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Volume 2015 (2015), Article ID 563414, 9 pages
http://dx.doi.org/10.1155/2015/563414
Research Article

Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences

1Department of Biotechnology, Assam University, Silchar, Assam 788011, India
2School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India

Received 8 June 2015; Revised 26 August 2015; Accepted 30 August 2015

Academic Editor: Derek Caetano-Anolles

Copyright © 2015 Shailendra Yadav et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. G. Yvon-Durocher, A. P. Allen, D. Bastviken et al., “Methane fluxes show consistent temperature dependence across microbial to ecosystem scales,” Nature, vol. 507, no. 7493, pp. 488–491, 2014. View at Publisher · View at Google Scholar · View at Scopus
  2. S. D. Bridgham, H. Cadillo-Quiroz, J. K. Keller, and Q. Zhuang, “Methane emissions from wetlands: biogeochemical, microbial, and modeling perspectives from local to global scales,” Global Change Biology, vol. 19, no. 5, pp. 1325–1346, 2013. View at Publisher · View at Google Scholar · View at Scopus
  3. J. T. Houghton, Y. Ding, D. J. Griggs et al., Climate Change 2001: The Scientific Basis, vol. 881, Cambridge University Press, Cambridge, Mass, USA, 2001.
  4. S. Solomon, Climate Change 2007—The Physical Science Basis: Working Group I Contribution to the Fourth Assessment Report of the IPCC, vol. 4, Cambridge University Press, Cambridge, UK, 2007.
  5. R. Angel, P. Claus, and R. Conrad, “Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions,” The ISME Journal, vol. 6, no. 4, pp. 847–862, 2012. View at Publisher · View at Google Scholar · View at Scopus
  6. A. R. Daquiado, K. M. Cho, T. Y. Kim, S. C. Kim, H.-H. Chang, and Y. B. Lee, “Methanogenic archaea diversity in Hanwoo (Bos taurus coreanae) rumen fluid, rectal dung, and barn floor manure using a culture-independent method based on mcrA gene sequences,” Anaerobe, vol. 27, pp. 77–81, 2014. View at Publisher · View at Google Scholar · View at Scopus
  7. R. S. Oremland, “Biogeochemistry of methanogenic bacteria,” in Biology of Anaerobic Microorganisms, pp. 641–705, John Wiley & Sons, 1988. View at Google Scholar
  8. S. H. Zinder, “Physiological ecology of methanogens,” in Methanogenesis, pp. 128–206, Springer, Berlin, Germany, 1993. View at Google Scholar
  9. J.-L. Garcia, B. K. C. Patel, and B. Ollivier, “Taxonomic, phylogenetic, and ecological diversity of methanogenic Archaea,” Anaerobe, vol. 6, no. 4, pp. 205–226, 2000. View at Publisher · View at Google Scholar · View at Scopus
  10. É. Bapteste, C. Brochier, and Y. Boucher, “Higher-level classification of the Archaea: evolution of methanogenesis and methanogens,” Archaea, vol. 1, no. 5, pp. 353–363, 2005. View at Publisher · View at Google Scholar · View at Scopus
  11. J. N. Reeve, J. Nölling, R. M. Morgan, and D. R. Smith, “Methanogenesis: genes, genomes, and who's on first?” Journal of Bacteriology, vol. 179, no. 19, pp. 5975–5986, 1997. View at Google Scholar
  12. R. K. Thauer, A.-K. Kaster, H. Seedorf, W. Buckel, and R. Hedderich, “Methanogenic archaea: ecologically relevant differences in energy conservation,” Nature Reviews Microbiology, vol. 6, no. 8, pp. 579–591, 2008. View at Publisher · View at Google Scholar · View at Scopus
  13. C. C. Mitigation, IPCC Special Report on Renewable Energy Sources and Climate Change Mitigation, 2011.
  14. D. Mayumi, J. Dolfing, S. Sakata et al., “Carbon dioxide concentration dictates alternative methanogenic pathways in oil reservoirs,” Nature Communications, vol. 4, article 1998, 2013. View at Publisher · View at Google Scholar · View at Scopus
  15. S. Gupta, N. Choudhary, and B. J. Alappat, “Bioreactor landfill for MSW disposal in Delhi,” in Proceedings of the International Conference on Sustainable Solid Waste Management, Chennai, India, September 2007.
  16. M. Rawat and A. Ramanathan, “Assessment of methane flux from municipal solid waste (MSW) landfill areas of Delhi, India,” Journal of Environmental Protection, vol. 2, no. 4, pp. 399–407, 2011. View at Publisher · View at Google Scholar
  17. V. Talyan, R. P. Dahiya, S. Anand, and T. R. Sreekrishnan, “Quantification of methane emission from municipal solid waste disposal in Delhi,” Resources, Conservation and Recycling, vol. 50, no. 3, pp. 240–259, 2007. View at Publisher · View at Google Scholar · View at Scopus
  18. L. B. Hansen, K. Finster, H. Fossing, and N. Iversen, “Anaerobic methane oxidation in sulfate depleted sediments: effects of sulfate and molybdate additions,” Aquatic Microbial Ecology, vol. 14, no. 2, pp. 195–204, 1998. View at Publisher · View at Google Scholar · View at Scopus
  19. A. A. Bloom, P. I. Palmer, A. Fraser, S. R. David, and C. Frankenberg, “Large-scale controls of methanogenesis inferred from methane and gravity spaceborne data,” Science, vol. 327, no. 5963, pp. 322–325, 2010. View at Publisher · View at Google Scholar · View at Scopus
  20. V. Singh and A. Mittal, “Toxicity analysis and public health aspects of municipal landfill leachate: a case study of Okhla Landfill, Delhi,” in Proceedings of the 8th World Wide Workshop for Young Environmental Scientists WWW-YES 2009: Urban Waters: Resource or Risks? 2–5 June 2009, 2011.
  21. D. Liu, W. Ding, Z. Jia, and Z. Cai, “The impact of dissolved organic carbon on the spatial variability of methanogenic archaea communities in natural wetland ecosystems across China,” Applied Microbiology and Biotechnology, vol. 96, no. 1, pp. 253–263, 2012. View at Publisher · View at Google Scholar · View at Scopus
  22. B. P. Walter, M. Heimann, R. D. Shannon, and J. R. White, “A process-based model to derive methane emissions from natural wetlands,” Geophysical Research Letters, vol. 23, no. 25, pp. 3731–3734, 1996. View at Publisher · View at Google Scholar
  23. L. S. Chasar, J. P. Chanton, P. H. Glaser, and D. I. Siegel, “Methane concentration and stable isotope distribution as evidence of rhizospheric processes: Comparison of a fen and bog in the glacial Lake Agassiz Peatland complex,” Annals of Botany, vol. 86, no. 3, pp. 655–663, 2000. View at Publisher · View at Google Scholar · View at Scopus
  24. G. B. Avery Jr., R. D. Shannon, J. R. White, C. S. Martens, and M. J. Alperin, “Controls on methane production in a tidal freshwater estuary and a peatland: methane production via acetate fermentation and CO2 reduction,” Biogeochemistry, vol. 62, no. 1, pp. 19–37, 2003. View at Publisher · View at Google Scholar · View at Scopus
  25. L.-N. Huang, Y.-Q. Chen, H. Zhou, S. Luo, C.-Y. Lan, and L.-H. Qu, “Characterization of methanogenic Archaea in the leachate of a closed municipal solid waste landfill,” FEMS Microbiology Ecology, vol. 46, no. 2, pp. 171–177, 2003. View at Publisher · View at Google Scholar · View at Scopus
  26. W. Laloui-Carpentier, T. Li, V. Vigneron, L. Mazéas, and T. Bouchez, “Methanogenic diversity and activity in municipal solid waste landfill leachates,” Antonie van Leeuwenhoek, vol. 89, no. 3-4, pp. 423–434, 2006. View at Publisher · View at Google Scholar · View at Scopus
  27. L. M. Steinberg and J. M. Regan, “Phylogenetic comparison of the methanogenic communities from an acidic, oligotrophic fen and an anaerobic digester treating municipal wastewater sludge,” Applied and Environmental Microbiology, vol. 74, no. 21, pp. 6663–6671, 2008. View at Publisher · View at Google Scholar · View at Scopus
  28. Q. Ban, J. Li, L. Zhang, Y. Zhang, and A. K. Jha, “Phylogenetic diversity of methanogenic archaea and kinetics of methane production at slightly acidic conditions of an anaerobic sludge,” International Journal of Agriculture and Biology, vol. 15, no. 2, pp. 347–351, 2013. View at Google Scholar · View at Scopus
  29. S. G. Tringe and E. M. Rubin, “Metagenomics: DNA sequencing of environmental samples,” Nature Reviews Genetics, vol. 6, no. 11, pp. 805–814, 2005. View at Publisher · View at Google Scholar · View at Scopus
  30. R. D. Bardgett and W. H. van der Putten, “Belowground biodiversity and ecosystem functioning,” Nature, vol. 515, no. 7528, pp. 505–511, 2014. View at Publisher · View at Google Scholar · View at Scopus
  31. N. R. Pace, “New perspective on the natural microbial world: molecular microbial ecology,” ASM News, vol. 62, no. 9, pp. 463–470, 1996. View at Google Scholar
  32. J. L. Kirk, L. A. Beaudette, M. Hart et al., “Methods of studying soil microbial diversity,” Journal of Microbiological Methods, vol. 58, no. 2, pp. 169–188, 2004. View at Publisher · View at Google Scholar · View at Scopus
  33. R. I. Amann, W. Ludwig, and K.-H. Schleifer, “Phylogenetic identification and in situ detection of individual microbial cells without cultivation,” Microbiological Reviews, vol. 59, no. 1, pp. 143–169, 1995. View at Google Scholar · View at Scopus
  34. M. Keller and K. Zengler, “Tapping into microbial diversity,” Nature Reviews Microbiology, vol. 2, no. 2, pp. 141–150, 2004. View at Publisher · View at Google Scholar · View at Scopus
  35. Y. F. Cheng, S. Y. Mao, J. X. Liu, and W. Y. Zhu, “Molecular diversity analysis of rumen methanogenic Archaea from goat in eastern China by DGGE methods using different primer pairs,” Letters in Applied Microbiology, vol. 48, no. 5, pp. 585–592, 2009. View at Publisher · View at Google Scholar · View at Scopus
  36. A.-D. G. Wright and C. Pimm, “Improved strategy for presumptive identification of methanogens using 16S riboprinting,” Journal of Microbiological Methods, vol. 55, no. 2, pp. 337–349, 2003. View at Publisher · View at Google Scholar
  37. P. Ghosh, A. Gupta, and I. S. Thakur, “Combined chemical and toxicological evaluation of leachate from municipal solid waste landfill sites of Delhi, India,” Environmental Science and Pollution Research, vol. 22, no. 12, pp. 9148–9158, 2015. View at Publisher · View at Google Scholar · View at Scopus
  38. S. Roy and A. Gupta, “Water quality assessment of river barak and tributaries in Assam, India,” Pollution Research, vol. 31, no. 3, pp. 445–450, 2012. View at Google Scholar · View at Scopus
  39. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990. View at Publisher · View at Google Scholar · View at Scopus
  40. K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, “MEGA6: molecular evolutionary genetics analysis version 6.0,” Molecular Biology and Evolution, vol. 30, no. 12, pp. 2725–2729, 2013. View at Publisher · View at Google Scholar · View at Scopus
  41. M. Kimura, “A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences,” Journal of Molecular Evolution, vol. 16, no. 2, pp. 111–120, 1980. View at Publisher · View at Google Scholar · View at Scopus
  42. T. Watanabe, M. Kimura, and S. Asakawa, “Diversity of methanogenic archaeal communities in Japanese paddy field ecosystem, estimated by denaturing gradient gel electrophoresis,” Biology and Fertility of Soils, vol. 46, no. 4, pp. 343–353, 2010. View at Publisher · View at Google Scholar · View at Scopus
  43. G. Borrel, H. M. B. Harris, W. Tottey et al., “Genome sequence of ‘Candidatus Methanomethylophilus alvus’ Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens,” Journal of Bacteriology, vol. 194, no. 24, pp. 6944–6945, 2012. View at Publisher · View at Google Scholar · View at Scopus
  44. H. Juottonen, Archaea, Bacteria, and methane production along environmental gradients in fens and bogs [Ph.D. thesis], University of Helsinki, Helsinki, Finland, 2008.
  45. G. Borrel, P. W. O'Toole, H. M. B. Harris, P. Peyret, J.-F. Brugère, and S. Gribaldo, “Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis,” Genome Biology and Evolution, vol. 5, no. 10, pp. 1769–1780, 2013. View at Publisher · View at Google Scholar · View at Scopus
  46. V. Iverson, R. M. Morris, C. D. Frazar, C. T. Berthiaume, R. L. Morales, and E. V. Armbrust, “Untangling genomes from metagenomes: revealing an uncultured class of marine euryarchaeota,” Science, vol. 335, no. 6068, pp. 587–590, 2012. View at Publisher · View at Google Scholar · View at Scopus
  47. K. G. Lloyd, L. Schreiber, D. G. Petersen et al., “Predominant archaea in marine sediments degrade detrital proteins,” Nature, vol. 496, no. 7444, pp. 215–218, 2013. View at Publisher · View at Google Scholar · View at Scopus
  48. I. Anderson, R. Wirth, S. Lucas et al., “Complete genome sequence of Staphylothermus hellenicusP8T,” Standards in Genomic Sciences, vol. 5, no. 1, p. 12, 2011. View at Publisher · View at Google Scholar · View at Scopus
  49. C. Brochier-Armanet, S. Gribaldo, and P. Forterre, “Spotlight on the thaumarchaeota,” The ISME Journal, vol. 6, no. 2, pp. 227–230, 2012. View at Publisher · View at Google Scholar · View at Scopus
  50. P. E. Galand, H. Fritze, R. Conrad, and K. Yrjälä, “Pathways for methanogenesis and diversity of methanogenic archaea in three boreal peatland ecosystems,” Applied and Environmental Microbiology, vol. 71, no. 4, pp. 2195–2198, 2005. View at Publisher · View at Google Scholar · View at Scopus
  51. M. Ikenaga, S. Asakawa, Y. Muraoka, and M. Kimura, “Methanogenic archaeal communities in rice roots grown in flooded soil pots: estimation by PCR-DGGE and sequence analyses,” Soil Science and Plant Nutrition, vol. 50, no. 5, pp. 701–711, 2004. View at Publisher · View at Google Scholar · View at Scopus
  52. A. Spang, A. Poehlein, P. Offre et al., “The genome of the ammonia-oxidizing Candidatus nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations,” Environmental Microbiology, vol. 14, no. 12, pp. 3122–3145, 2012. View at Publisher · View at Google Scholar · View at Scopus
  53. P. P. Chaudhary, L. Brablcová, I. Buriánková, and M. Rulík, “Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments,” Applied Microbiology and Biotechnology, vol. 97, no. 17, pp. 7553–7562, 2013. View at Publisher · View at Google Scholar · View at Scopus
  54. A. V. Piterina and J. T. Pembroke, “Use of PCR-DGGE based molecular methods to analyse microbial community diversity and stability during the thermophilic stages of an ATAD wastewater sludge treatment process as an aid to performance monitoring,” ISRN Biotechnology, vol. 2013, Article ID 162645, 13 pages, 2013. View at Publisher · View at Google Scholar
  55. T. Watanabe, M. Kimura, and S. Asakawa, “Community structure of methanogenic archaea in paddy field soil under double cropping (rice-wheat),” Soil Biology and Biochemistry, vol. 38, no. 6, pp. 1264–1274, 2006. View at Publisher · View at Google Scholar · View at Scopus
  56. T. Watanabe, M. Kimura, and S. Asakawa, “Dynamics of methanogenic archaeal communities based on rRNA analysis and their relation to methanogenic activity in Japanese paddy field soils,” Soil Biology and Biochemistry, vol. 39, no. 11, pp. 2877–2887, 2007. View at Publisher · View at Google Scholar · View at Scopus
  57. L. Brablcová, I. Buriánková, P. Badurová, P. P. Chaudhary, and M. Rulík, “Methanogenic archaea diversity in hyporheic sediments of a small lowland stream,” Anaerobe, vol. 32, pp. 24–31, 2015. View at Publisher · View at Google Scholar · View at Scopus
  58. V. Mach, M. B. Blaser, P. Claus, P. P. Chaudhary, and M. Rulík, “Methane production potentials, pathways, and communities of methanogens in vertical sediment profiles of river Sitka,” Frontiers in Microbiology, vol. 6, article 506, 2015. View at Publisher · View at Google Scholar
  59. G. Muyzer, “DGGE/TGGE a method for identifying genes from natural ecosystems,” Current Opinion in Microbiology, vol. 2, no. 3, pp. 317–322, 1999. View at Publisher · View at Google Scholar · View at Scopus
  60. G. Muyzer, E. C. De Waal, and A. G. Uitterlinden, “Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA,” Applied and Environmental Microbiology, vol. 59, no. 3, pp. 695–700, 1993. View at Google Scholar · View at Scopus
  61. S. J. Macnaughton, J. R. Stephen, A. D. Venosa, G. A. Davis, Y.-J. Chang, and D. C. White, “Microbial population changes during bioremediation of an experimental oil spill,” Applied and Environmental Microbiology, vol. 65, no. 8, pp. 3566–3574, 1999. View at Google Scholar · View at Scopus
  62. Y. Yu, C. Lee, J. Kim, and S. Hwang, “Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction,” Biotechnology and Bioengineering, vol. 89, no. 6, pp. 670–679, 2005. View at Publisher · View at Google Scholar · View at Scopus