Microbial-mediated Changes during the Brine–Shale–Microorganism Interaction Process

References

• Ahmed E, Holmström SJM. 2015. Microbe-mineral interactions: the impact of surface attachment on mineral weathering and element selectivity by microorganisms. Chem Geol. 403:13–23.
   Web of Science ®Google Scholar
• Ai H, Xu J, Huang W, He Q, Ni B, Wang Y. 2016. Mechanism and kinetics of biofilm growth process influenced by shear stress in sewers. Water Sci Technol. 73(7):1572–1582.
   PubMed Web of Science ®Google Scholar
• Ali G, Ling Z, Saif I, Usman M, Jalalah M, Harraz FA, Al-Assiri MS, Salama ES, Li X. 2021. Biomethanation and microbial community response during agricultural biomass and shrimp chaff digestion. Environ Pollut. 278:116801.
   PubMed Web of Science ®Google Scholar
• Barker WW, Welch SA, Chu S, Banfield JF. 1998. Experimental observations of the effects of bacteria on aluminosilicate weathering. Am. Mineral. 83(11-12 Part 2):1551–1563.
   Web of Science ®Google Scholar
• Barker WW, Banfield JF. 1996. Biologically versus inorganically mediated weathering reactions: relationships between minerals and extracellular microbial polymers in lithobiontic communities. Chem Geol. 132(1-4):55–69.
   Web of Science ®Google Scholar
• Bennett PC, Hiebert FK, Rogers JR. 2000. Microbial control of mineral groundwater equilibria: Macroscale to microscale. Hydrogeol J. 8(1):47–62.
   Web of Science ®Google Scholar
• Boquet E, Boronat A, Ramos-Cormenzana A. 1973. Production of calcite (calcium carbonate) crystals by soil bacteria is a general phenomenon. Nature. 246(5434):527–529.
   Web of Science ®Google Scholar
• Borton MA, Hoyt DW, Roux S, Daly RA, Welch SA, Nicora CD, Purvine S, Eder EK, Hanson AJ, Sheets JM, et al. 2018. Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales. Proc Natl Acad Sci U S A. 115(28):E6585–E6594.
   PubMed Web of Science ®Google Scholar
• Bottero S, Picioreanu C, Enzien MV, Van Loosdrecht M, Bruining J, Heimovaara T. 2010. Formation damage and impact on gas flow caused by biofilms growing within proppant packing used in hydraulic fracturing. Paper presented at: SPE International Symposium and Exhibition on Formation Damage, Lafayette, Louisiana, USA, 128066.
   Google Scholar
• Braissant O, Decho A, Dupraz C, Glunk K, Przekop KM, Visscher PT. 2007. Exopolymeric substances of sulfate-reducing bacteria: interactions with calcium at alkaline pH and implication for formation of carbonate minerals. Geobiology. 5(4):401–411.
   Web of Science ®Google Scholar
• Brehm U, Gorbushina A, Mottershead D. 2005. The role of microorganisms and biofilms in the breakdown and dissolution of quartz and glass. Palaeogeogr Palaeoclimatol Palaeoecol. 219(1-2):117–129.
   Web of Science ®Google Scholar
• Castanier S, Le Métayer-Levrel G, Perthuisot J-P. 1999. Ca-carbonates precipitation and limestone genesis—the microbiogeologist point of view. Sediment Geol. 126(1-4):9–23.
   Web of Science ®Google Scholar
• Chen Y, Li Y-L, Zhou G-T, Li H, Lin Y-T, Xiao X, Wang F-P. 2014. Biomineralization mediated by anaerobic methane-consuming cell consortia. Sci Rep. 4(1):1–9.
   Google Scholar
• Cheng Y, Hubbard CG, Geller JT, Chou C, Voltolini M, Engelbrektson AL, Coates JD, Ajo-Franklin JB, Wu Y. 2019. Biofilm feedbacks alter hydrological characteristics of fractured rock impacting sulfidogenesis and treatment. Energy Fuels. 33(11):10476–10486.
   Web of Science ®Google Scholar
• Cluff MA, Hartsock A, MacRae JD, Carter K, Mouser PJ. 2014. Temporal changes in microbial ecology and geochemistry in produced water from hydraulically fractured Marcellus shale gas wells. Environ Sci Technol. 48(11):6508–6517.
   PubMed Web of Science ®Google Scholar
• Cokar M, Ford B, Gieg LM, Kallos MS, Gates ID. 2013. Reactive reservoir simulation of biogenic shallow shale gas systems enabled by experimentally determined methane generation rates. Energy Fuels. 27(5):2413–2421.
   Web of Science ®Google Scholar
• Collet C, Gaudard O, Peringer P, Schwitzguebel JP. 2005. Acetate production from lactose by Clostridium thermolacticum and hydrogen-scavenging microorganisms in continuous culture-effect of hydrogen partial pressure. J Biotechnol. 118(3):328–338.
   PubMed Web of Science ®Google Scholar
• Colosimo F, Thomas R, Lloyd JR, Taylor KG, Boothman C, Smith AD, Lord R, Kalin RM. 2016. Biogenic methane in shale gas and coal bed methane: a review of current knowledge and gaps. Int J Coal Geol. 165:106–120.
   Web of Science ®Google Scholar
• Daly RA, Borton MA, Wilkins MJ, Hoyt DW, Kountz DJ, Wolfe RA, Welch SA, Marcus DN, Trexler RV, MacRae JD, et al. 2016. Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales. Nat Microbiol. 1(10):16146.
   PubMed Web of Science ®Google Scholar
• Daly RA, Roux S, Borton MA, Morgan DM, Johnston MD, Booker AE, Hoyt DW, Meulia T, Wolfe RA, Hanson AJ, et al. 2019. Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing. Nat Microbiol. 4(2):352–361.
   PubMed Web of Science ®Google Scholar
• Edgar RC. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 10(10):996–998.
   PubMed Web of Science ®Google Scholar
• Ehrlich H, Demadis KD, Pokrovsky OS, Koutsoukos PG. 2010. Modern views on desilicification: biosilica and abiotic silica dissolution in natural and artificial environments. Chem Rev. 110(8):4656–4689.
   PubMed Web of Science ®Google Scholar
• Fein JB, Scott S, Rivera N. 2002. The effect of Fe on Si adsorption by Bacillus subtilis cell walls: insights into non-metabolic bacterial precipitation of silicate minerals. Chem Geol. 182(2-4):265–273. ‚
   Web of Science ®Google Scholar
• Fernandez-Gonzalez N, Pedizzi C, Lema JM, Carballa M. 2019. Air-side ammonia stripping coupled to anaerobic digestion indirectly impacts anaerobic microbiome. Microb Biotechnol. 12(6):1403–1416.
   PubMed Web of Science ®Google Scholar
• Flythe MD, Russell JB. 2004. The effect of pH and a bacteriocin (bovicin HC5) on Clostridium sporogenes MD1, a bacterium that has the ability to degrade amino acids in ensiled plant materials1. FEMS Microbiol Ecol. 47(2):215–222.
   PubMed Web of Science ®Google Scholar
• Fredrickson JK, McKinley JP, Bjornstad BN, Long PE, Ringelberg DB, White DC, Krumholz LR, Suflita JM, Colwell FS, Lehman RM, et al. 1997. Pore‐size constraints on the activity and survival of subsurface bacteria in a late cretaceous shale‐sandstone sequence, northwestern New Mexico. Geomicrobiol J. 14(3):183–202.
   Web of Science ®Google Scholar
• Gallagher KL, Kading TJ, Braissant O, Dupraz C, Visscher PT. 2012. Inside the alkalinity engine: the role of electron donors in the organomineralization potential of sulfate-reducing bacteria. Geobiology. 10(6):518–530.
   PubMed Web of Science ®Google Scholar
• Gallert C, Bauer S, Winter J. 1998. Effect of ammonia on the anaerobic degradation of protein by a mesophilic and thermophilic biowaste population. Appl Microbiol Biotechnol. 50(4):495–501.
   PubMed Web of Science ®Google Scholar
• Gong XP, Tang HM, Zhao F, Wang JJ, Xiong H. 2016. Quantitative characterization of pore structure in shale reservoir of Longmaxi formation in Sichuan basin. Lithol Reserv. 28(03):48–57.
   Google Scholar
• Gregory KB, Vidic RD, Dzombak DA. 2011. Water management challenges associated with the production of shale gas by hydraulic fracturing. Elements. 7(3):181–186.
   Web of Science ®Google Scholar
• Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, et al. 2011. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 21(3):494–504.
   PubMed Web of Science ®Google Scholar
• Hahnke S, Langer T, Koeck DE, Klocke M. 2016. Description of Proteiniphilum saccharofermentans sp. nov., Petrimonas mucosa sp. nov. and Fermentimonas caenicola gen. nov., sp. nov., isolated from mesophilic laboratory-scale biogas reactors, and emended description of the genus Proteiniphilum. Int J Syst Evol Microbiol. 66(3):1466–1475.
   PubMed Web of Science ®Google Scholar
• Han W, Zhou G, Gao D, Zhang Z, Wei Z, Wang H, Yang H. 2020. Experimental analysis of the pore structure and fractal characteristics of different metamorphic coal based on mercury intrusion‑nitrogen adsorption porosimetry. Powder Technol. 362:386–398.
   Web of Science ®Google Scholar
• Hodot B. 1966. Outburst of Coal and Coalbed Gas (Chinese Translation). Beijing: China Coal Industry Press.
   Google Scholar
• Hu XW, Li S, Rong Y, Li Y. 2014. The research on biofilm composed by different EPS to adsorb Cu2. +China Environ Sci. 34(7):1749–1753.
   Google Scholar
• JY/T 0587-2020. 2020. General rules of polycrystalline X-ray diffraction method. Ministry of Education of PRC. Available at https://www.chinesestandard.net/
   Google Scholar
• Kargbo DM, Wilhelm RG, Campbell DJ. 2010. Natural gas plays in the Marcellus shale challenges and potential opportunities. Environ Sci Technol. 44(15):5679–5684.
   PubMed Web of Science ®Google Scholar
• Kayhanian M. 1999. Ammonia inhibition in high-solids biogasification: an overview and practical solutions. Environ Technol. 20(4):355–365.
   Web of Science ®Google Scholar
• Kirk MF, Martini AM, Breecker DO, Colman DR, Takacs-Vesbach C, Petsch ST. 2012. Impact of commercial natural gas production on geochemistry and microbiology in a shale-gas reservoir. Chem Geol. 332-333:15–25.
   Web of Science ®Google Scholar
• Kniemeyer O, Musat F, Sievert SM, Knittel K, Wilkes H, Blumenberg M, Michaelis W, Classen A, Bolm C, Joye SB, et al. 2007. Anaerobic oxidation of short-chain hydrocarbons by marine sulphate-reducing bacteria. Nature. 449(7164):898–901.
   PubMed Web of Science ®Google Scholar
• Kuivila KM, Murray JW, Devol AH, Novelli PC. 1989. Methane production, sulfate reduction and competition for substrates in the sediments of Lake Washington. Geochim Cosmochim Acta. 53(2):409–416.
   Web of Science ®Google Scholar
• Liu K, Ostadhassan M, Sun L, Zou J, Yuan Y, Gentzis T, Zhang Y, Carvajal-Ortiz H, Rezaee R. 2019. A comprehensive pore structure study of the Bakken Shale with SANS, N2 adsorption and mercury intrusion. Fuel. 245:274–285.
   Web of Science ®Google Scholar
• Liu X, Nie B. 2016. Fractal characteristics of coal samples utilizing image analysis and gas adsorption. Fuel. 182:314–322.
   Web of Science ®Google Scholar
• Ma XF, Zhang SC, Lang Z. 2004. Calculation of dimension of pore structure by using subsection regression method. J Univ Pet China. 28(06):54–56.
   Google Scholar
• Martini AM, Walter LM, McIntosh JC. 2008. Identification of microbial and thermogenic gas components from Upper Devonian black shale cores, Illinois and Michigan basins. Bulletin. 92(3):327–339.
   Google Scholar
• Matias PM, Pereira IA, Soares CM, Carrondo MA. 2005. Sulphate respiration from hydrogen in Desulfovibrio bacteria: a structural biology overview. Prog Biophys Mol Biol. 89(3):292–329.
   PubMed Web of Science ®Google Scholar
• Meng M, Ge H, Shen Y, Ji W. 2020. Fractal characterization of pore structure and its influence on salt ion diffusion behavior in marine shale reservoirs. Int J Hydrogen Energy. 45(53):28520–28530.
   Web of Science ®Google Scholar
• Meslé M, Périot C, Dromart G, Oger P. 2015. Methanogenic microbial community of the Eastern Paris Basin: potential for energy production from organic-rich shales. Int J Coal Geol. 149:67–76.
   Web of Science ®Google Scholar
• Mohan AM, Hartsock A, Bibby KJ, Hammack RW, Vidic RD, Gregory KB. 2013. Microbial community changes in hydraulic fracturing fluids and produced water from shale gas extraction. Environ Sci Technol. 47(22):13141–13150.
   PubMed Web of Science ®Google Scholar
• Mouser PJ, Borton M, Darrah TH, Hartsock A, Wrighton KC. 2016. Hydraulic fracturing offers view of microbial life in the deep terrestrial subsurface. FEMS Microbiol Ecol. 92(11):fiw166.
   PubMed Web of Science ®Google Scholar
• Paulo LM, Stams AJM, Sousa DZ. 2015. Methanogens, sulphate and heavy metals: a complex system. Rev Environ Sci Biotechnol. 14(4):537–553.
   Web of Science ®Google Scholar
• Qian J, Wu WT, Zhou YF, Yue ZB, Wang C. 2019. Effect of sulfate reducing bacteria on the crystallization process of calcium carbonate. J Chin Ceram Soc. 47(01):109–116.
   Google Scholar
• Qian W, Peng Y, Li X, Zhang Q, Ma B. 2017. The inhibitory effects of free ammonia on ammonia oxidizing bacteria and nitrite oxidizing bacteria under anaerobic condition. Bioresour Technol. 243:1247–1250.
   PubMed Web of Science ®Google Scholar
• Sharma S, Agrawal V, Akondi RN. 2020. Role of biogeochemistry in efficient shale oil and gas production. Fuel. 259:116207.
   Web of Science ®Google Scholar
• Sheng GP, Yu HQ, Li XY. 2010. Extracellular polymeric substances (EPS) of microbial aggregates in biological wastewater treatment systems: a review. Biotechnol Adv. 28(6):882–894.
   PubMed Web of Science ®Google Scholar
• Sim JH, Kamaruddin AH, Long WS, Najafpour G. 2007. Clostridium aceticum—a potential organism in catalyzing carbon monoxide to acetic acid: application of response surface methodology. Enzyme Microb Technol. 40(5):1234–1243.
   Web of Science ®Google Scholar
• Strong LG, Kasinkas L, Sadowsky MJ, Aksan A, Wackett LP. 2014. Biodegradation in waters from hydraulic fracturing: chemistry, microbiology, and engineering. J Environ Eng. 140(5SI):B4013001.
   Google Scholar
• Sun J, Hu S, Sharma KR, Ni BJ, Yuan Z. 2014. Stratified microbial structure and activity in sulfide- and methane-producing anaerobic sewer biofilms. Appl Environ Microbiol. 80(22):7042–7052.
   PubMed Web of Science ®Google Scholar
• Teng JB. 2020. Origin and evidence of calcite in shale oil reservoir of Dongying Sag. Pet Geol Recov Effic. 27(2):18–25.
   Google Scholar
• Tucker YT, Kotcon J, Mroz T. 2015. Methanogenic archaea in Marcellus shale: a possible mechanism for enhanced gas recovery in unconventional shale resources. Environ Sci Technol. 49(11):7048–7055.
   PubMed Web of Science ®Google Scholar
• Tucker YT, Mroz T. 2018. Microbes in Marcellus shale: extremophiles living more than two kilometers inside the Earth? Fuel. 234:1205–1211.
   Web of Science ®Google Scholar
• Valentine DL, Reeburgh WS. 2000. New perspectives on anaerobic methane oxidation. Environ Microbiol. 2(5):477–484.
   PubMed Web of Science ®Google Scholar
• Washburn E. 1921. Note on a method of determining the distribution of pore sizes in a porous material. Proc Natl Acad Sci U S A. 7(4):115–116.
   PubMedGoogle Scholar
• Welch SA, ‚Barker WW, Banfield JF. 1999. Microbial extracellular polysaccharide sand plagioclase dissolution. Geochim Cosmochim Acta. 63(9):1405–1419.
   Web of Science ®Google Scholar
• Wiegel J, Tanner R, Rainey FA. 2006. An introduction to the family Clostridiaceae. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K, Stackebrandt E, editors. The Prokaryotes. New York: Springer, p654–678.
   Google Scholar
• Yang Z, Shi X, Wang C, Wang L, Guo R. 2015. Magnetite nanoparticles facilitate methane production from ethanol via acting as electron acceptors. Sci Rep. 5:16118.
   PubMed Web of Science ®Google Scholar
• Zehnder AJ, Brock TD. 1979. Methane formation and methane oxidation by methanogenic bacteria. J Bacteriol. 137(1):420–432.
   PubMed Web of Science ®Google Scholar
• Zhang JC, Jin ZJ, Ms Y. 2004. Reservoiring mechanism of shale gas and its distribution. Nat Gas Ind. 24(7):15–18.
   Google Scholar
• Zhang JC, Tang Y, He D, Sun P, Zou X. 2020. Full-scale nanopore system and fractal characteristics of clay-rich lacustrine shale combining FE-SEM, nano-CT, gas adsorption and mercury intrusion porosimetry. Appl Clay Sci. 196:105758.
   Web of Science ®Google Scholar
• Zhao W, Li J, Yang T, Wang S, Huang J. 2016. Geological difference and its significance of marine shale gases in South China. Pet Explor Dev. 43(4):547–559.
   Web of Science ®Google Scholar
• Zhu JF, Liu JZ, Yang YM, Cheng J, Zhou JH, Cen KF. 2016. Fractal characteristics of pore structures in 13 coal specimens: relationship among fractal dimension, pore structure parameter, and slurry ability of coal. Fuel Process Technol. 149:256–267.
   Web of Science ®Google Scholar