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Applied Microbiology and Biotechnology

, Volume 97, Issue 17, pp 7553–7562 | Cite as

Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments

  • Prem Prashant Chaudhary
  • Lenka Brablcová
  • Iva Buriánková
  • Martin Rulík
Mini-Review

Abstract

Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research.

Keywords

Methanogens Diversity Sediments Microbial diversity Ribosomal RNA and mcrA 

Notes

Acknowledgments

The authors are thankful to the European Social Fund and state budget of the Czech Republic for providing the financial support during this study. This work is a part of the POSTUP II project CZ.1.07/2.3.00/30.0041, which is mutually financed by the previously stated funding agencies.

References

  1. Acinas SG, Rodrıiguez-Valera F, Pedros-Alio C (1997) Spatial and temporal variation in marine bacterioplankton diversity as shown by RFLP fingerprinting of PCR amplified 16S rDNA. FEMS Microb Ecol 24:27–40CrossRefGoogle Scholar
  2. Antony CP, Murrell JC, Shouche YS (2012) Molecular diversity of methanogens and identification of Methanolobus sp. as active methylotrophic Archaea in Lonar crater lake sediments. FEMS Microbiol Ecol 81:43–51PubMedCrossRefGoogle Scholar
  3. Bhattarai S, Ross KA, Schmid M, Anselmetti FS, Bürgmann H (2012) Local conditions structure unique archaeal communities in the anoxic sediments of meromictic Lake Kivu. Microb Ecol 64(2):291–310PubMedCrossRefGoogle Scholar
  4. Biderre-Petit C, Jézéquel D, Dugat-Bony E, Lopes F, Kuever J, Borrel G, Viollier E, Fonty G, Peyret P (2011) Identification of microbial communities involved in the methane cycle of a freshwater meromictic lake. FEMS Microbiol Ecol 77:533–545PubMedCrossRefGoogle Scholar
  5. Cahyani VR, Matsuya K, Asakawa S, Kimura M (2004) Succession and phylogenetic profile of methanogenic archaeal communities during the composting process of rice straw estimated by PCR-DGGE analysis. Soil Sci and Plant Nut 50:555–563CrossRefGoogle Scholar
  6. Capone DG, Kiene RP (1988) Comparison of microbial dynamics in marine and freshwater sediments: contrasts in anaerobic carbon catabolism. Limnol Oceanogr 33:725–749CrossRefGoogle Scholar
  7. Cetecioğlu Z, Ince BK, Kolukirik M, Ince O (2009) Biogeographical distribution and diversity of bacterial and archaeal communities within highly polluted anoxic marine sediments from the Marmara Sea. Mar Pollut Bull 58:384–395PubMedCrossRefGoogle Scholar
  8. Chaudhary PP (2009) Methanomicrobium phylotype are the dominant methanogen phylotype in the Murrah buffaloes. Lett Appl Microbiol 48:386PubMedCrossRefGoogle Scholar
  9. Chaudhary PP, Sirohi SK (2009) Dominance of Methanomicrobium phylotype in rumen (Bubalus bubalis ) methanogens from India. Lett Appl Microbiol 49:274–277PubMedCrossRefGoogle Scholar
  10. Chaudhary PP, Sirohi SK, Saxena J (2012) Diversity analysis of methanogens in rumen of Bubalus bubalis by 16S riboprinting and sequence analysis. Gene 493:13–17PubMedCrossRefGoogle Scholar
  11. Chaudhary PP, Sirohi SK, Singh D, Saxena J (2011) Methyl coenzyme M reductase (mcrA) gene based phylogenetic analysis of methanogens population in Murrah buffaloes (Bubalus bubalis). J Microbiol 49:558–561PubMedCrossRefGoogle Scholar
  12. Cicerone RJ, Oremland RS (1988) Biogeochemical aspects of atmospheric methane. Global Biogeochem Cy 1:61–86Google Scholar
  13. Conrad R (2009) The global methane cycle: recent advances in understanding the microbial processes involved. Environ Microbiol Rep 1:285–292PubMedCrossRefGoogle Scholar
  14. Dang H, Zhou H, Yang J, Ge H, Jiao N, Luan X, Zhang C, Klotz MG (2013) Thaumarchaeotal signature gene distribution in sediments of the northern South China Sea: an indicator of the metabolic intersection of the marine carbon, nitrogen, and phosphorus cycles? Appl Environ Microbiol 79:2137–2147PubMedCrossRefGoogle Scholar
  15. DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685–5689PubMedCrossRefGoogle Scholar
  16. Dhillon A, Lever M, Lloyd KG, Albert DB, Sogin ML, Teske A (2005) Methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A (mcrA) genes in hydrothermal sediments of the Guaymas Basin. Appl Environ Microbiol 71:4592–4601PubMedCrossRefGoogle Scholar
  17. Earl J, Pickup RW, Ritchie DA, Edwards C (2005) Development of temporal temperature gradient electrophoresis for characterising methanogen diversity. Microb Ecol 50:327–336PubMedCrossRefGoogle Scholar
  18. Ehhalt D, Prather M (2001) Atmospheric chemistry and greenhouse gases. In: Dentener F, Derwent R, Dlugokencky E, Holland E, Isaksen I, Katima J, Kirchhoff V, Matson P, Midgley P, Wang M (eds) Climate change: the scientific basis. Cambridge University Press, Cambridge, pp 239–287Google Scholar
  19. Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65:4630–4636PubMedGoogle Scholar
  20. Forster P, Ramaswamy V, Artaxo P, Berntsen T, Betts R, Fahey DW, Haywood J, Lean J, Lowe DC, Myhre G, Nganga J, Prinn R, Raga G, Schulz M, Dorland RV (2007) Changes in atmospheric constituents and in radiative forcing. In: Solomon S, Qin D, Manning M, Chen Z, Marquis M, Averyt KB, Tignor M, Miller HL (eds) Climate change 2007: the physical science basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, CambridgeGoogle Scholar
  21. Ganzert L, Jurgens G, Münster U, Wagner D (2007) Methanogenic communities in permafrost-affected soils of the Laptev Sea coast, Siberian Arctic, characterized by 16S rRNA gene fingerprints. FEMS Microbiol Ecol 59:476–488PubMedCrossRefGoogle Scholar
  22. Garcia JL (1990) Taxonomy and ecology of methanogens. FEMS Microbiol Rev 87:297–308CrossRefGoogle Scholar
  23. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63PubMedCrossRefGoogle Scholar
  24. (2007) Global warming potentials. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate ChangeGoogle Scholar
  25. Goffredi SK, Wilpiszeski R, Lee R, Orphan VJ (2008) Temporal evolution of methane cycling and phylogenetic diversity of archaea in sediments from a deep-sea whale-fall in Monterey Canyon, California. ISME J 2:204–220PubMedCrossRefGoogle Scholar
  26. Grosskopf R, Stubner S, Liesack W (1998) Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl Environ Microb 64:4983–4989Google Scholar
  27. Hristova KR, Lutenegger CM, Scow KM (2001) Detection and quantification of methyl tert-butyl ether-degrading strain PM1 by real-time TaqMan PCR. Appl Environ Microbiol 67:5154–5160PubMedCrossRefGoogle Scholar
  28. Ikenaga M, Asakawa S, Muraoka Y, Kimura M (2004) Methanogenic archaeal communities in rice roots grown in flooded soil pots: estimation by PCR-DGGE and sequence analyses. Soil Sci and Plant Nut 50:701–711CrossRefGoogle Scholar
  29. Jiang L, Zheng Y, Chen J, Xiao X, Wang F (2011) Stratification of Archaeal communities in shallow sediments of the Pearl River Estuary, Southern China. Anton Van Leeuwenhoek 99:739–751CrossRefGoogle Scholar
  30. Kanokratana P, Chanapan S, Pootanakit K, Eurwilaichitr L (2004) Diversity and abundance of Bacteria and Archaea in the Bor Khlueng Hot Spring in Thailand. J Basic Microbiol 44:430–444PubMedCrossRefGoogle Scholar
  31. Karr EA, Ng JM, Belchik SM, Sattley WM, Madigan MT, Achenbach LA (2006) Biodiversity of methanogenic and other archaea in the permanently frozen Lake Fryxell, Antarctica. Appl Environ Microbiol 72:1663–1666PubMedCrossRefGoogle Scholar
  32. Keyser M, Witthuhn RC, Lamprecht C, Coetzee MP, Britz TJ (2006) PCR based DGGE fingerprinting and identification of methanogens detected in three different types of UASB granules. Syst Appl Microbiol 29:77–84PubMedCrossRefGoogle Scholar
  33. Kojima H, Tsutsumi M, Ishikawa K, Iwata T, Mußmann M, Fukui M (2012) Distribution of putative denitrifying methane oxidizing bacteria in sediment of a freshwater lake, Lake Biwa. Syst Appl Microbiol 35:233–238PubMedCrossRefGoogle Scholar
  34. Kumar S, Dagar SS, Mohanty AK, Sirohi SK, Puniya M, Kuhad RC, Sangu KP, Griffith GW, Puniya AK (2011) Enumeration of methanogens with a focus on fluorescence in situ hybridization. Naturwissenschaften 98:457–472PubMedCrossRefGoogle Scholar
  35. Lazar CS, Dinasquet J, L'Haridon S, Pignet P, Toffin L (2011) Distribution of anaerobic methane-oxidizing and sulfate-reducing communities in the G11 Nyegga pockmark, Norwegian Sea. Anton Van Leeuwenhoek 100:639–653CrossRefGoogle Scholar
  36. Lazar CS, John Parkes R, Cragg BA, L'Haridon S, Toffin L (2012) Methanogenic activity and diversity in the centre of the Amsterdam Mud Volcano, Eastern Mediterranean Sea. FEMS Microbiol Ecol 81:243–254PubMedCrossRefGoogle Scholar
  37. McDonald SM, Sarno D, Scanlan DJ, Zingone A (2007) Genetic diversity of eukaryotic ultraphytoplankton in the Gulf of Naples during an annual cycle. Aquat Microb Ecol 50:75–89CrossRefGoogle Scholar
  38. McSweeney CS, Denman SE, Wright ADG, Yu Z (2007) Application of recent DNA/RNA-based techniques in rumen ecology. Asian-Aust J Anim Sci 20:283–294Google Scholar
  39. Miyashita A, Mochimaru H, Kazama H, Ohashi A, Yamaguchi T, Nunoura T, Horikoshi K, Takai K, Imachi H (2009) Development of 16S rRNA gene-targeted primers for detection of archaeal anaerobic methanotrophs (ANMEs). FEMS Microbiol Lett 297:31–37PubMedCrossRefGoogle Scholar
  40. Munson MA, Nedwell DB, Embley TM (1997) Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Appl Environ Microbiol 63:4729–4733PubMedGoogle Scholar
  41. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700PubMedGoogle Scholar
  42. Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Anton van Leeuwenhoek 73:127–141CrossRefGoogle Scholar
  43. Nedwell DB (1984) The input and mineralization of organic carbon in anaerobic aquatic sediments. Adv Microb Ecol 7:93–130CrossRefGoogle Scholar
  44. Nocker A, Burr M, Camper AK (2007) Genotypic microbial community profiling: a critical technical review. Microb Ecol 54:276–289PubMedCrossRefGoogle Scholar
  45. Nolla-Ardèvol V, Strous M, Sorokin DY, Merkel AY, Tegetmeyer HE (2012) Activity and diversity of haloalkaliphilic methanogens in Central Asian soda lakes. J Biotechnol 161:167–173PubMedCrossRefGoogle Scholar
  46. Orphan VJ, Jahnke LL, Embaye T, Turk KA, Pernthaler A, Summons RE, DES Marais DJ (2008) Characterization and spatial distribution of methanogens and methanogenic biosignatures in hypersaline microbial mats of Baja California. Geobiology 6:376–393PubMedCrossRefGoogle Scholar
  47. Peng M, Smith AH, Rehberger TG (2011) Quantification of Propionibacterium acidipropionici P169 bacteria in environmental samples by use of strain-specific primers derived by suppressive subtractive hybridization. Appl Environ Microbiol 77:3898–3902PubMedCrossRefGoogle Scholar
  48. Purdy KJ, Munson MA, Nedwell DB, Martin Embley T (2002) Comparison of the molecular diversity of the methanogenic community at the brackish and marine ends of a UK estuary. FEMS Microb Ecol 39:17–21CrossRefGoogle Scholar
  49. Putkinen A, Juottonen H, Juutinen S, Tuittila ES, Fritze H, Yrjälä K (2009) Archaeal rRNA diversity and methane production in deep boreal peat. FEMS Microbiol Ecol 70:87–98PubMedCrossRefGoogle Scholar
  50. Rastogi G, Barua S, Sani RK, Peyton BM (2011) Investigation of microbial populations in the extremely metal-contaminated Coeur d'Alene River sediments. Microb Ecol 62:1–13PubMedCrossRefGoogle Scholar
  51. Rigby M, Prinn RG, Fraser PJ, Simmonds PG, Langenfelds RL, Huang J, Cunnold DM, Steele LP, Krummel PB, Weiss RF, Doherty SO, Salameh PK, Wang H J, Harth CM, Mühle J, Porter LW (2008) Renewed growth of atmospheric methane. Geophys Res Lett 35(22). doi: 10.1029/2008GL036037
  52. Rulik M, Bednarik A, Mach V, Brablcova L, Buriankova I, Badurova P, Gratzova K (2013) Methanogenic system of a small lowland stream Sitka, Czech Republic. Biomass Now-Cultivation Utilization Chapter 17:395–426Google Scholar
  53. Savichtcheva O, Debroas D, Kurmayer R, Villar C, Jenny JP, Arnaud F, Perga ME, Domaizon I (2011) Quantitative PCR enumeration of total/toxic Planktothrix rubescens and total cyanobacteria in preserved DNA isolated from lake sediments. Appl Environ Microbiol 77:8744–8753PubMedCrossRefGoogle Scholar
  54. Schutte UM, Abdo Z, Bent SJ, Shyu C, Williams CJ, Pierson JD, Forney LJ (2008) Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Appl Microbiol Biotechnol 80:365–380PubMedCrossRefGoogle Scholar
  55. Sharma A, Chaudhary PP, Sirohi SK, Saxena J (2011) Structure modeling and inhibitor prediction of NADP oxidoreductase enzyme from Methanobrevibacter smithii. Bioinformation 6:15–19PubMedCrossRefGoogle Scholar
  56. Sirohi SK, Singh N, Dagar SS, Puniya AK (2012) Molecular tools for deciphering the microbial community structure and diversity in rumen ecosystem. Appl Microbiol Biotechnol 95:1135–1154PubMedCrossRefGoogle Scholar
  57. Sirohi SK, Chaudhary PP, Singh N, Singh D, Puniya AK (2013) The 16S rRNA and mcrA gene based comparative diversity of methanogens in cattle fed on high fibre based diet. Gene 523:161–166PubMedCrossRefGoogle Scholar
  58. Surakasi VP, Wani AA, Shouche YS, Ranade DR (2007) Phylogenetic analysis of methanogenic enrichment cultures obtained from Lonar Lake in India: isolation of Methanocalculus sp. and Methanoculleus sp. Microb Ecol 54:697–704PubMedCrossRefGoogle Scholar
  59. Wani AA, Surakasi VP, Siddharth J, Raghavan RG, Patole MS, Ranade D, Shouche YS (2006) Molecular analyses of microbial diversity associated with the Lonar soda lake in India: an impact crater in a basalt area. Res Microbiol 157:928–937PubMedCrossRefGoogle Scholar
  60. Watanabe T, Asakawa S, Nakamura A, Nagaoka K, Kimura M (2004) DGGE method for analyzing 16S rDNA of methanogenic archaeal community in paddy field soil. FEMS Microbiol Lett 232(2):153–163PubMedCrossRefGoogle Scholar
  61. Weber S, Lueders T, Friedrich MW, Conrad R (2001) Methanogenic populations involved in the degradation of rice straw in anoxic paddy soil. FEMS Microbiol Ecol 38:11–20CrossRefGoogle Scholar
  62. Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576–4579PubMedCrossRefGoogle Scholar
  63. Yoshioka H, Maruyama A, Nakamura T, Higashi Y, Fuse H, Sakata S, Bartlett DH (2010) Activities and distribution of methanogenic and methane-oxidizing microbes in marine sediments from the Cascadia Margin. Geobiology 8:223–233PubMedCrossRefGoogle Scholar
  64. Young A (1992) DoE Report CWM039A+B/92. Available at http://en.wikipedia.org/w/index.php?title=Landfill_gas_migration&oldid=525869338
  65. Zeikus JG, Winfrey MR (1976) Temperature limitation of methanogenesis in aquatic sediments. Appl Environ Microbiol 31(1):99–107PubMedGoogle Scholar
  66. Zeleke J, Lu SL, Wang JG, Huang JX, Li B, Ogram AV, Quan ZX (2013) Methyl coenzyme M reductase A (mcrA) gene-based investigation of methanogens in the mudflat sediments of Yangtze River Estuary, China. Microb Ecol. doi: 10.1007/s00248-012-0155-2 PubMedGoogle Scholar
  67. Zepp Falz K, Holliger C, Grosskopf R, Liesack W, Nozhevnikova AN, Müller B, Wehrli B, Hahn D (1999) Vertical distribution of methanogens in the anoxic sediment of Rotsee (Switzerland). Appl Environ Microbiol 65:2402–2408PubMedGoogle Scholar
  68. Zhou M, McAllister TA, Guan LL (2011) Molecular identification of rumen methanogens: technologies, advances and prospects. Anim Feed Sci Technol 166–167:76–86CrossRefGoogle Scholar
  69. Zoetendal EG, Cheng B, Koike S, Mackie RI (2004) Molecular microbial ecology of the gastrointestinal tract: from phylogeny to function. Curr Issues Intest Microbiol 5:31–47PubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Prem Prashant Chaudhary
    • 1
  • Lenka Brablcová
    • 1
  • Iva Buriánková
    • 1
  • Martin Rulík
    • 1
  1. 1.Laboratory of Aquatic Microbial Ecology, Department of Ecology and Environmental Sciences, Faculty of SciencePalacky UniversityOlomoucCzech Republic

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