Advertisement

Protocols for Investigating the Microbiology of Coal-Bed-Produced Waters

  • Amy V. CallaghanEmail author
  • Boris Wawrik
Protocol
Part of the Springer Protocols Handbooks book series (SPH)

Abstract

Coal-bed methane (CBM) has emerged as a globally important source of natural gas, and recent studies have revealed that microbial production of methane in CBM formations plays a significant role. Coal-bed formations are complex ecosystems with large reservoirs of organic substrates comprised of aliphatic, aromatic, and heterocyclic compounds. The biotransformation of this organic matter to methane by microbial communities, however, is not well elucidated. The latter has important implications with regard to energy recovery from subsurface environments. Although coal beds and other deep subsurface systems pose significant challenges with respect to field sampling and analysis, recent methodological advances have provided novel insights into the ecology and metabolism of coal-bed microbial communities. Specifically, the availability of affordable sequencing technologies and advances in mass spectrometry have allowed an unprecedented ability to study in situ processes governing microbial metabolism in subsurface environments. The following protocols include methodologies for the collection of coal-bed-produced water for traditional cultivation and most probable number (MPN) techniques, community DNA extraction and sequence-based molecular analyses, and metabolite profiling. The described techniques are intended as primers for several cultivation, molecular, and mass spectrometry applications and are adaptable to a range of field and experimental conditions.

Keywords:

Coal-bed methane Cultivation Metabolomics Molecular surveys Most probable number Subsurface microbiology 

Notes

Acknowledgments

The preparation of this chapter was funded by National Science Foundation grants MCB-1329890 and OCE-0961900.

References

  1. 1.
    Strąpoć D, Mastalerz M, Dawson K, Macalady J, Callaghan AV, Wawrik B, Turich C, Ashby M (2011) Biogeochemistry of microbial coal-bed methane. Annu Rev Earth Plant Sci 39:617–656CrossRefGoogle Scholar
  2. 2.
    Guo H, Yu Z, Liu R, Zhang H, Zhong Q, Xiong Z (2012) Methylotrophic methanogenesis governs the biogenic coal bed methane formation in Eastern Ordos Basin, China. Appl Microbiol Biotechnol 96:1587–1597CrossRefPubMedGoogle Scholar
  3. 3.
    Scott AR, Kaiser WR, Ayers Jr. WB (1994) Thermogenic and secondary biogenic gases, San-Juan Basin, Colorado and New-Mexico - implications for coalbed gas producibility. Am Assoc Pet Geol Bull 78:1186–1209Google Scholar
  4. 4.
    Strąpoć D, Mastalerz M, Eble C, Schimmelmann A (2007) Characterization of the origin of coalbed gases in southeastern Illinois Basin by compound-specific carbon and hydrogen stable isotope ratios. Org Geochem 38:267–287CrossRefGoogle Scholar
  5. 5.
    Flores RM, Rice CA, Stricker GD, Warden A, Ellis MS (2008) Methanogenic pathways of coal-bed gas in the Powder River Basin, United States: the geologic factor. Int J Coal Geol 76:52–75CrossRefGoogle Scholar
  6. 6.
    Fry JC, Horsfield B, Sykes R, Cragg BA, Heywood C, Kim GT, Mangelsdorf K, Mildenhall DC, Rinna J, Vieth A, Zink K.-G, Sass H, Weightman AJ, Parkes RJ (2009) Prokaryotic populations and activities in an interbedded coal deposit, including a previously deeply buried section (1.6-2.3 km) above 150 Ma basement rock. Geomicrobiol J 26:163–178CrossRefGoogle Scholar
  7. 7.
    Li D, Hendry P, Faiz M (2008) A survey of the microbial populations in some Australian coalbed methane reservoirs. Int J Coal Geol 76:14–24CrossRefGoogle Scholar
  8. 8.
    Shimizu S, Akiyama M, Naganuma T, Fujioka M, Nako M, Ishijima Y (2007) Molecular characterization of microbial communities in deep coal seam groundwater of northern Japan. Geobiology 5:423–433CrossRefGoogle Scholar
  9. 9.
    Strąpoć D, Picardal FW, Turich C, Schaperdoth I, Macalady JL, Lipp JS, Lin Y.-S, Ertefai TF, Schubotz F, Hinrichs K.-U, Mastalerz M, Schimmelmann A (2008) Methane-producing microbial community in a coal bed of the Illinois basin. Appl Environ Microbiol 74:2424–2432CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Penner TJ, Foght JM, Budwill K (2010) Microbial diversity of western Canadian subsurface coal beds and methanogenic coal enrichment cultures. Int J Coal Geol 82:81–93CrossRefGoogle Scholar
  11. 11.
    Klein DA, Flores RM, Venot C, Gabbert K, Schmidt R, Stricker GD, Pruden A, Mandernack K (2008) Molecular sequences derived from Paleocene Fort Union Formation coals vs. associated produced waters: implications for CBM regeneration. Int J Coal Geol 76:3–13CrossRefGoogle Scholar
  12. 12.
    Wawrik B, Mendivelso M, Parisi VA, Suflita JM, Davidova IA, Marks CR, Van Nostrand JD, Liang, Y, Zhou J, Huizinga BJ, Strąpoć D, Callaghan AV (2012) Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin. FEMS Microbiol Ecol 81:26–42CrossRefPubMedGoogle Scholar
  13. 13.
    An D, Caffrey SM, Soh J, Agrawal A, Brown D, Budwill K, Dong X, Dunfield PF, Foght J, Gieg LM, Hallam SJ, Hanson NW, He Z, Jack TR, Klassen J, Konwar KM, Kuatsjah E, Li C, Larter S, Leopatra V, Nesbo CL, Oldenburg T, Pagé AP, Ramos-Padron E, Rochman FF, Saidi-Mehrabad A, Sensen CW, Sipahimalani P, Song YC, Wilson S, Wolbring G, Wong M.-L, Voordouw G (2013) Metagenomics of hydrocarbon resource environments indicates aerobic taxa and genes to be unexpectedly common. Environ Sci Technol 47:10708–10717CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Krüger M, Beckmann S, Engelen B, Thielemann T, Cramer B, Schippers A, Cypionka H (2008) Microbial methane formation from hard coal and timber in an abandoned coal mine. Geomicrobiol J 25:315–321CrossRefGoogle Scholar
  15. 15.
    Thielemann T, Cramer B, Schippers A (2004) Coalbed methane in the Ruhr Basin, Germany: a renewable energy source? Org Geochem 35:1537–1549CrossRefGoogle Scholar
  16. 16.
    Green MS, Flanegan KC, Gilcrease PC (2008) Characterization of a methanogenic consortium enriched from a coalbed methane well in the Powder River Basin, USA. Int J Coal Geol 76:34–45CrossRefGoogle Scholar
  17. 17.
    Harris SH, Smith RL, Barker CE (2008) Microbial and chemical factors influencing methane production in laboratory incubations of low-rank subsurface coals. Int J Coal Geol 76:46–51Google Scholar
  18. 18.
    Lawson PA, Wawrik B, Allen TD, Johnson CN, Marks CR, Tanner RS, Harriman BH, Strąpoć D, Callaghan AV (2014) Youngiibacter fragilis gen. nov., sp. nov., isolated from natural gas production-water and reclassification of Acetivibrio multivorans as Youngiibacter multivorans comb. nov. Int J Syst Evol Microbiol 64:198–205CrossRefPubMedGoogle Scholar
  19. 19.
    Callaghan AV (2013) Metabolomic investigations of anaerobic hydrocarbon-impacted environments. Curr Opin Biotechnol 24:506–515CrossRefPubMedGoogle Scholar
  20. 20.
    Agrawal A, Gieg LM (2013) In situ detection of anaerobic alkane metabolites in subsurface environments. Front Microbiol 4:140CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63CrossRefPubMedGoogle Scholar
  22. 22.
    Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41:e1CrossRefPubMedGoogle Scholar
  23. 23.
    Fadrosh DW, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J (2014) An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome 2:6CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625–630PubMedPubMedCentralGoogle Scholar
  25. 25.
    Pinto AJ, Raskin L (2012) PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One 7(8): e43093Google Scholar
  26. 26.
    Teixeira LCRS, Yergeau E (2012) Quantification of microorganisms using a functional gene approach. In: Filion M (ed) Quantitative real-time PCR in applied microbiology. Caister Academic Press, Norfolk, UKGoogle Scholar
  27. 27.
    Kaeberlein T, Lewis K, Epstein SS (2002) Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296:1127–1129CrossRefPubMedGoogle Scholar
  28. 28.
    Beller HR (2000) Metabolic indicators for detecting in situ anaerobic alkylbenzene degradation. Biodegradation 11:125–139CrossRefPubMedGoogle Scholar
  29. 29.
    Young LY, Phelps CD (2005) Metabolic biomarkers for monitoring in situ anaerobic hydrocarbon degradation. Environ Health Perspect 113:62–67CrossRefPubMedGoogle Scholar
  30. 30.
    Tanner RS (1989) Monitoring sulfate-reducing bacteria: comparison of enumeration media. J Microbiol Methods 10:83–90CrossRefGoogle Scholar
  31. 31.
    Wolin EA, Wolin MJ, Wolfe RS (1963) Formation of methane by bacterial extracts. J Biol Chem 238:2882–2886PubMedGoogle Scholar
  32. 32.
    Balch WE, Wolfe RS (1976) New approach to cultivation of methanogenic bacteria: 2-mercaptoethanesulfonic acid (HS-CoM)-dependent growth of Methanobacterium ruminantium in a pressurized atmosphere. Appl Environ Microbiol 32:781–791PubMedPubMedCentralGoogle Scholar
  33. 33.
    Miller TL, Wolin MJ (1974) Serum bottle modification of the Hungate technique for cultivating obligate anaerobes. Appl Microbiol 27:985–987PubMedPubMedCentralGoogle Scholar
  34. 34.
    Trüper HG, Schlegel HG (1964) Sulphur metabolism in Thiorhodaceae I. Quantitative measurements on growing cells of Chromatium okenii. Antonie Van Leeuwenhoek 30:225–238Google Scholar
  35. 35.
    Pachmayr F (1960) Vorkommen und Bestimmung von Schwefelverbindungen in Mineral-Wasser [PhD Thesis]. University of Munich, Munich, GermanyGoogle Scholar
  36. 36.
    Banwart GJ (1981) Basic food microbiology. AVI Publishing Co. Inc., Westport, CTGoogle Scholar
  37. 37.
    Gieg LM, Suflita JM (2002) Detection of anaerobic metabolites of saturated and aromatic hydrocarbons in petroleum-contaminated aquifers. Environ Sci Technol 36:3755–3762CrossRefPubMedGoogle Scholar
  38. 38.
    Beller HR (2002) Analysis of benzylsuccinates in groundwater by liquid chromatography/tandem mass spectrometry and its use for monitoring in situ BTEX biodegradation. Environ Sci Technol 36:2724–2728CrossRefPubMedGoogle Scholar
  39. 39.
    Alumbaugh RE, Gieg LM, Field JA (2004) Determination of alkylbenzene metabolites in groundwater by solid-phase extraction and liquid chromatography-tandem mass spectrometry. J Chromatogr A 1042:89–97CrossRefPubMedGoogle Scholar
  40. 40.
    Gieg LM, Suflita JM (2005) Metabolic indicators of anaerobic hydrocarbon biodegradation in petroleum-laden environments. In: Ollivier B, Magot M (eds) Petroleum microbiology. ASM Press, Washington DC, pp 337–356CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  1. 1.Department of Microbiology and Plant BiologyUniversity of OklahomaNormanUSA

Personalised recommendations