and chemical identification from complex mixtures. Analytical Chemistry 91, 10509-10517. trace chemical detection techniques such as ion mobility spectrometry (IMS) and differential mobility spectrometry (DMS) can be used in many settings, such as evaluating the health condition of patients or detecting explosives at airports. These devices separate chemical compounds in a mixture and provide information to identify specific chemical species of interest. Further, these types of devices operate well in both controlled lab environments and in-field applications. Frequently, the commercial versions of these devices are highly tailored for niche applications (e.g., explosives detection) because of the difficulty involved in reconfiguring instrumentation hardware and data analysis software algorithms. In order for researchers to quickly adapt these tools for new purposes and broader panels of chemical targets, it is critical to develop new algorithms and methods for generating libraries of these sensor responses. Microelectromechanical system (MEMS) technology has been used to fabricate DMS devices that miniaturize the platforms for easier deployment; however, concurrent advances in advanced data analytics are lagging. DMS generates complex three-dimensional dispersion plots for both positive and negative ions in a mixture. Although simple spectra of single chemicals are straightforward to interpret (both visually and via algorithms), it is exceedingly challenging to interpret dispersion plots from complex mixtures with many chemical constituents. This study uses image processing and computer vision steps to automatically identify features from DMS dispersion plots. We used the bag-of-words approach adapted from natural language processing and information retrieval to cluster and organize these features. Finally, a support vector machine (SVM) learning algorithm was trained using these features in order to detect and classify specific compounds in these represented conceptualized data outputs. Using this approach, we successfully maintain a high level of correct chemical identification, even when a gas mixture increases in complexity with interfering chemicals present.Yu, C., Hu, G., Chen, R.-y., 2019. Geochemical differences of pyrolysis gas of various coal-bearing source rocks and its application in the Sulige gas field, Ordos Basin, China. Journal of Natural Gas Geoscience 4, 151-160. order to study the gas generation process of different coaly source rocks, thermal simulation experiments were performed on coal, dark mudstone, and carbonaceous mudstone. Additionally, a series of geochemical analysis including chemical composition, carbon and hydrocarbon isotope composition, as well as light hydrocarbon analysis on thermal simulation gas were also carried out in this study. It revealed that coal has the highest gas production rate; in addition, it yields a large amount of CO2 gas in the early stage of the simulation experiment. The carbon and hydrocarbon isotope of the coal thermal simulation gas is slightly heavier than that of coaly mudstone and carbon mudstone gas. Prior to reaching 500 °C, the carbon and hydrogen isotopes of these three kinds of gas became lighter and higher with the increase of temperature, but after 500 °C, they became lighter all throughout. Carbon isotope series reversal is observed in this process. The coal thermal simulation gas has the highest content of benzene, toluene, and 2,3-methylpentane. This study specified three highlights on the Sulige gas field: (1) CO2, formed in the early stage of hydrocarbon generation, may have a direct relationship with the reservoir densification in the Sulige gas field. (2) According to the analysis of light hydrocarbon, coal should be the dominant contributor to the accumulation of the Sulige natural gas. However, the contribution of coaly mudstone and carbon mudstone should not be ignored.Yu, K., Cao, Y., Qiu, L., Sun, P., 2019. Depositional environments in an arid, closed basin and their implications for oil and gas exploration: The lower Permian Fengcheng Formation in the Junggar Basin, China. American Association of Petroleum Geologists Bulletin 103, 2073-2115. Fengcheng Formation is a nonmarine, carbonate-dominated succession that formed under arid climatic conditions in a hydrologically closed basin. Two transects and two seismic profiles were examined, the characteristics and environmental significance of different lithofacies were studied, and a model of depositional environment divisions was proposed. The sedimentary model involved an alkaline lake in which the depositional environments consisted of a shallow saline lake margin, slope, saline lake center, and steep lake margin from northeast to southwest. The perennial central salty lake was located in the southwestern part of the study area, whereas there were widespread, low-gradient lake margins in the northeast, east, southeast, and southern parts of the study area. Lake-level fluctuations had a major influence on the shallow saline lake system and complicated the depositional environments in these areas. The deposits are derived from bedrock reworking, volcanic eruptions, and authigenic minerals that precipitated from brine during the hypersaline phase. Fine-grained terrigenous clastic sediments, volcanic ashes and dusts, and authigenic minerals mixed in the depocenter (concentration center of the brine pool), which was covered by high-salinity brines, and the depositional environment was anoxic as a result of salinity-based brine stratification. A thick sodium carbonate succession occurred in the depocenter of the ancient Mahu lake, where bedded sodium carbonate alternated with fine-grained, organic-rich tuff or tuffaceous hydrocarbon source rocks. Microorganisms bloomed in the alkaline, high-salinity brine, and the organic matter was well preserved, which is similar to those modern alkaline saline lakes in eastern Africa and western North America. Thus, the Permian Fengcheng Formation contains source rocks that formed in an alkaline saline lake.Yu, M., Eglinton, T.I., Haghipour, N., Montlu?on, D.B., Wacker, L., Wang, Z., Jin, G.e., Zhao, M., 2019. Molecular isotopic insights into hydrodynamic controls on fluvial suspended particulate organic matter transport. Geochimica et Cosmochimica Acta 262, 78-91. sorting has been shown to strongly influence the composition and age of organic carbon (OC) during sediment transport and burial in the marine environment, yet sorting effects on terrestrial OC (OCterr) in fluvial systems remain poorly understood. We conducted size fractionation of suspended particle samples from the lower Yellow River, China, and examined variations in mass distribution and carbon isotopic (δ13C and Δ14C) composition of bulk OC and specific biomarkers among grain size fractions in order to investigate the influence of hydrodynamic sorting and selective transport on organic matter export. In general, the 16–32?μm and 32–63?μm fractions contributed the most of sediment mass while the majority of the OC resided in the 16–32?μm fraction. Over 80% of OC and n-fatty acids (FAs) were concentrated in <32?μm fractions. Significant differences in OC%, surface area (SA), Δ14COC, n-FAs contents, and compound-specific 13C and 14C compositions were found among size fractions. Of particular note was a progressive decrease of Δ14C values (i.e., increase in 14C age) of long-chain (C26+28+30) FAs with decreasing grain size. Taken together, the bulk and molecular characteristics imply two distinct types of selective OCterr transport in the Yellow River. Coarser particles (>32?μm), characterized by relatively low SA, OC%, and Δ14COC values, but higher Δ14C values of C26+28+30 FAs, are inferred to reflect a combination of bedrock-derived detrital sediment and fresh vascular-plant material (e.g., plant fragments). In contrast, finer particles (<32?μm), exhibiting higher SA, OC%, and lower Δ14C26+28+30FAs values, reflect preferential transport of pre-aged, mineral soil-derived OC that is susceptible to repeated mobilization, as well as widespread dispersal in marginal seas. The latter, once buried in marine sediments, could account for the high burial efficiency of OCterr in the adjacent Bohai Sea and Yellow Sea. Thus, hydrodynamic sorting processes induce heterogeneity of composition and selective transport of OC. Bulk and molecular 14C measurements of size-fractionated particles facilitate both elucidation of these processes and assessment of their impact on OC cycling in (and export from) rivers.Yu, Y., Qi, Z., Li, W., Fu, S., Yu, X., Xiong, D., 2019. Effects of physical parameters and chemical dispersant on the formation of oil-particle aggregates (OPAs) in marine environments. Marine Pollution Bulletin 148, 66-74. oil and sediments can interact to form oil-particle aggregates (OPAs) in marine environments. Laboratory batch experiments were conducted to investigate the effects of the concentration and size of sediment, temperature, oil types and chemical dispersant on the formation of OPAs. The results showed that the mass of OPAs and oil-particle aggregation rate are mainly related to the sediment concentration. Under the same mass concentration, more oil droplets can be trapped by smaller particles. Nevertheless, larger particles tend to interact more quickly with oil droplets. The effect of temperature on the formation of OPAs is substantially attributed to its influence on oil viscosity, and there is a threshold for oil viscosity which will bring about the maximum OPAs. Spilled oil with a high asphaltene can interact more effectively with the sediments. Appropriate addition of chemical dispersant is favorable for the formation of OPAs while excess addition will inhibit it.Zamirri, L., Ugliengo, P., Ceccarelli, C., Rimola, A., 2019. Quantum mechanical investigations on the formation of complex organic molecules on interstellar ice mantles. Review and perspectives. ACS Earth and Space Chemistry 3, 1499-1523. interstellar medium (ISM) is rich in molecules, from simple diatomic to complex organic ones, some of which have a biotic potential. A notable example, in this respect, is represented by the so-called interstellar complex organic molecules (iCOMs). Interestingly, the various phases involved in the formation of Solar-type planetary systems lead to an increasing chemical complexity, in which, at each step, more complex molecules form. In dark molecular clouds, dust grains are covered by ice mantles, mainly made up of H2O but also of other volatiles species such as CO, NH3, CO2, CH4, and CH3OH. Although their mass is one hundred times lower than the gas-phase matter, these ice-covered grains play a fundamental role in the interstellar chemical complexity as some important reactions are exclusively catalyzed by their surfaces. For example, one of the current paradigms on the iCOMs formation assumes that iCOMs are synthesized on the ice mantle surfaces, in which reactants accrete and diffuse to finally react. As the usual approaches employed in astrochemistry (i.e., spectroscopic astronomical observations, astrochemical modeling and laboratory experiments) cannot easily provide details on the iCOMs formation processes occurring on ice mantles at the atomic level, computational chemistry has recently become a complementary tool to fill in this gap. Indeed, it can provide an accurate description (i.e., structures and reactive energy profiles) of these processes. Accordingly, several recent studies simulating the formation of iCOMs on icy surfaces by means of quantum mechanical methods have appeared in the literature. This Review aims to comprehensively analyze most of these works, focusing not only on standard iCOMs but also on simpler organic compounds as well as biomolecules. Perspectives on possible future directions of research using computational chemistry are also proposed.Zelaya, A.J., Parker, A.E., Bailey, K.L., Zhang, P., Van Nostrand, J., Ning, D., Elias, D.A., Zhou, J., Hazen, T.C., Arkin, A.P., Fields, M.W., 2019. High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer. Water Research 164, 114917. microbial community structure and function within the subsurface is critical to assessing overall quality and maintenance of groundwater; however, the factors that determine microbial community assembly, structure, and function in groundwater systems and their impact on water quality remains poorly understood. In this study, three shallow wells (FW301, FW303, FW305) in a non-contaminated shallow aquifer in the ENIGMA-Oak Ridge Field Research Center (Oak Ridge, TN) were sampled approximately 3 times a week over a period of three months to measure changes in groundwater geochemistry and microbial diversity. It was expected that the sampled microbial diversity from two historic field wells (FW301, FW303) would be relatively stable, while diversity from a newer well (FW305) would be less stable over time. The wells displayed some degree of hydrochemical variability over time unique to each well, with FW303 being overall the most stable well and FW301 being the most dynamic based upon dissolved oxygen, conductivity, and nitrate. Community analysis via ss-rRNA paired-end sequencing and distribution-based clustering revealed higher OTU richness, diversity, and variability in groundwater communities of FW301 than the other two wells for diversity binned over all time points. Microbial community composition of a given well was on average?>?50% dissimilar to any other well at a given time (days), yet, functional gene diversity as measured with GeoChip remained relatively constant. Similarities in community structure across wells were observed with respect to the presence of 20 shared bacterial groups in all samples in all wells, although at varying levels over the tested time period. Similarity percentage (SIMPER) analysis revealed that variability in FW301 was largely attributed to low abundance, highly-transient populations, while variability in the most hydrochemically stable well (FW303) was due to fluctuations in more highly abundant and frequently present taxa. Additionally, the youngest well FW305 showed a dramatic shift in community composition towards the end of the sampling period that was not observed in the other wells, suggesting possible succession events over time. Time-series analysis using vector auto-regressive models and Granger causality showed unique relationships between richness and geochemistry over time in each well. These results indicate temporally dynamic microbial communities over short time scales, with day-to-day population shifts in local community structure influenced by available source community diversity and local groundwater hydrochemistry.Zhai, G., Shirzaei, M., Manga, M., Chen, X., 2019. Pore-pressure diffusion, enhanced by poroelastic stresses, controls induced seismicity in Oklahoma. Proceedings of the National Academy of Sciences 116, 16228-16233.: We develop a physics-based earthquake-forecasting model for evaluating seismic hazard due to fluid injection, considering both pore pressure and poroelastic stresses. Applying this model to complex settings like Oklahoma, we show that the regional induced earthquake timing and magnitude are controlled by the process of fluid diffusion in a poroelastic medium, and thus seismicity can be successfully forecasted by using a rate-and-state earthquake nucleation model. We find that pore-pressure diffusion controls the induced earthquakes in Oklahoma. However, its impact is enhanced by poroelastic effects. This finding has significant implications for induced earthquake-forecasting efforts by integrating the physics of fluid diffusion and earthquake nucleation.Abstract: Induced seismicity linked to geothermal resource exploitation, hydraulic fracturing, and wastewater disposal is evolving into a global issue because of the increasing energy demand. Moderate to large induced earthquakes, causing widespread hazards, are often related to fluid injection into deep permeable formations that are hydraulically connected to the underlying crystalline basement. Using injection data combined with a physics-based linear poroelastic model and rate-and-state friction law, we compute the changes in crustal stress and seismicity rate in Oklahoma. This model can be used to assess earthquake potential on specific fault segments. The regional magnitude–time distribution of the observed magnitude (M) 3+ earthquakes during 2008–2017 is reproducible and is the same for the 2 optimal, conjugate fault orientations suggested for Oklahoma. At the regional scale, the timing of predicted seismicity rate, as opposed to its pattern and amplitude, is insensitive to hydrogeological and nucleation parameters in Oklahoma. Poroelastic stress changes alone have a small effect on the seismic hazard. However, their addition to pore-pressure changes can increase the seismicity rate by 6-fold and 2-fold for central and western Oklahoma, respectively. The injection-rate reduction in 2016 mitigates the exceedance probability of M5.0 by 22% in western Oklahoma, while that of central Oklahoma remains unchanged. A hypothetical injection shut-in in April 2017 causes the earthquake probability to approach its background level by ～2025. We conclude that stress perturbation on prestressed faults due to pore-pressure diffusion, enhanced by poroelastic effects, is the primary driver of the induced earthquakes in Oklahoma.Zhan, L., Guo, B., Yu, Y., Hu, J., Wang, S., 2019. Source–reservoir chart for tight oil sweet spots evaluation and its application in Permian of Jimsar Sag, Junggar Basin. Journal of Petroleum Exploration and Production Technology 9, 1723-1731. spots control the production of the tight oil reservoir, so sweet spots evaluation is a critical work for tight oil exploration and development. This paper proposes a source–reservoir chart method for tight oil sweet spots evaluation and an application in Permian of Jimsar Sag, Junggar Basin. Firstly, the evaluation chart is plotted based on the relationships between the TOC and Ro parameters of source rocks, the porosity and the oil saturation of reservoirs through the experimental data of hydrocarbon generation simulation and mercury injection. Secondly, according to the evaluation criteria of TOC, Ro of source rock and porosity, oil saturation of reservoir in the study area, the chart is divided into three sweet spots zones and a non-sweet spots zone. Finally, each grid of the study area is assigned parameters and plotted in the chart of different zones, and the sweet spots are mapped. Production data show the reliability of the evaluation results. This method provides a convenient and efficient procedure for evaluating sweet spots of tight oil based on integrating the quality of source rocks and reservoirs.Zhang, B., Yao, S., Hu, W., Ding, H., Liu, B., Ren, Y., 2019. Development of a high-productivity and anoxic-euxinic condition during the late Guadalupian in the Lower Yangtze region: Implications for the mid-Capitanian extinction event. Palaeogeography, Palaeoclimatology, Palaeoecology 531, 108630. marine anoxia is considered one of the most important causes for the mid-Capitanian mass extinction. However, the mechanisms and subsequent sulfidic process for the mid-Capitanian mass extinction are still debated. Here, we focus on a comprehensive study including marine productivity and redox conditions of the Lower Yangtze area across the mid-Capitanian mass extinction based on multiple geochemical indicators. Our results show that the redox conditions and marine productivity have gone through three stages. The pre-extinction early-middle Capitanian is characterized by anoxic conditions with intermittent euxinic episodes and moderate-high productivity, whereas the middle Capitanian is dominated by stronger euxinic conditions and higher productivity. Subsequently, an oxic shallow water environment and low productivity are recognized by significant decreases in all of these geochemical indicators across the mid-Capitanian. The appearance and development of the anoxic-euxinic conditions was probably caused by high productivity related to enhanced upwelling, which led to the intensified heterotrophic respiration and subsequent oxygen-depletion of the water column. More sluggish oceanic circulation that resulted from the global warming associated with the eruption of the Emeishan Large Igneous Province and upward movement of the chemocline due to great regression also further exacerbated the euxinic conditions during the middle Capitanian. The development of these euxinic conditions may have played a major role in triggering the super-anoxic ocean and is also coincident with the mid-Capitanian biotic crisis, which suggests the possible causal link between them. With comprehensive analysis of profiles across the globe, sulfidic models showing that the sulfidic water first occurred in the deep water during the early-middle Capitanian and shoaled to shallow water in the middle-late Capitanian could be established, despite the fact that the temporally and spatially heterogeneous sulfidic processes in the late Guadalupian are still debated.Zhang, C., Chang, H., Wang, H., Zhu, Y., Zhao, X., He, Y., Sun, F., Wu, F., 2019. Spatial and temporal distributions of short-, medium-, and long-chain chlorinated paraffins in sediment cores from nine lakes in China. Environmental Science & Technology 53, 9462-9471. spatial and temporal distributions of short-, medium-, and long-chain chlorinated paraffins (SCCPs, MCCPs, and LCCPs) were studied in sediment cores and surface sediment from nine lakes in China. The highest total CP concentrations in surface sediment were found in the plateau lakes of southwest China, followed by lakes in the northeast, east, and remote northwest. The concentrations of three CP groups in cores showed an increasing trend from the 1970s to 2014, with the most rapid increase occurring from the late 2000s to 2014, consistent with the statistics on historical production of CPs in China. The three CP groups showed site-specific profiles in sediments from the nine lakes, and their percentages changed with sedimentary years. In sediment samples with dated year after 1980, MCCPs were dominant in sediment from Lakes Sihailongwan maar, Taihu, Erhai, and Chenghai, and LCCPs were predominant compounds in the other five lakes. The proportions of LCCPs rapidly increased after 1980, reflecting the increasing production and usage of LCCPs in China. The total burdens of ∑SCCPs, ∑MCCPs, and ∑LCCPs in sediment prior to 2006 were estimated to be 0.26–5100, 0.29–21000, and 0.07–4300 kg, respectively, which were 1.4–440-fold higher than those of ∑PBDEs.Zhang, D., 2019. Accumulation conditions and key technologies for exploration and development in Sebei gas field in Qaidam Basin, NW China. Petroleum Research 4, 191-211. Sebei gas field, located in the northern slope of the Sanhu depression in the eastern Qaidam Basin, is the largest inland biogas producing area in China. It is a typical Quaternary biogenetic gas reservoir composed of multiple layers of unconsolidated sandstone. Through systematic study of gas generating mechanism of source rock, reservoir-caprock combination and trap evolution, the unique biogas accumulation model characterized by “continuous hydrocarbon generation and dynamic accumulation” is established. Its uniqueness is reflected in the biogas generation mechanism under dual effect of low-temperature thermodynamics and microbial degradation, source-reservoir one body, self generation and self storage, dynamic source-reservoir-caprock assemblages and anticline trap formation mechanism of multi-factor mutual promotion. This understanding reveals the intrinsic factors for formation of large-scale biogas field under frigid climate, high salinity and low organic matter abundance. A number of exploration and development technologies have been worked out during the exploration and development of the Sebei gas field. Among them, the low-amplitude structure identification technique, multi-parameter gas-bearing detection technique, sand control and comprehensive water control technique for unconsolidated sandstone are well applied in discovering the gas field, increasing reserve, and increasing and maintaining gas production. The above understandings and key technologies have great reference significance and demonstration effect for biogas exploration and development in China and the world.Zhang, F., Algeo, T.J., Cui, Y., Shen, J., Song, H., Sano, H., Rowe, H.D., Anbar, A.D., 2019. Global-ocean redox variations across the Smithian-Spathian boundary linked to concurrent climatic and biotic changes. Earth-Science Reviews 195, 147-168. Smithian-Spathian boundary (SSB) was an interval characterized by a major global carbon cycle perturbation, climatic cooling from a middle/late Smithian boundary hyperthermal condition, and a major setback in the recovery of marine necto-pelagic faunas from the end-Permian mass extinction. Although the SSB has been linked to changes in oceanic redox conditions, key aspects of this redox variation (e.g., duration, extent, and triggering mechanisms) and its relationship to coeval climatic and biotic changes remain unresolved. Here, we report a high-resolution middle Smithian to middle Spathian U isotope (δ238U) record based on marine carbonates of the Zuodeng (South China) and Jesmond (British Columbia) sections to investigate the timing and global extent of ocean-redox variation across the SSB. Our δ238U record reveals values similar to or slightly heavier than modern seawater (-0.39‰) during the middle Smithian, a rapid negative shift to highly negative values during the early late Smithian, a positive shift at the SSB, and a rapid shift back to more negative values in the early-middle Spathian. A simple U-isotope mass balance modeling suggests that the global area of anoxic seafloor expanded strongly during the late Smithian and the early-middle Spathian (covering ~11% of total seafloor area), but that it contracted sharply during the SSB (~2%). The redox pattern documented by our δ238U record shows a good first-order correspondence to tropical sea-surface temperature (SST) data for the Smithian-Spathian. In particular, peak anoxia coincided with the middle/late Smithian boundary hyperthermal event, and diminished anoxia with a pronounced decline in SSTs at the SSB. The temporal correlation between anoxia and low biodiversity levels of many marine clades (e.g., conodonts and ammonoids) during the late Smithian indicates that oceanic anoxia may have played a role in the SSB biocrisis.Zhang, G., Tong, X., Xin, R., Wen, Z., Ma, F., Huang, T., Wang, Z., Yu, B., Li, Y., Chen, H., Liu, X., Liu, Z., 2019. Evolution of lithofacies and paleogeography and hydrocarbon distribution worldwide (I). Petroleum Exploration and Development 46, 664-686. using a large amount of geological and geophysical data, the geological characteristics such as lithofacies and paleogeography of 4981 geological units at thirteen key geological periods or epoches since the Precambrian in the world have been figured out. The global lithofacies and paleogeography charts have been compiled by ArcGis mapping technology. Combined with the results of plate-paleogeography reconstruction, the lithofacies and paleogeography as well as the prototype basins of these global paleoplates have been restored with the Gplate software. Results show that there are 22 kinds of lithofacies combinations and 10 types of paleogeography units developed since Precambrian. These features of lithofacies and paleogeography as well as their evolution were mainly controlled by the divergent and convergent movements of those plates. Taking the results of the lithofacis and paleogeography at the present and paleoplate location during the seven key geological periods from the Precambrian to Paleozoic for example, during the Late Precambrian and Cambrian, the large-scale disintegration of the Rodinia supercontinent resulted in reduction of uplift denudation area and clastic terrestrial facies area, the expansion of coastal-shallow marine facies and shallow-water carbonate platform. In Devonian, uplift denudation area and clastic terrestrial facies area began to increase and littoral-shallow marine facies area and shallow-water carbonate platform shrank as a result of the formation of Larussia supercontinent. In the Permian, with the formation of the Pangea continent, the development of the global uplift denudation area and clastic terrestrial facies reached its peak, while the littoral and shallow marine facies were very limited in distribution. The lithofacies and paleogeography features and evolution patterns of different stages lay a solid foundation for analyzing the formation conditions of geological elements, such as source rocks, reservoirs and cap rocks for oil and gas accumulation, and revealing the distribution regularity of oil and gas around the world.Zhang, J., Cao, J., Wang, Y., Li, J., Hu, G., Zhou, N., Shi, T., 2019. Geochemistry and genesis of oil and gas seeps in the Junggar Basin, NW China: Implications for hybrid petroleum systems. Geofluids 2019, 9732674. Junggar Basin of NW China is representative in containing oil and gas seeps worldwide as there are a wide variety of oil and gas seeps over a large area. However, the genesis of these seeps remains poorly known, limiting the understanding of their implications for petroluem geology and hydrocarbon exploration. Here, we investigate 26 samples of oil and gas seeps from nine outcrops within five areas along the margins of the Junggar Basin to determine the geochemical characteristics of the hydrocarbons, constrain their genesis, and discuss future exploration strategies. Results indicate one type of gas seeps and five types of oil seeps. The gas seeps are derived from low-maturity Jurassic source rocks and occur in the Wusu and Dushanzi areas in the western segment of the southern basin. Type 1 oil seeps, sourced from lower Permian rocks (P1f), occur on the northwestern margin. Type 2 oil seeps, derived from middle Permian source rocks (P2l/P2p), occur on the eastern segment of the southern margin and eastern margin of the Junggar Basin. Type 3 oil seeps, with Jurassic source rocks, occur in the Qigu area in the middle segment of the southern basin. Type 4 oil seeps, with Cretaceous source rocks, occur in the Anjihai and Huoerguosi areas within the middle segment of the southern basin. Type 5 oil seeps mainly have Paleogene source rocks with a minor contribution from Jurassic rocks and occur in the Wusu and Dushanzi areas in the western segment of the southern basin with the single-type gas seeps. These results indicate the presence of lacustrine hybrid petroleum systems within the Junggar Basin with complex oil and gas sources and migration-accumulation. Six potential areas along the basin margin were proposed for exploration in the future.Zhang, J., Chi, F., Wei, D., Zhou, B., Cai, S., Li, Y., Kuang, E., Sun, L., Li, L.-J., 2019. Impacts of long-term fertilization on the molecular structure of humic acid and organic carbon content in soil aggregates in black soil. Scientific Reports 9, 11908. aggregates are the basic units of soil structure, and their composition and carbon (C) stability directly affect soil fertility. As cementing agents, humic substances play an important role in the formation and stability of soil aggregates. Long-term fertilization not only changes the structure of humic acid (HA), but also affects the content and stability of organic C in soil aggregates. In this study, based on a long-term fertilization experiment, the relationship between the molecular structure of HA and the stability of organic C in the aggregates was examined. Compared with the non-fertilization control (CK), both the application of organic manure alone (M) and organic manure combined with inorganic fertilizer application (MNPK) increased organic C content in the bulk soil and in HA. In addition, the application of organic manure (M, MNPK) favored the formation of macroaggregates (>0.25?mm) and showed a higher organic C contents of soil aggregates with different sizes than the CK. Moreover, the content of aliphatic C, the ratios of aliphatic C/aromatic C and alkyl C/O-alkyl C was increased with the application of organic fertilizer. A significant negative correlation was observed between aromatic C and organic C content of the aggregates with sizes of >2?mm, 2–0.25?mm, and 0.25–0.053?mm (P?<?0.05). The findings indicated that organic fertilization treatments (M and MNPK) increased the aliphatic C content of HA, which favored the increase in the organic C content and stability of the aggregates.Zhang, J., He, S., Wang, Y., Wang, Y., Hao, X., Luo, S., Li, P., Dang, X., Yang, R., 2019. Main mechanism for generating overpressure in the Paleogene source rock series of the Chezhen depression, Bohai Bay Basin, China. Journal of Earth Science 30, 775-787. Chezhen depression, located in the south of Bohai Bay Basin, is an oil-producing basin in China. The third and fourth members of the Shahejie Formation (Es3 and Es4) are the main source rock series in the Chezhen depression. Widespread overpressures occurred in the Es3 and Es4 from the depths of approximately 2 000 to 4 600 m, with the maximum pressure coefficient of 1.98 from drillstem tests (DST). Among the sonic, resistivity and density logs, sonic-log is the only reliable pressure indicator and can be used to predict the pore pressure with Eaton’s method. All the overpressured mudstones in the source rock series have higher acoustic traveltimes compared with normally pressured mudstones at a given depth. The overpressured mudstones in the Es3 and Es4 units are characterized by a normal geothermal gradient, high average density values up to 2.5 g/cm3, strong present-day hydrocarbon generation capability, abundant mature organic matter and high contents of residual hydrocarbons estimated by the Rock-Eval S1 values and chloroform-soluble bitumen “A” values. All suggest that the dominant mechanism for overpressure in the mudstones of source rock series in the Chezhen depression is hydrocarbon generation. A comparison between the matrix porosity of the normally pressured sandstones and overpressured sandstones, the quantitative evaluation of porosity loss caused by compaction and the conventional thin section inspection demonstrate that the sandstones in the Chezhen depression were normally compacted. The high contents of hydrocarbons in the overpressured reservoirs prove that the overpressure in the sandstones of the source rock series was caused by pressure transmission from the source rocks.Zhang, J., Li, X., Chen, Z., Li, Q., Li, G., Lv, T., 2019. Numerical simulation of the improved gas production from low permeability hydrate reservoirs by using an enlarged highly permeable well wall. Journal of Petroleum Science and Engineering 183, 106404. production from low-permeability hydrate reservoirs is characterized by very low efficiency. In this work, the enlarged well wall with good permeability was first proposed to improve the gas production performance from low-permeability hydrate reservoir in Liwan 3 area of the South China Sea. The gas-water production behaviors, the spatial distributions and evolutions of hydrate reservoir parameters and gas-water flow characteristics, induced by constant-depressurization, were investigated and evaluated by numerical simulations under different radius of permeable well wall. Results show that the enlarged well wall provides a high-permeability channel around the production interval and increases the contact area between the production interval and hydrate layer, so the pressure drop propagation speed and distance, i.e. the depressurization efficiency in the hydrate-bearing sediments is increased. Both gas and water production performances are significantly improved, and the gas and water production rates, cumulates and gas to water ratio increase with the increase in permeable well wall radius. The cumulative CH4 and water produced increase by ca. 4 and 3 times, respectively, when the permeable well wall radius increases from 0 to 5?m. However, the heat supply by heat convection of geothermal water is still limited.Zhang, L., Huang, X., Wang, C., Yang, C., 2019. Insight into polycyclic aromatic hydrocarbons in unconventional oil via concentration-resolved fluorescence spectroscopy coupled with data mining techniques. Energy & Fuels 33, 7206-7215. exploration, production, and transportation of unconventional oils have attracted increasing attention for their economic value and environmental pressure. However, the previous analytical techniques of conventional oils encounter bottlenecks because of the separation difficulties of the unresolved complex mixtures. It is of great value to develop new methods to pursue a more detailed investigation of the chemical compositions of unconventional oil. Concentration-resolved fluorescence spectroscopy (CRFS) was developed to characterize the multi-dimensional fluorescence features of polycyclic aromatic hydrocarbons in unconventional oil samples. Laboratory simulation experiments of thermal evolution and biodegradation were designed to verify the effectiveness of CRFS compared to gas chromatography–flame ionization detector and gas chromatography–mass spectrometry. Dual-tree complex wavelet analysis and principal component analysis were used to remove redundant information and extract more detailed and effective information on CRFS spectra, and then a generalized regression neural network was used to classify and identify crude oil samples of different heavy oil species. With 100% accuracy, this computer data processing combined CRFS method is proven to be fast, accurate, and economical and is expected to be an effective method to solve the present problem of unconventional oil analysis.Zhang, L., Liu, X., Zhao, Y., Zhou, Y., Shan, B., 2019. Effect of pore throat structure on micro-scale seepage characteristics of tight gas reservoirs. Natural Gas Industry 38, 50-57. present, the effects of pore throat structure on micro-scale seepage characteristics of tight gas reservoirs are less researched, and traditional numerical simulation methods are faced with a great number of challenges in the study of micro-scale flow. In this paper, the flow pattern of tight gas was studied based on the actual temperature and pressure of tight gas reservoir and the characteristic size of reservoir pore throat, and the rationality of tight gas flow was simulated by means of lattice Boltzmann method. Then, considering the influences of micro-scale effect, slippage effect and other factors, a tight gas flow model was established on the basis of LBGK-D2Q9 model, and its calculation results were compared with the analytical solutions and the numerical solutions listed in the literature. Finally, the influential laws of pore throat structure on the micro-scale seepage characteristics of tight gas were discussed. And the following research results were obtained. First, when the pressure is in the range of 3–70 MPa and the temperature is in the range of 293.15–373.15 K, the Knudsen number (Kn) is less than 0.1 and the gas flow is in the pattern of slippage flow and weak continuous flow. And in this case, it is reasonable to adopt the LBGK-D2Q9 model to simulate tight gas flow. Second, the effect of the characteristic size of the flow channel on the Kn is much greater than that of the pressure change. When the pore–throat ratio is constant, the Kn increases slowly along the throat. And its increasing trend gets more obvious with the increase of pore–throat ratio. Third, the presence of the throat makes the non-linear distribution characteristics of the pressure in the pore throat significant, and the pressure drop mainly lies in the throat. And the higher the pore–throat ratio is, the larger the pressure drop range in the throat is. Fourth, the non-linear distribution of pressure decreases the gas flow speed significantly, thus reducing the mass flow rate in the flow channel. In conclusion, the simulation result of the model established in this paper is highly coincident with the analytical solutions and the numerical solutions calculated by DSMC and IP methods in the literature, which verifies that this proposed model is reliable. The research results reveal the importance of "connecting fracture and expanding throat" in the practical development engineering of tight gas reservoirs.Zhang, L., Orchard, M.J., Brayard, A., Algeo, T.J., Zhao, L., Chen, Z.-Q., Lyu, Z., 2019. The Smithian/Spathian boundary (late Early Triassic): A review of ammonoid, conodont, and carbon-isotopic criteria. Earth-Science Reviews 195, 7-36. transition from the Smithian substage to the Spathian substage of the Olenekian stage of the late Early Triassic was a critical time marked by a series of biological and environmental changes during the multimillion-year recovery interval following the end-Permian mass extinction. However, the Smithian/Spathian boundary (SSB) does not yet have an agreed definition, a shortcoming that complicates high-resolution analysis of events during the Smithian-Spathian transition. Here, we review key biostratigraphic (i.e., ammonoid and conodont) studies of the Smithian and Spathian substages in historically important regions (e.g., the Canadian Arctic for the Boreal realm, western North America for the eastern Panthalassic Ocean) and more recently re-studied locations (e.g., Pakistan and India in the southern Tethys, South China in the eastern Tethys) as well as the carbon isotope chemostratigraphy of 29 major Smithian-Spathian sections globally. Key ammonoid genera (e.g., Wasatchites, Anasibirites, Glyptophiceras and Xenoceltites of the late Smithian, and Bajarunia, Tirolites and Columbites of the early Spathian), conodont species (e.g., Scythogondolella milleri, Novispathodus waageni, and Borinella buurensis of the late Smithian, and ‘Triassospathodus’ hungaricus, Neogondolella aff. sweeti, and Icriospathodus spp. of the early Spathian), and carbonate carbon isotope excursions provide appropriate markers for constraining the SSB. Use of the first occurrence of the conodont Novispathodus pingdingshanensis as a potential marker of the SSB is also discussed. Based on correlations of biostratigraphic and carbon isotope data globally, we propose to revise previous placements of the SSB transition in some sections. Finally, we show that the Smithian Thermal Maximum (STM; herein named) was middle Smithian in age and not correlative with the SSB, as inferred in some earlier studies, and that the SSB coincided with a subsequent major global cooling event.Zhang, L., Peng, Y., Ge, Z., Xu, K., 2019. Fate of dissolved organic nitrogen during the Anammox process using ultra-high resolution mass spectrometry. Environment International 131, 105042. ammonium oxidation (Anammox) is a cost-effective process for treating highly nitrogenous wastewater. However, the fate of organic nitrogen during Anammox treatment is still unclear, which limits its practical application. In this work, the changes in the quality of dissolved organic nitrogen (DON) in coal liquefaction wastewater (CLW) during Anammox were studied in relation to its chemical composition, which was determined by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). The molecular-level characterization of extracellular polymeric substances (EPS) in the Anammox sludge is also reported for the first time in this paper. The relative contribution of N-containing compounds to the total dissolved organic matter (DOM) determined by summating the normalized intensities exceeded 30%, highlighting the complexity of the nitrogenous compounds in the influent. Additionally, Anammox appeared to be better suited to removing DON compounds with fewer carbonyl or carboxyl groups, more aromatic structures, and higher oxidative properties. Lignin-like substances were verified as the predominant component of N-containing compounds in Anammox EPS, followed by protein and substances with condensed aromatic structures. DON compounds with higher degrees of saturation, lower molecular weight, and higher lignin-like properties were more prone to absorption by Anammox EPS. A series of microbe-mediated pathways were demonstrated to be responsible for DON biodegradation, which revealed the organic and inorganic nitrogen removal mechanisms in the Anammox reactor. The obtained results provide great support to the ongoing efforts to optimize the Anammox process.Zhang, L., Wang, Y., Miao, X., Gan, M., Li, X., 2019. Geochemistry in geologic CO2 utilization and storage: A brief review. Advances in Geo-Energy Research 3, 304-313. this brief review, a comprehensive collection of previous studies about geochemistry in geologic CO2 utilization and storage is presented and discussed to demonstrate the importance of CO2-rock and CO2-wellbore cement interactions in geologic CO2 utilization and storage scenarios. For CO2-rock interaction, CO2 injection reduces the pH of brine in CO2 storage reservoir, which triggers dissolution of silicate and oxide minerals in the reservoir. Dissolution of silicate and oxide minerals causes concentration increase of cations and anions, which induces secondary precipitation of silica, silicates and carbonates. For CO2-cement interaction, the interaction between CO2 and wellbore cement results in formation of a unique “sandwich” structure in cement (i.e., one carbonate precipitation zone in the middle and two dissolution zones on two sides). For both CO2-rock and CO2-cement interactions, pH plays a key role in the extent of mineral dissolution and precipitation, and the extent is dependent on pH buffering capacity of the CO2 storage reservoir. The potential of CO2-induced contaminant mobilization in deep CO2 storage reservoir and shallow aquifer is also discussed, and the chance for CO2 injection and CO2 leakage to cause severe shallow aquifer contamination is low. Zhang, L., Zeng, Q., Liu, X., Chen, P., Guo, X., Ma, L.Z., Dong, H., Huang, Y., 2019. Iron reduction by diverse actinobacteria under oxic and pH-neutral conditions and the formation of secondary minerals. Chemical Geology 525, 390-399. reduction of Fe(III) is an important biogeochemical process in anoxic or acidic environments. However, this process under oxic and pH-neutral conditions is understudied, and the iron reduction capability of the phylum Actinobacteria is poorly known. In this study, we investigated the capacity of diverse actinobacteria to reduce Fe(III) in the presence of oxygen and at pH?7. From 277 actinobacterial strains isolated from deep sea and terrestrial soil, 109 strains (39.40%) belonging to 17 genera showed the capacity of reducing FeCl3 under oxic and initially neutral pH conditions. Among the 109 strains, 49 spanning 13 genera also reduced ferric iron oxides under the same conditions. Four non-filamentous strains from four genera were selected for further analyses. All the four strains showed the capacity to reduce goethite under oxic and pH?7 and 8 conditions. Microbial fuel cell (MFC) experiments showed a current enhancement when the strains were cultured in the presence of goethite. Living actinobacterial cells and their metabolites played a key role in reducing Fe(III). The strains produced organic acids and siderophores, which likely promoted Fe(III) reduction due to altered reduction potentials of complexed Fe(III) and inhibition of Fe(II) oxidization by oxygen. SEM/EDS and XRD analyses detected vivianite in the culture of Kocuria oceani FXJ8.057 with goethite, where, unexpectedly, K. oceani FXJ8.057 produced nanowire-like structures. These results demonstrate that actinobacteria are able to reduce Fe(III) in both aqueous and solid forms under oxic and pH-neutral conditions. The mechanisms, however, still need further investigation.Zhang, Q., Xiong, X., Pang, Z., Liu, R., Liang, F., Liang, P., Guo, W., Zhang, J., 2019. Composition effects on pore structure of transitional shale: A case study of the upper Carboniferous Taiyuan Formation in the eastern uplift of the Liaohe Depression, China. Marine and Petroleum Geology 110, 638-649. shale is very different from marine shale with respect to mineral composition and pore structure. Insights into the effects of rock composition on pore structure can aid understanding of the storage and migration mechanisms of shale gas in a reservoir. To investigate the compositional effects on pore structure, a combination of geochemical and petrophysical experiments were conducted on four bulk shale samples and their corresponding extracted organic matter (OM) and clay mineral samples. The experimental results show that the removal of OM using H2O2 during clay mineral extraction oxidizes and removes pyrite and siderite from the samples while other inorganic phases remain unaffected. OM hosted more abundant micropores compared with clay minerals, while mesopores and fine-macropores are dominant in clay minerals. Effects of the OM and clay minerals on pore volume and surface area are quantitatively evaluated on the basis of weight-normalized pore-size distribution (PSD) curves of extracted OM and clay mineral samples. In terms of the CO2 adsorption, contribution from OM and clay minerals to micropore volume (MIV) are 19.43–32.92% and 18.75–39.05% respectively, and to micropore surface area (MIS) are 19.30–32.28% and 16.42–35.72%. Other minerals (other than organic matter and clay minerals) account for 34.29–48.93% of the MIV and 39.75–52.98% of the MIS. N2 adsorption results reveal that the pore volume and surface area are mainly attributable to the clay minerals, providing 54.37–80.75% of the BJH pore volume (BJHV) (average 65.83%) and 70.68–87.04% of the BET surface area (BETS) (average 78.71%). The primary medium for pore development in marine shale is OM, whereas pores in the transitional shale are mostly found in the clay and other inorganic minerals. Therefore, the hydraulic fracturing design and drilling-related operations involved in the exploitation of transitional shale gas should be appropriately adjusted and improved in order to accommodate intrinsic characteristics of the transitional shale gas reservoir.Zhang, S., Zhang, X., Hao, Z., Wang, Z., Lin, J., Liu, M., 2019. Dissolution behavior and chemical characteristics of low molecular weight compounds from tectonically deformed coal under tetrahydrofuran extraction. Fuel 257, 116030. deformed coal (TDC) is formed by complex and variable tectonic stresses. The induced physical-chemical effects result in a variety of chemical compositions and structures in TDCs. In this work, medium volatile bituminous coals with four types of tectonic deformation were selected and extracted with tetrahydrofuran to investigate the dissolution behavior and distribution of low molecular weight compounds in TDCs. The results revealed that a higher degree of tectonic deformation in the coal produces a higher total extraction yield as the total extraction time increases. A diffusion model also establishes a good relationship between the extraction mass and extraction time, and the diffusion coefficient Dobs can be used to describe the extraction kinetics. Chemical analysis of the extracts using column chromatography and GC/MS further found that there are more binding points for forming non-covalent bonds in long chain aliphatic hydrocarbons. So the alkanes with more than 20 carbon atoms are often dissolved at the medium and late stages. Aromatic compounds, which are mostly dissolved at the medium stage, are essentially combined into the coal macromolecular structure by π–π stacking interactions or hydrogen bonds. While a large number of heteroatomic compounds are distributed widely in coals, resulting in diverse dissolution behaviors. Under the tectonic stresses, the type and content of low molecular weight compounds in TDCs increase compared to intact coal. Particularly, an increase in tectonic deformation appeared to produce more aromatic hydrocarbons and long chain alkanes in TDCs, whilst the presence of heteroatomic compounds becomes more complex.Zhang, T.-Y., Li, S., Zhu, Q.-F., Wang, Q., Hussain, D., Feng, Y.-Q., 2019. Derivatization for liquid chromatography-electrospray ionization-mass spectrometry analysis of small-molecular weight compounds. TrAC Trends in Analytical Chemistry 119, 115608. derivatization-based liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) technique is an effective analytical tool for trace small-molecular weight compounds analysis present in complex samples. Chemical derivatization technique can improve the detection sensitivity, selectivity, chromatographic separation and identification capability of LC-ESI-MS analysis. In this review, we summarized the progress of chemical derivatization-assisted LC-MS methods in the period of 2014–2018, according to the functional groups of analytes, such as carboxyls, amines, carbonyls, thiols, hydroxyls, phosphates, modified nucleic acids, conjugated dienes and carbon-carbon double bonds. We mainly focused on the reaction principles of representative derivatization reagents with some application cases highlighting the impact of chemical derivatization-assisted LC-MS technique, which would be helpful for the designing and synthesis of new derivatization reagents for the analysis of small-molecular weight compounds in complex samples.Zhang, W., Hu, W., Borjigin, T., Zhu, F., 2020. Pore characteristics of different organic matter in black shale: A case study of the Wufeng-Longmaxi Formation in the Southeast Sichuan Basin, China. Marine and Petroleum Geology 111, 33-43. matter (OM) pores are recognized to be the most important pore type in gas shales in the Ordovician Wufeng-Silurian Longmaxi Formation in the Sichuan Basin, China. However, the effects of the type and origin of organic matter on pore development in OM remain controversial. In this study, detailed scanning electron microscope (SEM) analysis of siliceous shales was conducted for core samples from the Wufeng-Longmaxi Formation, taken from five shale gas wells in the Southeast Sichuan Basin. In addition to bitumen, several types of morphologically distinct organic macerals were identified. Due to the high maturity (vitrinite reflectance (Ro)?>?2.2%) and compaction of the sample, confirming the origin of some OM types was difficult. However, each OM type is characterized by distinct pore features: (1) the pores in bitumen are normally well developed, with circular or irregular shapes; (2) spherical kerogen contains uneven pores, with irregular and angular pores at the periphery and few pores in the core; (3) algal fragments may have angular pores, the distribution and structure of which are influenced by the initial structure of the organic matter; (4) bacteria-like aggregates represent the accumulation of numerous microbial granules, and contain residual pores; (5) graptolites are relatively tight and usually have few or no pores. The findings indicate that bitumen and algal fragments are the most favourable hydrocarbon-generating organisms for OM pore development. Notably, organic matter originating from different biological sources can influence the extent, shape, and structure of the pores. Some organic pores are recognized as remained pores of sedimentary stage, which may be previously regarded as pores formed during the gas generation period.Zhang, W., Li, Y., Zhao, F., Han, W., Zhou, J., Holland, G., Zhou, Z., 2019. Quantifying the helium and hydrocarbon accumulation processes using noble gases in the North Qaidam Basin, China. Chemical Geology 525, 368-379. reserves and insecure resource supply have led to global shortage crises in helium, a vital gas for cryogenic engineering and other countless industrial manufacturing processes. Despite the attention drawn by global supply disruptions, the helium accumulation mechanism in natural gas fields remains poorly understood. Noble gases are excellent tracers for studying migration and accumulation processes of fluids in the subsurface and can be used to investigate the influence of subsurface fluids on helium accumulation. We present noble gas isotope and abundance data as well as major gas compositional data from 10 producing wells in three gas fields in the North Qaidam Basin, China. Helium is more concentrated in the Mabei and Dongping gas fields (2.06–48.4?×?10?4?cm3 STP/cm3) than in the Niudong gas field (1.15–1.42?×?10?4?cm3 STP/cm3). The helium is mainly radiogenic, with 3He/4He ratios of 0.01–0.05 Ra, where Ra is the atmospheric value of 3He/4He, and lacks significant contribution from the mantle (0.03–0.67%). The noble gases derived from air-saturated water (20Ne, 36Ar, 84Kr and 130Xe) can be explained by an oil-modified groundwater-exsolution model with excess heavy noble gases. The calculated Voil/Vwater and Vgas/Vwater ratios indicate that the Mabei region is the most oil-rich area and the Dongping region has the driest natural gas, which is consistent with the geological context. These ratios further support the fractionation models. The strong linear relationship between 4He and 20Ne (R2?=?0.98) suggested that 4He was dissolved into groundwater before migrating into the oil or gas phase. The initial 4He concentrations in groundwater can accumulate within 0.31–2.78 Myr assuming a 4He flux from the entire crustal section. According to the fractionation model, helium in groundwater partitions into the gas phase when contacting hydrocarbons. The different volume ratios among oil, gas and water during the equilibration process cause much greater variability in the helium concentrations in the gas phase (e.g., 6.08?×?10?4 to 2.01?×?10?3?cm3 STP/cm3 in Mabei) than those in the groundwater phase (e.g. 9.18?×?10?3 to 1.39?×?10?2?cm3 4He STP/cm3 H2O in Mabei). Hydrocarbons play a critical role in helium accumulation and dilution. Helium-rich natural gas fields are characterized by old groundwater systems and moderate hydrocarbon abundance. This study has succeeded in quantitatively assessing the helium accumulation process in natural gas fields in the North Qaidam Basin and revealed that both groundwater and hydrocarbon phases control the helium accumulation in the subsurface environment. This outcome has broad implications for the prediction of hydrocarbon and helium as resources.Zhang, W., Liang, J., Wei, J., Su, P., Lin, L., Huang, W., 2019. Origin of natural gases and associated gas hydrates in the Shenhu area, northern South China Sea: Results from the China gas hydrate drilling expeditions. Journal of Asian Earth Sciences 183, 103953. data for hydrate gases acquired from the GMGS3 and GMGS4 gas hydrate drilling expeditions conducted by the Guangzhou Marine Geological Survey (GMGS) are used to explore the origin of hydrate gases and their relationship to deep hydrocarbon reservoirs, and to evaluate the contribution of different genetic types of gases to the formation and accumulation of gas hydrates in the Shenhu area of the northern part of the South China Sea (SCS). Compositionally, methane is the dominant gas (>90%) in the void gas and pressure core gas. In addition, as much as ~3% of the gas is composed of C2+ hydrocarbons, including ethane, propane, iso-butane, butane, iso-pentane, and n-pentane. The δ13C-CH4 and δD-CH4 values indicate a mixed biogenic-thermogenic origin for the hydrate-forming gas. The methane isotope correlation indicates that the source of the hydrate gas is closely related to the deep conventional gas reservoirs discovered in the Baiyun Sag-Panyu Low Uplift area. Both the hydrate gases and the deep reservoir gases are sourced from the hydrocarbon kitchens in the Baiyun Sag, revealing a paragenetic relationship within the same petroleum system. The composition of the hydrocarbons and the isotopic variation of methane with depth suggest that the thermogenic gas was likely affected by compositional and isotopic fractionation during the long-distance migration from the deep source rocks to the shallow gas hydrate stability zone (GHSZ). The impact of biodegradation on a solely thermogenic gas could also affect the final composition of the hydrate-forming gas. Analysis of the GHSZ based on gas hydrate compositions suggests that the occurrence of thermogenic gas could also indicate the coexistence of structure I (SI) and structure II (SII) gas hydrates in the Shenhu area, with the SII hydrates accumulating in or below the lower part of the SI GHSZ. The confirmed presence of SII hydrates in the Shenhu area relocated the base of the GHSZ deeper than was indicated by the bottom simulating reflector, which warrants further study in future explorations for gas hydrates in the Shenhu area.Zhang, Y., 2019. Similarities in diverse polycyclic aromatic hydrocarbons of asphaltenes and heavy oils revealed by noncontact atomic force microscopy: Aromaticity, bonding, and implications for reactivity, in: Rahimi, P., Ovalles, C., Zhang, Y., Adams, J.J. (Eds.), Chemistry Solutions to Challenges in the Petroleum Industry. American Chemical Society, Washington DC, pp. 39-65. oils are enriched in polycyclic aromatic hydrocarbons (PAHs) (or polynuclear aromatic hydrocarbons), but characterization of their chemical structures has been a great challenge because of their tremendous diversity. Recently, with the advent of molecular imaging by noncontact atomic force microscopy (nc-AFM), the structures of molecules within petroleum have been imaged, and a diverse range of novel PAH structures have been revealed. Understanding these structures will help to explain their chemical reactivities and the mechanisms of their formation or conversion. Studies on aromaticity and bonding provide a means to recognize their intrinsic structural patterns, which is crucial to reconciling a small number of structures by AFM and predicting an infinite number of diverse molecules in the bulk. Four types of PAH structures can be categorized according to their relative stabilities and reactivities, and it was found that the most and least stable types are rarely observed by AFM, as most molecules form intermediate types in a subtle balance between kinetic reactivity and thermodynamic stability. Local aromaticity was found to be maximized when possible for both alternant and nonalternant PAHs revealed by the values of the nucleus-independent chemical shift as an aromaticity index. The unique role of five-membered rings in disrupting the electron distribution was recognized. In particular, the presence of partial double bonds in most petroleum PAHs was identified, and their implications for the structures and reactivities of petroleum molecules are discussed.Zhang, Y., Barber, T.J., Hu, Q., Bleuel, M., El-Sobky, H.F., 2019. Complementary neutron scattering, mercury intrusion and SEM imaging approaches to micro- and nano-pore structure characterization of tight rocks: A case study of the Bakken shale. International Journal of Coal Geology 212, 103252. angle neutron scattering (SANS) and ultra-small angle neutron scattering (USANS) techniques have been increasingly utilized to study tight rocks (e.g., mudrocks), due to their capabilities of detecting total pore spaces (both body and throat) across the nm-μm spectrum. Mercury injection capillary pressure (MICP) is a widely employed technique in the oil and gas industry, used to obtain a variety of petrophysical properties of porous rocks. In this study, we selected six samples from the three (i.e., lower, middle, and upper) members of the Bakken Formation (Late Devonian to Early Mississippian) in the Williston Basin, North Dakota. We utilized the complementary techniques of (U)SANS and MICP to characterize and differentiate their pore systems over a broad measurable range of pore/throat sizes from 1.25?nm to 50?μm. Detailed processing of (U)SANS scattering data is illustrated to show how the total porosity and pore size distribution are obtained and compared against MICP analyses. The results show that the lower/upper Bakken samples and the middle Bakken samples have distinct mineral compositions and organic matter contents, which could be important factors affecting their pore structure. Assisted with the field emission-scanning electron microscopy (FE-SEM) technique, it was found that organic matter-hosted pores contribute a significant portion of total porosity in the lower/upper Bakken shales, while the middle Bakken samples are mostly composed of mineral pores. Additionally, the porosities measured by the (U)SANS and MICP techniques are related to sample sizes employed for each approach, due to a limited pore accessibility of mudrocks; a larger sample size will possess a higher proportion of isolated pores. In general, the results for the Bakken samples in this study indicate that the combination of (U)SANS, MICP, and FE-SEM approaches gives a more complete picture of the pore structure of tight rocks.Zhang, Y., Zeng, J., Cai, J., Feng, S., Feng, X., Qiao, J., 2019. A mathematical model for determining oil migration characteristics in low-permeability porous media based on fractal theory. Transport in Porous Media 129, 633-652. migration processes are crucially important for determining oil reserve levels and distributions in low-permeability reservoirs. Previous researches have proved that the macroscopic parameters of oil migration processes are controlled by microscopic pore properties in low-permeability media. To analyze the relationship between pore-scale parameters and the oil migration process in low-permeability formations, a mathematical model combining the capillary bundle model and fractal theory is developed in this work. The accuracy of the proposed model is validated via comparisons with three well-designed oil charging experiments using natural core samples. Based on the validated model, the influence of four factors (pore fractal dimension, tortuosity fractal dimension, the wettability of the rock surface, and the formation water viscosity) on oil migration processes in low-permeability media is analyzed. Oil saturation and effective permeability are used as the output parameters for reflecting changes in the oil migration process. The calculation results indicate that oil saturation decreases as pore fractal dimension, tortuosity fractal dimension, the hydrophilicity of the rock surface, and brine viscosity increase. On the other hand, effective permeability decreases as tortuosity fractal dimension and formation water viscosity increase, but increases with pore fractal dimension. Moreover, the wettability dependence of effective permeability is relatively weak.Zhao, J., Wang, L., Tang, L., Ren, R., You, W., Farooq, R., Wang, Z., Zhang, Y., 2019. Changes in bacterial community structure and humic acid composition in response to enhanced extracellular electron transfer process in coastal sediment. Archives of Microbiology 201, 897-906. acids are one of the main organic matters in sediments and contribute importantly to the marine biogeochemical cycles. Extracellular electron transfer is a ubiquitous natural process and has potentials to change the macrostructure of humic acids which can act as an electron shuttle. By setting up marine sediment microbial fuel cells, the present study revealed that enhanced extracellular electron transfer process could increase the content of C and H, but decrease the O content in humic acids, which could result in an increased aromaticity and decreased polarity of humic acids, whereas no significant changes occurred to the humification degree of the humic acids. Specific bacterial groups as potential exoelectrogens including Proteobacteria (especially Pseudomonas strains) and Firmicutes were enriched under enhanced extracellular electron transfer process, indicating?that they were active to exchange electrons and might play important roles during the changes of humic acids, while the relative abundance of Verrucomicrobia and Bacteroidetes was reduced during these processes. The results of the present research shed lights on the relation between exoelectrogens and the transformation of humic acids in coastal sediment, while the microbial process and mechanisms behind it require further study.Zhao, L., Kaiser, R.I., Lu, W., Xu, B., Ahmed, M., Morozov, A.N., Mebel, A.M., Howlader, A.H., Wnuk, S.F., 2019. Molecular mass growth through ring expansion in polycyclic aromatic hydrocarbons via radical–radical reactions. Nature Communications 10, 3689. aromatic hydrocarbons (PAHs) represent key molecular building blocks leading to carbonaceous nanoparticles identified in combustion systems and extraterrestrial environments. However, the understanding of their formation and growth in these high temperature environments has remained elusive. We present a mechanism through laboratory experiments and computations revealing how the prototype PAH—naphthalene—can be efficiently formed via a rapid 1-indenyl radical—methyl radical reaction. This versatile route converts five- to six-membered rings and provides a detailed view of high temperature mass growth processes that can eventually lead to graphene-type PAHs and two-dimensional nanostructures providing a radical new view about the transformations of carbon in our universe.Zhao, P., Han, S., Li, X., Zhu, T., Tao, X., Guo, L., 2019. Comparison of RP-3 Pyrolysis reactions between surrogates and 45-component model by ReaxFF molecular dynamics simulations. Energy & Fuels 33, 7176-7187. work compares pyrolysis reactions of 3- and 4-component surrogate models of RP-3 aviation fuel by a ReaxFF molecular dynamics (MD) simulation method. To evaluate the reactivity of the two RP-3 surrogate models, a multi-component baseline model that consists of 45 components was constructed as a representative of real RP-3 fuel. Reactive MD simulations of RP-3 fuel pyrolysis were performed for the two simple surrogate models and the multi-component baseline model using the GPU code of GMD-Reax. Reaction pathways were analyzed with aid of the unique software of VARxMD. The main product yield and the initial reaction pathways in heat-up pyrolysis simulations of the two RP-3 surrogate models are found different from those in the 45-component model. In comparison to the 45-component baseline model, the weight fraction of C2H4 generated can be 15% higher for the 4-component surrogate model and 10% higher for the 3-component surrogate model. Because the C2H4 molecules in RP-3 pyrolysis are mainly produced through β-scission reactions of normal paraffins, the overestimation of the C2H4 yield in heat-up pyrolysis simulations by the two RP-3 surrogate models can be attributed to the much higher normal paraffin of the 4-component surrogate model (86.5%) and 3-component surrogate model (73.0%) over the 45-component model (26.7%). Accordingly, the multiple branched methylalkane radicals generated in ring-opening reactions of 1,3,5-trimethylcyclohexane are responsible for the overestimation of C3H6 production found in simulations of the 3-component surrogate model. The differences of the major product generation between the two surrogate models and the baseline model indicate that both the fuel component composition and molecular structures in RP-3 surrogate models are closely associated with their reactivity differences in pyrolysis. ReaxFF MD simulations can be a useful approach to provide clues for further refinement of compositions and molecular structures of RP-3 surrogate fuel.Zhao, P., Wang, L., Xu, C., Fu, J., Shi, Y., Mao, Z., Xiao, D., 2020. Nuclear magnetic resonance surface relaxivity and its advanced application in calculating pore size distributions. Marine and Petroleum Geology 111, 66-74. laboratory and downhole nuclear magnetic resonance (NMR) measurements are commonly used to calculate the pore size distribution (PSD) that is important in determining the reservoir storage capacity and evaluating producibility, etc. The surface relaxivity is a key parameter to calculate the PSD using NMR transversal relaxation time (T2) distributions. Accurate surface relaxivity value would result in a reasonable PSD. In order to comprehensively study surface relaxivity, the conventional sandstone, tight sandstone, and shale samples are selected to perform experiments including porosity, permeability, NMR, mercury injection capillary pressure (MICP) and low temperature nitrogen adsorption (LTNA), etc. Three approaches, including LTNA, MICP, and Kozeny's equation, are used to determine the surface relaxivity. We find that for all samples, the surface relaxivity determined with Kozeny's equation is greater than that using LTNA and MICP data, indicating that surface relaxivity of smaller pores is less than that of bigger pores. It is also observed that the surface relaxivity of conventional sandstone is greater than that of tight sandstone and shales. The surface relaxivity of sandstone and shale samples are both affected by clay content. For shale samples, the surface relaxivity ranges from 3.41?μm/s to 9.79?μm/s and is influenced by organic matter contents as well. An equation for predicting surface relaxivity of shale is established. Finally, we propose an advanced method for calculating reasonable PSDs of sandstone and shale formation by the combination of two surface relaxivities, which could be applied to laboratory and field wells.Zhao, S., Pu, W., Varfolomeev, M.A., Yuan, C., Qin, S., Wang, L., Emelianov, D.A., Khachatrian, A.A., 2019. Thermal behavior and kinetics of heavy crude oil during combustion by high pressure differential scanning calorimetry and accelerating rate calorimetry. Journal of Petroleum Science and Engineering 181, 106225. the thermal release correlates directly with the success of in-situ combustion (ISC) technology, this research performs a series of investigations concerning thermal behavior and kinetics of heavy crude oil during combustion using high pressure differential scanning calorimetry (HP-DSC) and accelerating rate calorimetry (ARC). The results obtained from HP-DSC profiles indicated that for oil alone and its mixtures with quartz sand/crushed core, the peak temperature was lowered, and the heat flow increased with increasing oxygen partial pressure. The heat enthalpy of low temperature oxidation (LTO) was higher than that of high temperature oxidation (HTO) under oxygen partial pressures of 0.5, 1 and 1.5 MPa, and the increase in heat enthalpy of LTO with oxygen partial pressure was more pronounced than that of HTO. Unlike the crushed core, the addition of quartz sand delayed exothermic oxidation reactions. Compared with oil only and oil + quartz sand, the LTO and HTO peak temperatures of oil + crushed core were considerably lowered, and the effect of crushed core on increasing heat release for LTO at oxygen partial pressure of 1.5 MPa was more prominent. It was observed that the heat enthalpy of LTO and HTO increased quasi-linearly with the oxygen partial pressure in both the presence and absence of quartz sand/crushed core. ISC might be considered as an appropriate candidate for Jiqi block, based on exothermic continuity of the ARC curves, with the near-wellbore zone of target block heated to 180 °C where the exothermic oxidation activity is notably intensified. The kinetic results showed that the LTO and HTO intervals were divided into 6 and 2 subintervals, respectively, which facilitated more precise modelling of the ISC process.Zhao, X., Pu, X., Jiang, W., Zhou, L., Jin, F., Xiao, D., Fu, L., Li, H., 2019. An exploration breakthrough in Paleozoic petroleum system of Huanghua Depression in Dagang Oilfield and its significance, North China. Petroleum Exploration and Development 46, 651-663. recent years, several wells in the Qibei and Wumaying buried hills of Dagang Oilfield tapped oil in the Carboniferous–Permian and Ordovician strata. This major breakthrough reveals that the deep Paleozoic in the Bohai Bay is a new petroleum system. Through re-evaluating the Paleozoic source rock, reservoir-cap combinations and traps, it is found the oil and gas mainly come from Carboniferous–Permian source rock. The study shows that the Paleozoic strata are well preserved in the central-south Huanghua Depression and developed two kinds of reservoirs, Upper Paleozoic clastic rock and Lower Paleozoic carbonate rock, which form favorable source-reservoir assemblages with Carboniferous–Permian coal measure source rock. The Carboniferous–Permian coal-bearing source rock is rich in organic matters, which are mainly composed of type II2 and III kerogens, and minor II1 kerogen in partial areas. Multi-stage tectonic movements resulted in two stages of hydrocarbon generation of the source rocks. The period from the deposition of Kongdian Formation to now is the second stage of hydrocarbon generation. The matching between large-scale oil and gas charging, favorable reservoir-cap combinations and stable structure determines the enrichment of oil and gas. According to the new comprehensive evaluation of Paleozoic petroleum system, the primary oil and gas resources of the Paleozoic in the Bohai Bay Basin are over 1×1012 m3. The exploration breakthrough in Paleozoic petroleum system, especially Carboniferous–Permian petroleum system in Huanghua Depression is inspirational for oil and gas exploration in similar provinces of Bohai Bay Basin.Zhao, Y., Xiao, Z., Lv, J., Shen, W., Xu, R., 2019. A novel approach to enhance the urease activity of Sporosarcina pasteurii and its application on microbial-induced calcium carbonate precipitation for sand. Geomicrobiology Journal 36, 819-825. is involved in the formation of carbonate sediments by microbial-induced calcium carbonate precipitation (MICP), and Sporosarcina pasteurii used extensively in this technique owing to its high urease production. In this study, a simple two-step culture method with the appropriate medium was developed to enhance the urease activity of S. pasteurii. Urea played an important role in the culture process, particularly during the pre-cultivation step and the newly developed method improved both urease activity and specific urease activity. Furthermore, the increase in urease activity by MICP resulted in increased production of calcium carbonate and better strength of bio-cemented sand.Zhou, W., Jiang, Z., Qiu, H., Jin, X., Wang, R., Cen, W., Tang, X., Li, X., Wang, G., Cao, X., Sun, Y., 2019. Shale gas accumulation conditions and prediction of favorable areas for the Lower Carboniferous Luzhai Formation in Guizhong depression Acta Petrolei Sinica 40, 798-812. on field investigation and cores observation,in combination with the data of geochemistry,scanning electron microscopy,X-ray diffraction and low-temperature gas adsorption,this study analyzes the geological conditions of shale gas accumulation such as mud shale distribution,geochemical parameters,reservoir characteristics and gas-bearing characteristics in the Lower Carboniferous Luzhai Formation in Guizhong depression. The study shows that the shale from the Lower Carboniferous Luzhai Formation in Guizhong depression is dominated by deep-water continental shelf sediments. The organic-rich shale is distributed widely,generally with the sedimentary thickness from 50m to 300m and moderate buried depth. The organic carbon content in shale is above 1.5%,and the organic matter reaches the high mature or over mature stage. That brittle minerals,pore spaces and gas adsorption performances are well developed in the reservoir indicate favorable geological conditions for shale gas accumulation. In combination with the comprehensive information that Guizhong depression has large erosion thickness,experiencing multi-stage faults and magmatism and poor shale gas preservation environment,it is believed that the Liuzhou-Luzhai area and the Hechi-Yizhou area are favorable areas for shale gas exploration in the Lower Carboniferous Luzhai Formation,Guizhong depression.Zhu, Z., Oakes, J., Eyre, B., Hao, Y., Sia, E.S.A., Jiang, S., Müller, M., Zhang, J., 2019. The non-conservative distribution pattern of organic matter in Rajang, a tropical river with peatland in its estuary. Biogeosciences Discussions 2019, 1-32. Asian peatland-draining rivers have attracted much attention due to their high dissolved organic carbon (DOC) yield and high CO2 emissions under anthropogenic activities. In August 2016, we carried out a field investigation of the Rajang river and estuary, a tropical system located in Sarawak, Malaysia. The Rajang has peatland in its estuary while the river basin is covered by tropical rainforest. DOC δ13C in the Rajang ranged from ?28.7?‰ to ?20.1?‰ and a U-shaped trend from river to estuary was identified. For particulate organic carbon (POC), the δ13C ranged between ?29.4?‰ to ?31.1?‰ in the river and a clear increasing trend towards more δ13C -enriched with higher salinity existed in the estuary. In the estuary, there was a linear conservative dilution pattern for dissolved organic matter composition (as quantified by D/L amino acids enantiomers) plotted against DOC δ13C, whereas when plotted against salinity dissolved D/L amino acids enantiomers values were higher than the theoretical dilution value. Together, these data indicate that the addition of DOC in estuary (by peatland) not only increased the DOC concentration, but also altered its composition, by adding more bio-degraded, 13C-depleted organic matter into the bulk dissolved organic matter. Alteration of organic matter composition (adding of more degraded subpart) was also apparent for the particulate phase, but patterns were less clear. The Rajang was characterized by DOC?/?DON ratios of 50 in the river section, with loss of DON in the estuary increased the ratio to 140, suggesting the unbalanced export pattern for organic carbon and nitrogen, respectively. Under anthropogenic activities, further assessment of organic carbon to nitrogen ratio is needed.Zindorf, M., M?rz, C., Wagner, T., Gulick, S.P.S., Strauss, H., Benowitz, J., Jaeger, J., Schnetger, B., Childress, L., LeVay, L., van der Land, C., La Rosa, M., 2019. Deep Sulfate-Methane-Transition and sediment diagenesis in the Gulf of Alaska (IODP Site U1417). Marine Geology 417, 105986. samples from the Gulf of Alaska (GOA, IODP Expedition 341, Site U1417) have been analyzed to understand present and past diagenetic processes that overprint the primary sediment composition. No Sulfate-Methane Transition Zone (SMTZ) was observed at the zone of sulfate depletion, but a >200?m thick sulfate- and methane-free sediment interval occurred between the depth of sulfate depletion (~200?m) and the onset of methanogenesis (~440?m). We suggest that this apparent gap in biogeochemical processing of organic matter is caused by anaerobic oxidation of methane fueled by sulfate which is released during dissolution of barites at the upper boundary of the methane rich layer. Beneath the methanogenic zone, at ~650?m depth, pore-water sulfate concentrations increase again, indicating sulfate supply from greater depth feeding into a deep, inverse SMTZ. A likely explanation for the availability of sulfate in the deep sub-seafloor at U1417 is the existence of a deep aquifer related to plate bending fractures, which actively transports sulfate-rich water to, and potentially along, the interface between sediments and oceanic crust. Such inverse diagenetic zonations have been previously observed in marine sediments, but have not yet been linked to subduction-related plate bending. With the discovery of a deep inverse SMTZ in an intra-oceanic plate setting and the blocking of upward methane diffusion by sulfate released from authigenic barite dissolution, Site U1417 provides new insights into sub-seafloor pore-fluid and gas dynamics, and their implications for global element cycling and the deep biosphere.Zolkos, S., Tank, S.E., Striegl, R.G., Kokelj, S.V., 2019. Thermokarst effects on carbon dioxide and methane fluxes in streams on the Peel Plateau (NWT, Canada). Journal of Geophysical Research: Biogeosciences 124, 1781-1798.: Thermokarst can rapidly mobilize vast amounts of sediment, solutes, and organic carbon previously maintained in frozen soils to inland waters. Streams provide a critical pathway for transforming these materials into carbon dioxide (CO2) and methane (CH4), yet the direct effects of thermokarst on fluvial C gas efflux from streams to the atmosphere are largely unknown. Working on the Peel Plateau in the western Canadian Arctic, we show that CO2 efflux in rill runoff thaw streams (runoff) within retrogressive thaw slumps (RTSs) was four times greater than in adjacent streams and contributed modestly but disproportionately to efflux at the landscape scale. In contrast, CH4 efflux was generally greater in adjacent streams than in RTS runoff and, overall, was within the range of values reported for other northern streams. While RTS occurrence was a primary driver of CO2 efflux, CH4 efflux was more strongly associated with conditions reflective of biological activity. Transects downstream of two RTSs revealed that CH4 consistently and rapidly degassed to the atmosphere, while elevated CO2 was sustained downstream of one RTS feature. At the watershed scale, streams adjacent to RTSs rather than runoff streams within RTSs dominated fluvial CO2 and CH4 efflux. Intensifying thermokarst activity in the western Canadian Arctic will likely amplify contributions from runoff streams in RTSs to watershed‐scale fluvial C gas efflux.Plain Language Summary: Rapid Arctic warming is thawing perennially frozen ground (permafrost) and driving terrain subsidence in ice‐rich areas (thermokarst). In glaciated permafrost landscapes, thermokarst features called retrogressive thaw slumps, which are caused by thawing of ice‐rich permafrost, release sediment, solutes, and organic materials that have been preserved in permafrost for millennia. Following thaw, permafrost carbon can rapidly transform into the greenhouse gas carbon dioxide and methane in streams. Yet the effects of thermokarst on fluvial gas flux are largely unknown. Working on the Peel Plateau in northwest Canada, we found that carbon dioxide efflux to the atmosphere from runoff draining from thaw slumps was four times greater than in streams adjacent to thaw slumps. In contrast, methane efflux in adjacent streams was twice that in runoff streams and both were similar to streams in other northern regions. While thaw slump occurrence was a primary driver of carbon dioxide efflux, methane efflux was more strongly associated with conditions reflective of biological activity. Generally, both carbon dioxide and methane were rapidly degassed downstream. While efflux of carbon dioxide and methane in thaw slumps were a small component of watershed‐scale fluvial C gas efflux, these fluxes will likely increase as regional thermokarst activity accelerates.Zou, J., Rezaee, R., Xie, Q., You, L., 2019. Characterization of the combined effect of high temperature and moisture on methane adsorption in shale gas reservoirs. Journal of Petroleum Science and Engineering 182, 106353. a significant amount of methane stored in shales in the form of adsorbed gas, it is important to understand the controlling factors of the methane adsorption capacity. Under actual reservoir conditions, the high temperature and moisture are always coexisting which can affect gas adsorption capacity. This paper studied the methane adsorption of shale at different temperatures in dry and wet conditions. The adsorption results indicated that the moisture and high temperature can reduce the adsorbed gas content in shales individually, and the two factors have a synergistic-negative effect on methane adsorption in shales. Thermodynamic parameters showed that the heat of adsorption shows a decreased tendency and the entropy of adsorption becomes less negative after moisturizing the samples. The combined effect of the two factors is sufficiently important in the evaluation of gas adsorption capacity in shale gas systems.Zwahlen, C., Wogelius, R., Hollis, C., Holland, G., 2019. Reaction path modelling illustrating the fluid history of a natural CO2-H2S reservoir. Applied Geochemistry 109, 104391. the increasing interest in geologic co-sequestration of CO2 and H2S, the long-term consequences of the chemical interactions involved in this process remain largely unknown on a reservoir scale. A Mississippian aged CO2-H2S reservoir in LaBarge Field, Wyoming, USA is an ideal study site to investigate mineral and fluid reactions related to gaseous H2S and CO2. We conducted two reaction path models based on mineralogical, fluid, gas, and stable isotope compositional data to discern the role of CO2 influx upon the generation of H2S through thermochemical sulphate reduction (TSR). We discriminate between two models-one in which TSR is triggered by temperature at a given burial depth and one where TSR is triggered by ingress of CO2. The reaction path model based upon burial-controlled TSR and later CO2 influx is consistent with mineralogical observations and stable isotope measurements from drill cores. The models show that CO2 influx leads to calcite precipitation which is only limited by the calcium concentration in the fluid. This modelling approach is useful in constraining the timing of fluid flux in the reservoir and gives further insight into the mineralogical consequences of the gas, water, and rock interactions occurring in the reservoir. In terms of geologic co-sequestration this implies that the addition of CO2 into a reducing carbonate system can result in calcite precipitation, instead of anhydrite as previously thought. Furthermore, it is only limited by the availability of Ca2+ and will therefore not diminish the amount of H2S in the system. ................
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