Abstract
Microorganisms that are present in drilling fluids, hydraulic fracturing fluids, and natural gas reservoirs cause a number of problems (e.g., souring of natural gas, corrosion of field infrastructure) that lead to significant costs for the natural gas industry. In spite of their importance, relatively little is known about the abundance, diversity, and community structure of the microbial guilds in (1) fluids that are used to construct natural gas wells or (2) natural gas reservoirs prior to well construction. This chapter provides protocols that can be used to study the microbiology of drilling fluids, hydraulic fracturing fluids, and natural gas reservoirs. The chapter also includes procedures for (1) the timely collection, preservation, transport, and handling of samples from relevant locations; (2) the enumeration of microorganisms that have been implicated in deleterious processes that occur within natural gas wells; (3) the use of cultivation-independent, nucleic acids-based approaches for the characterization and quantification of microorganisms in samples from natural gas wells; and (4) handling and interpreting nucleic acid sequence data in samples from natural gas wells. Relevant information regarding suppliers of equipment, troubleshooting techniques that can be used to overcome problems that may be encountered while studying the microbiological properties of natural gas wells, and research questions that need to be addressed in future studies are also discussed.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Miller RG, Sorrell SR (2014) The future of oil supply. Philos T R Soc A 372:1–27
Witze A (2007) Energy: that’s oil, folks. Nature 445:14–17
Curtis JB, Montgomery SL (2002) Recoverable natural gas resource of the United States: summary of recent estimates. AAPG Bull 86:1671–1678
Zhang H, Chen J, Guo S (2008) Preparation of natural gas adsorbents from high-sulfur petroleum coke. Fuel 87:304–311
Kerr RA (2010) Natural gas from shale bursts onto the scene. Science 328:1624–1626
Arthur JD, Bohm B, Layne M (2008) Hydraulic fracturing considerations for natural gas wells of the Marcellus Shale. Paper presented at ground water protection council annual forum, Cincinnati, OH
Pollastro RM (2007) Total petroleum system assessment of undiscovered resources in the giant Barnett Shale continuous (unconventional) gas accumulation, Fort Worth Basin, Texas. AAPG Bull 91:551–578
Struchtemeyer CG, Davis JP, Elshahed MS (2011) Influence of the drilling mud formulation process on the bacterial communities in thermogenic natural gas wells of the Barnett Shale. Appl Environ Microbiol 77:4744–4753
Johnson K et al (2008) Use of microbiocides in Barnett Shale gas well fracturing fluids to control bacteria related problems. Presented at corrosion conference, New Orleans, LA
Darley HCH, Gray GR (1988) Composition and properties of drilling and completion fluids. Gulf Professional Publishing, Houston
Baldi F et al (1996) Dissolution of Barium from Barite in Sewage Sludges and Cultures of Desulfovibrio desulfuricans. Appl Environ Microbiol 62:2398–2404
Lie TJ, Godchaux W, Leadbetter ER (1999) Sulfonates as terminal electron acceptors for growth of sulfite-reducing bacteria (Desulfitobacterium spp.) and sulfate-reducing bacteria: effects of inhibitors of sulfidogenesis. Appl Environ Microbiol 65:4611–4617
Pereyra L et al (2010) Detection and quantification of functional genes of cellulose-degrading, fermentative, and sulfate-reducing bacteria and methanogenic archaea. Appl Environ Microbiol 76:2192–2202
Struchtemeyer C, Elshahed M (2012) Bacterial communities associated with hydraulic fracturing fluids in thermogenic natural gas wells in North Central Texas, USA. FEMS Microbiol Ecol 81:13–25
Moore SL, Cripps CM (2012) Bacterial survival in fractured Shale-Gas wells of the Horn River Basin. J Canadian Petroleum Technol 51:283–289
Veil JA (2010) Water management technologies used by Marcellus Shale Gas Producers. National laboratory, Argonne
James A, Burns B (1984) Microbial alteration of subsurface natural gas accumulations. AAPG Bull 68:957–960
Murali MA et al (2013) Microbial communities in flowback water impoundments from hydraulic fracturing for recovery of shale gas. FEMS Microbiol Ecol 86:567–580
Wuchter C et al (2013) Microbial diversity and methanogenic activity of Antrim Shale formation waters from recently fractured wells. Front Microbiol 4, 10.3389/fmicb.2013.00367
Strong LC et al (2014) Biodegradation in waters from hydraulic fracturing: chemistry, microbiology, and engineering. J Environ Eng-ASCE 140. doi:10.1061/(ASCE)EE.1943-7870.0000792
Struchtemeyer CG et al (2005) Evidence for aceticlastic methanogenesis in the presence of sulfate in a gas condensate-contaminated aquifer. Appl Environ Microbiol 71:5348–5353
Wagner M et al (1998) Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J Bacteriol 180:2975–2982
Ben-Dov E, Brenner A, Kushmaro A (2007) Quantification of sulfate-reducing bacteria in industrial wastewater, by real-time polymerase chain reaction (PCR) using dsrA and apsA genes. Microb Ecol 54:439–451
Hamady M et al (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 5:235–237
Caporaso JG et al (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6:1621–1624
Caporaso JG et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336
Cole JR et al (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–145
Schloss PD et al (2009) Introducing Mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541
Evans J, Sheneman L, Foster J (2006) Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method. J Mol Evol 62:785–792
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313
Alexander M, Clark FE (1965) Nitrifying bacteria. In: Black CA, Evans DD, White JL, Ensminger LE, Clark FE (eds) Methods of soil analysis, part 2. American Society of Agronomy, Madison, pp 1477–1483
Oblinger JL, Koburger JA (1975) Understanding and teaching the most probable number technique. J Milk Food Technol 38:540–545
Balch WE, Wolfe R (1976) New approach to the cultivation of methanogenic bacteria: 2-mercaptoethanesulfonic acid (HS-CoM)-dependent growth of Methanobacterium ruminantium in a pressurized atmosphere. Appl Environ Microbiol 32:781–791
Bryant MP (1972) Commentary on the Hungate technique for culture of anaerobic bacteria. Am J Clin Nutr 25:1324–1328
Webster G et al (2009) Subsurface microbiology and biogeochemistry of a deep, cold-water carbonate mound from the Porcupine Seabight (IODP Expedition 307). Environ Microbiol 11:239–257
Einen J, Thorseth IH, Ovreas L (2008) Enumeration of Archaea and Bacteria in seafloor basalt using real-time quantitative PCR and fluorescence microscopy. FEMS Microbiol Lett 282:182–187
Varon-Lopez M et al (2014) Sulphur-oxidizing and sulphate-reducing communities in Brazilian mangrove sediments. Environ Microbiol 16:845–855
Gabarro J et al (2013) Nitrous oxide reduction genetic potential from the microbial community of an intermittently aerated partial nitritation SBR treating mature landfill leachate. Water Res 47:7066–7077
Liu Z et al (2008) Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res 36, 10.1093/nar/gkn1491
Liu Z et al (2007) Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res 35, 10.1093/nar/gkm1541
Youssef N et al (2009) Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys. Appl Environ Microbiol 75:5227–5236
Schloss PD, Handelsman J (2006) Toward a census of bacteria in soil. PLoS Comput Biol 2, 10.1371/journal.pcbi.0020092
DeSantis TZ et al (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072
Quast C et al (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596
Struchtemeyer CG, Morrison MD, Elshahed MS (2012) A critical assessment of the efficacy of biocides used during the hydraulic fracturing process in shale natural gas wells. Int Biodeter Biodegr 71:15–21
Muthukumar N et al (2003) Microbiologically influenced corrosion in petroleum product pipelines–a review. Indian J Exp Biol 41:1012–1022
Fujioka RS (2002) Microbial indicators of coastal water quality. In: Hurst CJ, Crawford RL, Knudsen GR, McInerney MJ, Stetzenbach LD (eds) Manual of environmental microbiology, 2nd edn. ASM, Washington, DC, pp 234–243
Schrader C et al (2012) PCR inhibitors–occurrence, properties and removal. J Appl Microbiol 113:1014–1026
Braid MD, Daniels LM, Kitts CL (2003) Removal of PCR inhibitors from soil DNA by chemical flocculation. J Microbiol Meth 52:389–393
Miller D et al (1999) Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol 65:4715–4724
Youssef NH, Elshahed MS, McInerney MJ (2009) Microbial processes in oil fields: Culprits, problems, and opportunities. Adv Appl Microbiol 66:141–251
Agrawal A, Vanbroekhoven K, Lal B (2010) Diversity of culturable sulfidogenic bacteria in two oil–water separation tanks in the north-eastern oil fields of India. Anaerobe 16:12–18
Obuekwe C, Westlake D (1987) Occurrence of bacteria in Pembina crude oil pipeline system and their potential role in corrosion process. Appl Microbiol Biotechnol 26:389–393
Obuekwe C, Westlake D, Cook F (1983) Corrosion of Pembina crude oil pipeline. Eur J Appl Microbiol Biotechnol 17:173–177
Liang R et al (2014) Roles of thermophilic thiosulfate-reducing bacteria and methanogenic archaea in the biocorrosion of oil pipelines. Front Microbiol 5, 10.3389/fmicb.2014.00089
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer-Verlag Berlin Heidelberg
About this protocol
Cite this protocol
Struchtemeyer, C.G., Youssef, N.H., Elshahed, M.S. (2014). Protocols for Investigating the Microbiology of Drilling Fluids, Hydraulic Fracturing Fluids, and Formations in Unconventional Natural Gas Reservoirs. In: McGenity, T., Timmis, K., Nogales , B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2014_8
Download citation
DOI: https://doi.org/10.1007/8623_2014_8
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-662-53116-7
Online ISBN: 978-3-662-53118-1
eBook Packages: Springer Protocols