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12 - The Microbiology of Shale Gas Extraction

from Part II - Environmental Analysis

Published online by Cambridge University Press:  28 July 2022

By
Sophie L. Nixon
Edited by
John Stolz ,
Daniel Bain  and
Michael Griffin
John Stolz
Affiliation:
Duquesne University, Pittsburgh
Daniel Bain
Affiliation:
University of Pittsburgh
Michael Griffin
Affiliation:
Carnegie Mellon University, Pennsylvania
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Summary

Pristine shale formations are limited subsurface microbial habitats owing to their limited physical space. However, the process of drilling and hydraulic fracturing to recover natural gas from these formations greatly enhances their habitability for microbial life. Drawing upon over a decade of research, this chapter introduces fractured shales as dynamic microbial ecosystems, with particular emphasis on microbial processes that negatively impact on shale gas extraction, including input fluid degradation, biogenic sulfide production and biofilm formation. Collectively, these processes have the potential to sour natural gas, corrode extraction infrastructure, restrict the flow of gas and generally increase costs of resource recovery. The use and efficacy of biocides to control these impacts is discussed. This review presents a biogeographical overview of the fractured shale formations studied to date, highlighting a paucity of information on fractured shales outside the United States, and concludes with a discussion on the remaining knowledge gap.

Keywords

biofilmbiocidedegradationresistance
Type
Chapter
Information
Environmental Impacts from the Development of Unconventional Oil and Gas Reserves , pp. 292 - 310
Publisher: Cambridge University Press
Print publication year: 2022

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References

Akob, DM, Cozzarelli, IM, Dunlap, DS, Rowan, EL, and Lorah, MM. (2015). Organic and inorganic composition and microbiology of produced waters from Pennsylvania shale gas wells. Applied Geochemistry. 60: 116–125.Google Scholar
Booker, AE, Borton, MA, Daly, RA et al. (2017). Sulfide generation by dominant Halanaerobium microorganisms in hydraulically fractured shales. mSphere. 2(4): e00257–17.Google Scholar
Booker, AE, Hoyt, DW, Meulia, T et al. (2019). Deep-subsurface pressure stimulates metabolic plasticity in shale-colonizing Halanaerobium spp. Applied and Environmental Microbiology. 85(12): e00018–19.CrossRefGoogle ScholarPubMed
Borton, MA, Daly, RA, O’Banion, B et al. (2018a). Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured. Environmental Microbiology. 20(12): 4596–4611.CrossRefGoogle ScholarPubMed
Borton, MA, Hoyt, DW, Roux, S et al. (2018b). Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales. Proceedings of the National Academy of Sciences. 115(28): E6585–E6594.Google Scholar
Bowman, JP, McCammon, SA, Nichols, DS et al. (1997). Shewanella gelidimarina sp. nov. and Shewanella frigidimarina sp. nov., novel Antarctic species with the ability to produce eicosapentaenoic acid (20:5ω3) and grow anaerobically by dissimilatory Fe(III) reduction. International Journal of Systematic Bacteriology. 47(4): 1040–1047.Google Scholar
Campa, MF, Wolfe, AK, Techtmann, SM, Harik, A, and Hazen, TC. (2019). Unconventional oil and gas energy systems: an unidentified hotspot of antimicrobial resistance? Frontiers in Microbiology. 10: 2392.Google Scholar
Cliffe, L, Nixon, SL, Daly, RA et al. (2020). Identification of persistent sulfidogenic bacteria in shale gas produced waters. Frontiers in Microbiology. 11: 286.Google Scholar
Cluff, MA, Hartsock, A, MacRae, JD, Carter, K, and Mouser, PJ. (2014). Temporal changes in microbial ecology and geochemistry in produced water from hydraulically fractured Marcellus shale gas wells. Environmental Science & Technology. 48(11): 6508–6517.Google Scholar
Colwell, FS, Onstott, TC, Delwiche, ME et al. (1997). Microorganisms from deep, high temperature sandstones: constraints on microbial colonization. FEMS Microbiology Reviews. 20: 425–435.CrossRefGoogle Scholar
Craciun, S and Balskus, EP. (2012). Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme. Proceedings of the National Academy of Sciences. 109(52): 21307–21312.CrossRefGoogle ScholarPubMed
Daly, RA, Borton, MA, Wilkins, MJ et al. (2016). Microbial metabolism in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales. Nature Microbiology. 1(10): 16146.Google Scholar
Daly, RA, Roux, S, Borton, MA et al. (2019). Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing. Nature Microbiology. 4: 352–361.Google Scholar
Davis, JP, Struchtemeyer, CG, and Elshahed, MS. (2012). Bacterial communities associated with production facilities of two newly drilled thermogenic natural gas wells in the Barnett Shale (Texas, USA). Microbial Ecology. 64(4): 942–954.Google Scholar
Elsner, M and Hoelzer, K. (2016). Quantitative survey and structural classification of hydraulic fracturing chemicals reported in unconventional gas production. Environmental Science & Technology. 50: 3290–3314.CrossRefGoogle ScholarPubMed
Evans, MV, Getzinger, G, Luek, JL et al. (2019). In situ transformation of ethoxylate and glycol surfactants buu shale-colonizing microorganisms during hydraulic fracturing. ISME Journal. 13: 2690–2700.Google Scholar
Evans, MV, Panescu, J, Hanson, AJ et al. (2018). Members of Marinobacter and Arcobacter influence system biogeochemistry during early production of hydraulically fractured natural gas wells in the Appalachian basin. Frontiers in Microbiology. 9: 2646.Google Scholar
Fichter, J, Wunch, K, Moore, R et al. (2012). How hot is too hot for bacteria? A technical study assessing bacterial establishment in downhole drilling, fracturing and stimulation operations. In CORROSION 2012, March 11–15, Salt Lake City, Utah. NACE International.Google Scholar
Fredrickson, JK, McKinley, JP, Bjornstad, BN et al. (1997). Pore-size constraints on the activity and survival of subsurface bacteria in a late Cretaceous shale-sandstone sequence, northwestern New Mexico. Geomicrobiology Journal. 14: 182–202.CrossRefGoogle Scholar
Huang, R. (2008). Shale-Derived Dissolved Organic Matter as a Substrate for Subsurface Methanogenic Communities in the Antrim Shale Michigan Basin, USA. Masters thesis. Department of Geosciences, University of Massachusetts Amherst.Google Scholar
Johnson, K, French, K, Fichter, JK, and Oden, R. (2008). Use of microbiocides in Barnett Shale gas well fracturing fluids to control bacteria related problems. In CORROSION 2008, March 16–20, New Orleans, Louisiana. NACE International.Google Scholar
Kahrilas, GA, Blotevogul, J, Stewart, PS, and Borch, T. (2015) Biocides in hydraulic fracturing fluids: A critical review of their usage, mobility, degradation and toxicity. Environmental Science & Technology. 49(1): 16–32.Google Scholar
Kashefi, K and Lovley, DR. (2003) Extending the upper temperature limit for life. Science. 301(5635): 934.Google Scholar
Kekacs, D, Drollette, BD, Brooker, M, Plata, DL, and Mouser, PJ. (2015). Aerobic biodegradation of organic compounds in hydraulic fracturing fluids. Biodegradation. 26(4): 271–287.Google Scholar
Kirk, MF, Martini, AM, Breecker, SO et al. (2012). Impact of commercial natural gas production on geochemistry and microbiology in a shale-gas reservoir. Chemical Geology. 332–333: 15–25.CrossRefGoogle Scholar
Krumholz, LR, McKinley, JP, Ulrich, GA, and Suflita, JM. (1997). Confined subsurface microbial communities in cretaceous rock. Nature. 386: 64–66.Google Scholar
Liang, R, Davidova, IA, Marks, CR et al. (2016). Metabolic capability of a predominant Halanaerobium sp. in hydraulically fractured gas wells and its implication in pipeline corrosion. Frontiers in Microbiology. 7: 988.Google Scholar
Lipus, D, Ross, D, Bibby, K, and Gulliver, D. (2017a). Draft genome sequence of Pseudomonas sp. BDAL1 reconstructed from a Bakken shale hydraulic fracturing-produced water storage tank metagenome. Genome Announcements. 5: e00033–17.Google Scholar
Lipus, D, Roy, D, Khan, E et al. (2018). Microbial communities in Bakken region produced water. FEMS Microbiology Letters. 365(12): fny107.Google Scholar
Lipus, D, Vikram, A, Ross, D et al. (2017b). Predominance and metabolic potential of Halanaerobium spp. in produced water in hydraulically fractured Marcellus shale wells. Applied Environmental Microbiology. 83(8): e02659–16.Google Scholar
Martini, AM, Walter, LM, Budai, JM et al. (1998). Genetic and temporal relations between formation waters and biogenic methane: Upper Devonian Antrim Shale, Michigan Basin, USA. Geochimica et Cosmochimica Acta. 62(10): 1699–1720.Google Scholar
Mouser, PJ, Borton, M, Darrah, TH, Hartsock, A, and Wrighton, KC. (2016). Hydraulic fracturing offers a view of microbial life in the deep terrestrial subsurface. FEMS Microbiology Ecology. 92(11).CrossRefGoogle ScholarPubMed
Murali Mohan, A, Hartsock, A, Bibby, KJ et al. (2013a). Microbial community changes in hydraulic fracturing fluids and produced water from shale gas extraction. Environmental Science & Technology. 47(22): 13141–13150.Google Scholar
Murali Mohan, A, Hartsock, A, Hammack, RW, Vidic, RD, and Gregory, KB. (2013b). Microbial communities in flowback water impoundments from hydraulic fracturing for recovery of shale gas. FEMS Microbiology Ecology. 86(3): 567–580.Google Scholar
Nixon, SL, Daly, RA, Borton, MA et al. (2019). Genome-resolved metagenomics extends the environmental distribution of the Verrucomicrobia phylum to the deep terrestrial subsurface. mSphere. 4: e00613–19.Google Scholar
Nixon, SL, Walker, L, Streets, MDT et al. (2017). Guar gum stimulates biogenic sulfide production at elevated pressures: Implications for shale gas extraction. Frontiers in Microbiology. 8: 679.Google Scholar
Onstott, TC, Phelps, TJ, Colwell, FS et al. (1998). Observations pertaining to the origin and ecology of microorganisms recovered from the deep subsurface of Taylorsville Basin, Virginia. Geomicrobiology Journal. 15: 353–385.Google Scholar
Santillan, EFU, Choi, W, Bennett, PC, and Leyris, JD. (2015). The effects of biocide use on the microbiology and geochemistry of produced water in the Eagle Ford formation, Texas, U.S.A. Journal of Petroleum Science and Engineering. 135: 1–9.Google Scholar
Schlegel, ME, McIntosh, JC, Bates, BL, Kirk, MF, and Martini, AM. (2011). Comparison of fluid geochemistry and microbiology of multiple organic-rich reservoirs in the Illinois Basin, USA: Evidence for controls on methanogenesis and microbial transport. Geochimica et Cosmochimica Acta. 75: 1903–1919.CrossRefGoogle Scholar
Strong, LC, Gould, T, Kasinkas, L et al. (2013). Biodegradation in waters from hydraulic fracturing: Chemistry, microbiology, and engineering. Journal of Environmental Engineering. 140(5): B4013001.Google Scholar
Struchtemeyer, CG. (2018). Microbiology of oil- and natural gas-producing shale formations: An overview. In Steffan, R (ed) Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation. Springer Nature Switzerland AG, pp. 215–232.Google Scholar
Struchtemeyer, CG and Elshahed, MS. (2012). Bacterial communities associated with hydraulic fracturing fluids in thermogenic natural gas wells in North Central Texas, USA. FEMS Microbiol Ecology. 81(1): 13–25.CrossRefGoogle ScholarPubMed
Struchtemeyer, CG, Davis, JP, and Elshahed, MS. (2011). Influence of drilling mud formation process on the bacterial communities in thermogenic natural wells of the Barnett Shale. Applied and Environmental Microbiology. 77(14): 4744–4753.Google Scholar
Struchtemeyer, CG, Morrison, MD, and Elshahed, MS. (2012). A critical assessment of the efficacy of biocides used during the hydraulic fracturing process in shale natural gas wells. International Biodeterioration & Biodegradation. 71: 15–21.Google Scholar
Struchtemeyer, CG, Youssef, NH, and Elshahed, MS. (2017). Protocols for investigating the microbiology of drilling fluids, hydraulic fracturing fluids, and formations in unconventional natural gas reservoirs. In McGenity, TJ, Timmis, KN, Fernandez, BN (eds.) Hydrocarbon and Lipid Microbiology Protocols. Springer-Verlag, pp. 1–25.Google Scholar
Tucker, YT, Kotcon, J, and Mroz, T. (2015). Methanogenic archaea in Marcellus shale: A possible mechanism for enhanced gas recovery in unconventional shale resources. Environmental Science & Technology. 49(11): 7048–7055.Google Scholar
Vandenbroucke, M and Largeau, C. (2007). Kerogen origin, evolution and structure. Organic Geochemistry. 38: 719–833.CrossRefGoogle Scholar
Venkateswaran, K, Moser, DP, Dollhopf, ME et al. (1999). Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. International Journal of Systematic Bacteriology. 49: 705–724.Google Scholar
Vikram, A, Lipus, D, and Bibby, K. (2014). Produced water exposure alters bacterial response to biocides. Environmental Science & Technology. 48(21): 13001–13009.Google Scholar
Vikram, A, Lipus, D, and Bibby, K. (2016). Metatranscriptome analysis of active microbial communities in produced water samples from the Marcellus Shale. Microbial Ecology. 72: 571.Google Scholar
Waldron, PJ, Petsch, ST, Martini, AM, and Nüsslein, K. (2007). Salinity constrains on subsurface archaeal diversity and methanogenesis in sedimentary rock rich in organic matter. Applied and Environmental Microbiology. 73: 4171–4179.Google Scholar
Wang, H, Lu, L, Chen, X, Bian, Y, and Ren, ZJ. (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 Res. 164: 114942.Google Scholar
Wuchter, C, Banning, E, Mincer, T, Drenzek, NJ, and Coolen, MJ. (2013). Microbial diversity and methanogenic activity of Antrim Shale formation waters from recently fractured wells. Frontiers in Microbiology. 4: 367.Google Scholar
Zhang, Y, Yu, Z, Zhang, H, and Thompson, IP. (2017). Microbial distribution and variation in produced water from separators to storage tanks of shale gas wells in Sichuan Basin, China. Environmental Science: Water Research & Technology. 3(2): 340–351.Google Scholar
Zhong, C, Li, J, Flynn, SL et al. (2019). Temporal changes in microbial community composition and geochemistry in flowback and produced water from the Duvernay formation. ACS Earth Space Chem. 3: 1047–1057.Google Scholar

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