Skip to main content
SpringerLink
Log in

Cultivation-independent analysis of archaeal and bacterial communities of the formation water in an Indian coal bed to enhance biotransformation of coal into methane

  • Bioenergy and biofuels
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

An Erratum to this article was published on 07 February 2012

Abstract

Biogenic origin of the significant proportion of coal bed methane has indicated the role of microbial communities in methanogenesis. By using cultivation-independent approach, we have analysed the archaeal and bacterial community present in the formation water of an Indian coal bed at 600–700 m depth to understand their role in methanogenesis. Presence of methanogens in the formation water was inferred by epifluorescence microscopy and PCR amplification of mcrA gene. Archaeal 16S rRNA gene clone library from the formation water metagenome was dominated by methanogens showing similarity to Methanobacterium, Methanothermobacter and Methanolinea whereas the clones of bacterial 16S rRNA gene library were closely related to Azonexus, Azospira, Dechloromonas and Thauera. Thus, microbial community of the formation water consisted of predominantly hydrogenotrophic methanogens and the proteobacteria capable of nitrogen fixation, nitrate reduction and polyaromatic compound degradation. Methanogenic potential of the microbial community present in the formation water was elucidated by the production of methane in the enrichment culture, which contained 16S rRNA gene sequences showing close relatedness to the genus Methanobacterium. Microcosm using formation water as medium as well as a source of inoculum and coal as carbon source produced significant amount of methane which increased considerably by the addition of nitrite. The dominance of Diaphorobacter sp. in nitrite amended microcosm indicated their important role in supporting methanogenesis in the coal bed. This is the first study indicating existence of methanogenic and bacterial community in an Indian coal bed that is capable of in situ biotransformation of coal into methane.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Ahmed M, Smith JW (2001) Biogenic methane generation in the degradation of eastern Australian Permian coals. Organic Geochem 32:809–816

    Article  CAS  Google Scholar 

  • Altschu SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Google Scholar 

  • Bailey JE, Ollis DF (1986) Biochemical engineering fundamentals, 2nd edn. McGraw-Hill, New York

    Google Scholar 

  • Baker KH (1994) Bioremediation of surface and subsurface soils. In: Baker KH, Herson DS (eds) Bioremediation. McGraw-Hill, New York, pp 203–259

    Google Scholar 

  • Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS (1979) Methanogens: reevaluation of a unique biological group. Microbiol Rev 43:260–296

    CAS  Google Scholar 

  • Banat IM, Nedwell DB, Balba MT (1983) Stimulation of methanogenesis by slurries of saltmarsh sediment after the addition of molybdate to inhibit sulphate-reducing bacteria. J Gen Microbiol 129:123–129

    CAS  Google Scholar 

  • Chakraborty R, Coates JD (2005) Hydroxylation and carboxylation—two crucial steps of anaerobic benzene degradation by Dechloromonas strain RCB. Appl Environ Microbiol 71:5427–5432

    Article  CAS  Google Scholar 

  • Chowdhury SP, Khanna S, Verma SC, Tripathi AK (2004) Molecular diversity of tannic acid degrading bacteria isolated from tannery soil. J Appl Microbiol 97:1210–1219

    Article  CAS  Google Scholar 

  • Coates JD, Chakraborty R, Lack JG, Connor SMO, Cole KA, Bender KS, Achenbach LA (2001) Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas. Nature 411:1039–1043

    Article  CAS  Google Scholar 

  • Cookson JT Jr (1995) Bioremediation engineering design and application. McGraw-Hill, New York

    Google Scholar 

  • Faison BD (1992) The chemistry of low rank coal and its relationship to the biochemical mechanisms of coal biotransformation. In: Crawford DL (ed) Microbial transformations of low rank coals. CRC, Boca Raton, pp 1–26

    Google Scholar 

  • Faiz M, Hendry P (2006) Significance of microbial activity in Australian coal bed methane reservoirs—a review. Bull Can Petrol Geol 54:261–272

    Article  Google Scholar 

  • Fakoussa RM, Hofrichter M (1999) Biotechnology and microbiology of coal degradation. Appl Microbiol Biotechnol 52:25–40

    Article  CAS  Google Scholar 

  • Flores RM, Rice CA, Stricker GD, Warden A, Ellis MS (2008) Methanogenic pathways of coalbed gas in the Powder River Basin, United States: the geologic factor. Int J Coal Geol 76:52–75

    Google Scholar 

  • Garrity GM (ed) (2005) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York

    Google Scholar 

  • Gockay CF, Kolankaya N, Dilek FB (2001) Microbial solubilization of lignites. Fuel 80:1421–1433

    Article  Google Scholar 

  • Godon JJ, Zumstein E, Dabert P, Habouzit F, Moletta R (1997) Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl Environ Microbiol 63:2802–2813

    CAS  Google Scholar 

  • Green MS, Flanegan KC, Gilcrease PC (2008) Characterization of a methanogenic consortium enriched from a coalbed methane well in the Powder River Basin, U.S.A. Int J Coal Geol 76:34–45

    Article  CAS  Google Scholar 

  • Hales BA, Edward C, Ritchie DA, Hall G, Pickup RW, Saunders JR (1996) Isolation and identification of methanogen-specific DNA from blanket bog peat by PCR amplification and sequence analysis. Appl Environ Microbiol 62:668–675

    CAS  Google Scholar 

  • Harding R, Czarnecki S, Isbister J, Barik S (1993) Biogasification of low-rank coal. TR-101572. ARCTECH, Inc. for Electric Power Research Institute, Chantilly, p 9

    Google Scholar 

  • Hyvik H, Eskilt JP, Hovland JS (1997) Method for removing hydrogen sulphide from oil-containing water and equipment therefor. Biotechnol Adv 15:734–735

    Google Scholar 

  • Jin S, Fallgren P, Luo H (2010) Feasibility of enhanced biodegradation of petroleum compounds in groundwater under denitrifying conditions. Bull Environ Contam Toxicol 84:357–361

    Article  CAS  Google Scholar 

  • Khan ST, Hiraishi A (2002) Diaphorobacter nitroreducens gen. nov., sp. nov., a poly (3-hydroxybutyrate)-degrading denitrifying bacterium isolated from activated sludge. J Gen Appl Microbiol 48:299–308

    Article  CAS  Google Scholar 

  • King GM, Wiebe JM (1980) Tracer analysis of methanogenesis in salt marsh soil. Appl Environ Microbiol 39:877–881

    CAS  Google Scholar 

  • Klankeo P, Nopcharoenkul W, Pinyakong O (2009) Two novel pyrene-degrading Diaphorobacter sp. and Pseudoxanthomonas sp. isolated from soil. J Biosci Bioengg 108:488–495

    Article  CAS  Google Scholar 

  • Klein DA, Flores RM, Venot C, Gabbert K, Schmid R, Stricker GD, Pruden A, Mandernac K (2008) Molecular sequences derived from Paleocene Fort Union formation coals vs. associated produced waters: implications for CBM regeneration. Int J Coal Geol 76:3–13

    Article  CAS  Google Scholar 

  • Kluber HD, Conrad R (1998a) Effects of nitrate, nitrite, NO and N2O on methanogenesis and other redox processes in anoxic rice field soil. FEMS Microbiol Ecol 25:301–318

    Article  CAS  Google Scholar 

  • Kluber HD, Conrad R (1998b) Inhibitory effects of nitrate, nitrite, NO and N2O on methanogenesis by Methanosarcina barkeri and Methanobacterium bryantii. FEMS Microbiol Ecol 25:331–339

    Article  CAS  Google Scholar 

  • Li D, Hendry P, Faiz M (2008) A survey of the microbial populations in some Australian coalbed methane reservoirs. Int J Coal Geol 76:14–24

    Article  CAS  Google Scholar 

  • LUCA Technologies, LLC (2004) Active biogenesis of methane in Wyoming’s Powder river Basin. http://www.lucatechnologies.com/content/index.cfm?fuseaction=showContent&contentID=22&navID=22

  • Mandal D, Tewari DC, Rautela MS (2004) Analysis of micro-fractures in coal for the coal bed methane exploitation in Jharia Coal field. Abstract 5th conference and exposition on petroleum geophysics, Hyderabad-2004, India, pp 904–909

  • Mazumder S, Wolf KH-AA (2004) An overview of the potential and prospects of coalbed methane exploration and exploitation in the Permo-carboniferous coal measures of the Barakar formation, Jharia basin India. Geolo Bel 7:147–156

    CAS  Google Scholar 

  • McInerney MJ, Bryant MP (1981) Review of methane fermentation fundamentals. In: Wise DL (ed) Fuel gas production from biomass. CRC, Boca Raton, pp 19–46

    Google Scholar 

  • Midgley DJ, Hendry P, Pinetown KL, Fuentes D, Se Gong FD, Mitchell DL, Faiz M (2010) Characterisation of a microbial community associated with a deep, coal seam methane reservoir in the Gippsland Basin, Australia. Int J Coal Geol 82:232–239

    Article  CAS  Google Scholar 

  • Mikucki JA, Liu Y, Delwiche M, Colwell FS, Boone DR (2003) Isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of Methanoculleus submarinus sp. Nov. Appl Environ Microbiol 69:3311–3316

    Article  CAS  Google Scholar 

  • Mochimaru H, Yoshioka H, Tamaki H, Nakamura K, Kaneko N, Sakata S, Imachi H, Sekiguchi Y, Uchiyama H, Kamagata Y (2007a) Microbial diversity and methanogenic potential in a high temperature natural gas field in Japan. Extremophiles 11:453–461

    Article  CAS  Google Scholar 

  • Mochimaru H, Uchiyama H, Yoshioka H, Imachi H, Hoaki T, Tamaki H, Nakamura K, Sekiguchi Y, Kamagata Y (2007b) Methanogen diversity in deep subsurface gas-associated water at the Minami-Kanto gas field in Japan. Geomicrobiol 24:93–100

    Article  CAS  Google Scholar 

  • Narasimhan KS, Mukherjee AK, Sengupta S, Singh SM, Alam MM (1998) Coal bed methane potential in India. Fuel 77:1865–1866

    Article  CAS  Google Scholar 

  • Ogram AV, Jessup RE, Ou LT, Rao PSC (1985) Effects of sorption on biological degradation rates of (2, 4-dichlorophenoxy) acetic acid in soils. Appl Environ Microbiol 49:582–587

    CAS  Google Scholar 

  • Paster BJ, Parola EC (1982) Physiological diversity of rumen Spirochetes. Appl Environ Microbiol 43:686–693

    CAS  Google Scholar 

  • Penner TJ, Foght JM, Budwill K (2010) Microbial diversity of western Canadian subsurface coal beds and methanogenic coal enrichment cultures. Int J Coal Geol 82:81–93

    Article  CAS  Google Scholar 

  • Ramaswami A, Luthy RG (1997) Measuring and modeling physicochemical limitations to bioavailability and biodegradation. In: Hurst CJ (ed) Manual of environmental microbiology. ASM, Washington, DC, pp 721–729

    Google Scholar 

  • Reilly CO, Colleran E (2005) Toxicity of nitrite toward mesophilic and thermophilic sulphate-reducing, methanogenic and syntrophic populations in anaerobic sludge. J Ind Microbiol Biotechnol 32:46–52

    Article  Google Scholar 

  • Roy R, Conrad R (1999) Effect of methanogenic precursors (acetate, hydrogen, propionate) on the suspension of methane production by nitrate in anoxic rice field soil. FEMS Microbiol Ecol 28:49–61

    Article  CAS  Google Scholar 

  • Scott AR (1999) Improving coal gas recovery with microbially enhanced coalbed methane. In: Mastalerz M, Glikson M, Golding SD (eds) Coalbed methane: scientific, environmental and economic evaluation. Kluwer, Dordrecht, pp 89–110

    Google Scholar 

  • Sekiguchi Y, Kagamata Y, Syutsubo K, Ohashi A, Harada H (1998) Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA gene analysis. Microbiology 144:2655–2665

    Article  CAS  Google Scholar 

  • 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 5:423–433

    Article  CAS  Google Scholar 

  • Singh AK, Sharma M, Singh MP (2009) Genesis of natural cokes: some Indian examples. Int J Coal Geol 75:40–48

    Article  Google Scholar 

  • Skladany GJ, Baker KH (1994) Laboratory biotreatability studies. In: Baker KH, Herson DS (eds) Bioremediation. McGraw-Hill, New York, pp 97–172

    Google Scholar 

  • Strąpoc D, Picardal FW, Turich C, Schaperdoth I, Macalady JL, Lipp JS, Lin YS, Ertefai TF, Schubotz F, Hinrichs KU, Mastalerz M, Schimmelmann A (2008) Methane-producing microbial community in a coal bed of the Illinois Basin. Appl Environ Microbiol 74:2424–2432

    Article  Google Scholar 

  • Thielemann T, Cramer B, Schippers A (2004) Coalbed methane in the Ruhr Basin, Germany: a renewable energy source? Org Geochem 35:1537–1549

    CAS  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  CAS  Google Scholar 

  • Tierney M (2006) Naphthalene degradation by denitrifying bacteria. ProQuest dissertations and theses, Rutgers, The State University of New Jersey, New Brunswick, 164 p. http://search.proquest.com/docview/305291617?accountid=26421

  • Volkwein JC, Schoeneman AL, Clausen EG, Gaddy JL, Johnson ER, Basu R, Ju N, Klasson KT (1994) Biological production of methane from bituminous coal. Fuel Process Technol 40:339–345

    Article  CAS  Google Scholar 

  • Widdel F (1986) Growth of methanogenic bacteria in pure culture with 2-propanol and other alcohols as hydrogen donors. Appl Environ Microbiol 51:1056–1062

    CAS  Google Scholar 

  • Willmann G, Fakoussa RM (1997) Extracellular oxidative enzymes of coal-attacking fungi. Fuel Process Technol 52:27–41

    Article  CAS  Google Scholar 

  • Winfrey MR, Zeikus JG (1977) Effect of sulfate on carbon and electron flow during microbial methanogenesis in freshwater sediments. Appl Environ Microbiol 33:275–281

    CAS  Google Scholar 

  • Wolin EA, Wolin MJ, Wolfe RS (1963) Formation of methane by bacterial extracts. J Biol Chem 238:2882–2886

    CAS  Google Scholar 

  • Zhao Y, Zhang H, Boone DR, Mah RA (1986) Isolation and characterization of a fast-growing, thermophilic Methanobacterium species. Appl Environ Microbiol 52:1227–1229

    CAS  Google Scholar 

  • Zinder SH (1993) Physiological ecology of methanogens. In: Ferry JG (ed) Methanogenesis: ecology, physiology, biochemistry and genetics. Chapman and Hall, New York, pp 128–206

    Google Scholar 

Download references

Acknowledgements

This work was carried out jointly by School of Biotechnology, Banaras Hindu University and Institute of Reservoir Studies, Ahmedabad with financial support from Oil and Natural gas Commission, New Delhi and Department of Biotechnology, Government of India. DNS was supported by a Junior/Senior Research Fellowship from the University Grants Commission, New Delhi. We appreciate the critical help and advice received from Dr D. M. Kale (ONGC, New Delhi); Dr R. V. Marathe, Dr S. Bateja and Dr T. R. Misra (Institute of Reservoir Studies, Ahmedabad), Dr D. R. Ranade (Agarkar Research Institute, Pune) and Dr S. P. Chowdhury (Helmholtz Zentrum, Muenchen).

Author information

Authors and Affiliations

  1. School of Biotechnology, Banaras Hindu University, Varanasi, 221105, India

    Durgesh Narain Singh, Ashok Kumar & Anil Kumar Tripathi

  2. Institute of Reservoir Studies, Oil and Natural Gas Commission, Ahmedabad, 380005, India

    Munish Prasad Sarbhai

Authors
  1. Durgesh Narain Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ashok Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Munish Prasad Sarbhai
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Anil Kumar Tripathi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Anil Kumar Tripathi.

Additional information

An erratum to this article can be found at http://dx.doi.org/10.1007/s00253-012-3879-5.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Singh, D.N., Kumar, A., Sarbhai, M.P. et al. Cultivation-independent analysis of archaeal and bacterial communities of the formation water in an Indian coal bed to enhance biotransformation of coal into methane. Appl Microbiol Biotechnol 93, 1337–1350 (2012). https://doi.org/10.1007/s00253-011-3778-1

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-011-3778-1

Keywords

Search

Navigation