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Dominance of Methanosarcinales Phylotypes and Depth-Wise Distribution of Methanogenic Community in Fresh Water Sediments of Sitka Stream from Czech Republic

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Abstract

The variation in the diversity of methanogens in sediment depths from Sitka stream was studied by constructing a 16S rRNA gene library using methanogen-specific primers and a denaturing gradient gel electrophoresis (DGGE)-based approach. A total of nine different phylotypes from the 16S rRNA library were obtained, and all of them were clustered within the order Methanosarcinales. These nine phylotypes likely represent nine new species and at least 5–6 new genera. Similarly, DGGE analysis revealed an increase in the diversity of methanogens with an increase in sediment depth. These results suggest that Methanosarcinales phylotypes might be the dominant methanogens in the sediment from Sitka stream, and the diversity of methanogens increases as the depth increases. Results of the present study will help in making effective strategies to monitor the dominant methanogen phylotypes and methane emissions in the environment.

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References

  1. Biderre-Petit C, Jézéquel D, Dugat-Bony E, Lopes F, Kuever J, Borrel G et al (2011) Identification of microbial communities involved in the methane cycle of a freshwater meromictic lake. FEMS Microbiol Ecol 77:533–545

    Article  PubMed  CAS  Google Scholar 

  2. Bretschko G, Klemens WE (1986) Quantitative methods and aspects in the study of the interstitial fauna of running waters. Stygologia 2:297–316

    Google Scholar 

  3. Buriánková I, Brablcová L, Mach V, Hýblová A, Badurová P, Cupalová J et al (2012) Methanogens and methanotrophs distribution in the hyporheic sediments of a small lowland stream. Fund Appl Limnol 181:87–102

    Article  Google Scholar 

  4. Buriánková I, Brablcová L, Mach V, Dvořák P, Chaudhary PP, Rulik M (2013) Identification of methanogenic archaea in the Hyporheic Sediment of Sitka Stream. PLoS ONE 8(11):e80804. doi:10.1371/journal.pone.0080804

    Article  PubMed  PubMed Central  Google Scholar 

  5. Chan OC, Claus P, Casper P, Ulrich A, Lueders T, Conrad R (2005) Vertical distribution of structure and function of the methanogenic archaeal community in Lake Dagow sediment. Environ Microbiol 7:1139–1149

    Article  PubMed  CAS  Google Scholar 

  6. Chaudhary PP (2009) Methanomicrobium phylotype are the dominant methanogen phylotype in the Murrah buffaloes. Lett Appl Microbiol 48:386

    Article  PubMed  CAS  Google Scholar 

  7. Chaudhary PP, Brablcová L, Buriánková I, Rulík M (2013) Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments. Appl Microbiol Biotechnol 97:7553–7562

    Article  PubMed  CAS  Google Scholar 

  8. Chunleuchanon S, Sooksawang A, Teaumroong N, Boonkerd N (2003) Diversity of nitrogen-fixing cyanobacteria under various ecosystems of Thailand: population dynamics as affected by environmental factors. World J Microbiol Biotechnol 19:167–173

    Article  CAS  Google Scholar 

  9. Chaudhary PP, Sirohi SK, Saxena J (2012) Diversity analysis of methanogens in rumen of Bubalus bubalis by 16S riboprinting and sequence analysis. Gene 493:13–17

    Article  PubMed  CAS  Google Scholar 

  10. Chaudhary PP, Sirohi SK (2009) Dominance of Methanomicrobium phylotype in rumen (Bubalus bubalis) methanogens from India. Lett Appl Microbiol 49:274–277

    Article  PubMed  CAS  Google Scholar 

  11. Cicerone RJ, Oremland RS (1988) Biogeochemical aspects of atmospheric methane. Global Biogeochem Cy 1:61–86

    Google Scholar 

  12. Conrad R (2009) The global methane cycle: recent advances in understanding the microbial processes involved. Environ Microbiol Rep 1:285–292

    Article  PubMed  CAS  Google Scholar 

  13. 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 71:4592–4601

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  14. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  15. Ferry JG (1993) Methanogenesis: ecology, physiology, biochemistry & genetics. Chapman & Hall, New York, 536 pp

    Book  Google Scholar 

  16. Fortuna A (2012) The Soil Biota. Nature Education Knowledge 3:1

    Google Scholar 

  17. Franzolin R, St-Pierre B, Northwood K, Wright ADG (2012) Analysis of rumen methanogen diversity in water buffaloes (Bubalus bubalis) under three different diets. Microb Ecol 64:131–139

    Article  PubMed  CAS  Google Scholar 

  18. Garcia JL, Patel BKC, Ollivier B (2000) Taxonomic, phylogenetic, and ecological diversity of methanogenic archaea. Anaerobe 6:205–226

    Article  PubMed  CAS  Google Scholar 

  19. 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 64:4983–4989

    CAS  Google Scholar 

  20. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G et al (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21:494–504

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  21. Hlaváčová E, Rulík M, Čáp L (2005) Anaerobic microbial metabolism in hyporheic sediment of a gravel bar in a small lowland stream. River Res Appl 21:1003–1011

    Article  Google Scholar 

  22. Hlaváčová E, Rulík M, Čáp L, Mach V (2006) Greenhouse gases (CO2, CH4, N2O) emissions to the atmosphere from a small lowland stream. Arch Hydrobiol 165:339–353

    Article  Google Scholar 

  23. Huang S, Chen C, Wu Y, Wu Q, Zhang R (2011) Characterization of depth-related bacterial communities and their relationships with the environmental factors in the river sediments. World J Microbiol Biotechnol 27:2655–2664

    Article  CAS  Google Scholar 

  24. 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 Plant Nutr 50:701–711

    Article  CAS  Google Scholar 

  25. 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 99:739–751

    Article  CAS  Google Scholar 

  26. 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 72:1663–1666

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  27. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  PubMed  CAS  Google Scholar 

  28. Koch K, Knoblauch C, Wagner D (2009) Methanogenic community composition and anaerobic carbon turnover in submarine permafrost sediments of the Siberian Laptev Sea. Environ Microbiol 11(3):657–668

    Article  PubMed  CAS  Google Scholar 

  29. 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 81:243–254

    Article  PubMed  CAS  Google Scholar 

  30. Lee GC, Watanabe T, Murase J, Asakawa S, Kimura M (2012) Growth of methanogens in an oxic soil microcosm: Elucidation by a DNA-SIP experiment using 13C-labeled dried rice callus. Appl Soil Ecol 58:37–44

    Article  Google Scholar 

  31. Leichtfried M (1988) Bacterial substrates in gravel beds of a second order alpine stream (Project Ritrodat-Lunz, Austria). Verh Internat Verein Limnol 23:1325–1332

    CAS  Google Scholar 

  32. Madden TL, Tatusov RL, Zhang J (1996) Applications of network BLAST server. In: Russell, F.D. (Ed.), Method Enzymol Academic Press:131–141

  33. Munson MA, Nedwell DB, Embley TM (1997) Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Appl Environ Microbiol 63:4729–4733

    PubMed  CAS  PubMed Central  Google Scholar 

  34. Newberry CJ, Webster G, Cragg BA, Parkes RJ, Weightman AJ, Fry JC (2004) Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190. Environ Microbiol 6(3):274–287

    Article  PubMed  Google Scholar 

  35. Orphan VJ, Jahnke LL, Embaye T, Turk KA, Pernthaler A, Summons RE et al (2008) Characterization and spatial distribution of methanogens and methanogenic biosignatures in hypersaline microbial mats of Baja California. Geobiology 6:376–393

    Article  PubMed  CAS  Google Scholar 

  36. 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 39:17–21

    Article  CAS  Google Scholar 

  37. 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 70:87–98

    Article  PubMed  CAS  Google Scholar 

  38. 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 62:1–13

    Article  PubMed  Google Scholar 

  39. Rulík M, Čáp L, Hlaváčová E (2000) Methane in the hyporheic zone of a small lowland stream (Sitka, Czech Republic). Limnologica 30:359–366

    Article  Google Scholar 

  40. Rulik M, Bednarik A, Mach V, Brablcova L, Buriankova I, Badurova P et al (2013) Methanogenic system of a small lowland stream Sitka, Czech Republic. Biomass Now-Cultivation Utilization Chapter 17:395–426

    Google Scholar 

  41. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  42. Sanders IA, Heppell CM, Cotton JA, Wharton G, Hildrew AG, Flowers EJ et al (2007) Emissions of methane from chalk streams has potential implications for agricultural practices. Freshwater Biol 52:1176–1186

    Article  CAS  Google Scholar 

  43. Sanz JL, Rodríguez N, Díaz EE, Amils R (2011) Methanogenesis in the sediments of Rio Tinto, an extreme acidic river. Environ Microbiol 13:2336–2341

    Article  PubMed  CAS  Google Scholar 

  44. Schindler JE, Krabbenhoft DP (1998) The hyporheic zone as a source of dissolved organic carbon and carbon gases to a temperate forested stream. Biogeochemistry 43:157–174

    Article  CAS  Google Scholar 

  45. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB et al (2009) Introducing MOTHUR: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  46. Schwarz JIK, Eckert W, Conrad R (2007) Community structure of Archaea and Bacteria in a profundal lake sediment Lake Kinneret (Israel). Syst Appl Microbiol 30:239–254

    Article  PubMed  CAS  Google Scholar 

  47. 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 54:697–704

    Article  PubMed  Google Scholar 

  48. Takezaki N, Rzhetsky A, Nei M (2004) Phylogenetic test of the molecular clock and linearized trees. Mol Biol Evol 12:823–833

    Google Scholar 

  49. Tamura KNM, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 101:11030–11035

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  50. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Bio Evol 28:2731–2739

    Article  CAS  Google Scholar 

  51. 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 232:153–163

    Article  PubMed  CAS  Google Scholar 

  52. Watanabe T, Hosen Y, Agbisit R, Llorca L, Fujita D, Asakawa S et al (2010) Changes in community structure and transcriptional activity of methanogenic archaea in a paddy field soil brought about by a water-saving practice—Estimation by PCR-DGGE and qPCR of 16S rDNA and 16S rRNA. 19th World Congress of Soil Solutions for a Changing World. Brisbane, Australia, pp 5–8

    Google Scholar 

  53. 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 38:11–20

    Article  CAS  Google Scholar 

  54. Wilcock RJ, Sorrell BK (2008) Emissions of greenhouse gases CH4 and N2O from low gradient streams in agriculturally developed catchments. Water Air Soil Poll 188:155–170

    Article  CAS  Google Scholar 

  55. Wilms R, Kopke B, Sass H, Chang TS, Cypionka H, Engelen B (2006) Deep biosphere-related bacteria within the subsurface of tidal flat sediments. Environ Microbiol 8:709–719

    Article  PubMed  CAS  Google Scholar 

  56. Wright ADG, Pimm C (2003) Improved strategy for presumptive identification of methanogens using 16S riboprinting. J Microbiol Methods 55:337–349

    Article  PubMed  CAS  Google Scholar 

  57. Wright ADG, Auckland CH, Lynn DH (2007) Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada. Appl Environ Microbiol 73:4206–4210

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  58. Wright ADG, Ma X, Obispo NE (2008) Methanobrevibacter phylotypes are the dominant methanogens in sheep from Venezuela. Microb Ecol 56:390–394

    Article  PubMed  Google Scholar 

  59. Xingqing Z, Liuyan Y, Zhenyang Y, Naiying P, Lin X, Daqiang Y et al (2008) Characterization of depth-related microbial communities in lake sediment by denaturing gradient gel electrophoresis of amplified 16S rRNA fragments. J Environ Sci 20:224–230

    Article  Google Scholar 

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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.

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Authors and Affiliations

  1. Laboratory of Aquatic Microbial Ecology, Department of Ecology and Environmental Sciences, Faculty of Science, Palacky University, Šlechtitelů 11, 783 71, Olomouc, Czech Republic

    Prem Prashant Chaudhary, Lenka Brablcová, Iva Buriánková, Adam Bednařík & Martin Rulík

  2. Department of Animal Science, University of Vermont, 570 Main Street, Burlington, VT, 05405, USA

    André-Denis G. Wright

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  1. Prem Prashant Chaudhary
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  2. André-Denis G. Wright
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Correspondence to Prem Prashant Chaudhary.

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Chaudhary, P.P., Wright, AD.G., Brablcová, L. et al. Dominance of Methanosarcinales Phylotypes and Depth-Wise Distribution of Methanogenic Community in Fresh Water Sediments of Sitka Stream from Czech Republic. Curr Microbiol 69, 809–816 (2014). https://doi.org/10.1007/s00284-014-0659-8

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