1887

Microbiology Society logo

Volume 148, Issue 11

The gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill

bThe GenBank accession numbers for the sequences reported in this paper are AF414034–AF414051 (see Fig. 2) and AF414007–AF414033 (environmental isolates in Fig. 3).

Free

Abstract

Inferred amino acid sequences of the methyl coenzyme-M reductase () gene from five different methanogen species were aligned and two regions with a high degree of homology flanking a more variable region were identified. Analysis of the DNA sequences from the conserved regions yielded two degenerate sequences from which a forward primer, a 32-mer, and a reverse primer, a 23-mer, could be derived for use in the specific PCR-based detection of methanogens. The primers were successfully evaluated against 23 species of methanogen representing all five recognized orders of this group of , generating a PCR product between 464 and 491 bp. Comparisons between the and 16S small subunit rRNA gene sequences using PHYLIP demonstrated that the tree topologies were strikingly similar. Methods were developed to enable the analysis of methanogen populations in landfill using the gene as the target. Two landfill sites were examined and 63 clones from a site in Mucking, Essex, and 102 from a site in Odcombe, Somerset, were analysed. Analysis revealed a far greater diversity in the methanogen population within landfill material than has been seen previously.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): detection , identification , MCR, methyl coenzyme-M reductase , methanogenic Archaea , methyl coenzyme-M reductase and OTU, operational taxonomic unit
© Microbiology Society
Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-148-11-3521
2002-11-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/micro/148/11/1483521a.html?itemId=/content/journal/micro/10.1099/00221287-148-11-3521&mimeType=html&fmt=ahah

References

  1. Allmansberger R, Bollschweiler C, Konheiser U, Muller B, Muth E, Pasti G., Klein A. 1986; Arrangement and expression of methyl CoM reductase genes in Methanococcus voltae . Syst Appl Microbiol 7:13–17
     [Google Scholar]
  2. Archer D. B., Peck M. W. 1989; The microbiology of methane production in landfills. In Microbiology of Extreme Environments and its Potential for Biotechnology pp 187–204 Edited by Costa M. S. Da., Duarte J. C., Williams R. A. D. London: Elsevier;
     [Google Scholar]
  3. Barlaz M. A. 1997; Microbial studies of landfills and anaerobic refuse decomposition. In Manual of Environmental Microbiology pp 541–557 Edited by Hurst C. J., Knudsen G. R., McInerney M. J., Stetzenbach L. D., Walter M. V. Washington, DC: American Society for Microbiology;
     [Google Scholar]
  4. Bidle K. A, Kastner M., Bartlett D. H. 1999; A phylogenetic analysis of microbial communities associated with methane hydrate containing marine fluids and sediments in the Cascadia margin (ODP site 892B). FEMS Microbiol Lett 177:101–108
     [Google Scholar]
  5. Bokranz M., Klein A. 1987; Nucleotide sequence of the methyl coenzyme M reductase gene cluster from Methanosarcina barkeri . Nucleic Acids Res 15:4350–4351
     [Google Scholar]
  6. Bokranz M, Baumner G, Allmansberger R, Ankel-Fuchs D., Klein A. 1988; Cloning and characterization of the methyl coenzyme M reductase genes from Methanobacterium thermoautotrophicum . J Bacteriol 170:568–577
     [Google Scholar]
  7. Boone D. R, Whitman W. B., Rouviere P. 1993; Diversity and taxonomy of methanogens. In Methanogenesis: Ecology, Physiology, Biochemistry and Genetics pp 35–80 Edited by Ferry J. G. New York: Chapman & Hall;
     [Google Scholar]
  8. Burggraf S, Stetter K. O, Rouviere P., Woese C. R. 1991; Methanopyrus kandleri : an archaeal methanogen unrelated to all other known methanogens. Syst Appl Microbiol 14:346–351
     [Google Scholar]
  9. Chandler D. P, Fredrickson J. K., Brockman F. J. 1997; Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol Ecol 6:475–482
     [Google Scholar]
  10. Compton T. 1990; Degenerate primers for DNA amplification. In PCR Protocols: a Guide to Methods and Applications pp 38–45 Edited by Innis M. A., Gelfand D. H., Sninisky J. J., White T. J. San Diego: Academic Press;
     [Google Scholar]
  11. Cram D. S, Sherf B. A, Libby R. T, Mattaliano R. J, Ramachandran K. L., Reeve J. N. 1987; Structure and expression of the genes, mcrBDCGA , which encode the subunits of component C of methyl coenzyme M reductase in Methanococcus vannielii . Proc Natl Acad Sci USA 84:3992–3996
     [Google Scholar]
  12. Felsenstein J. 1995 phylip (Phylogeny Inference Package) version 3.57c Seattle: Department of Genetics, University of Washington;
     [Google Scholar]
  13. Fielding E. R., Archer D. B. 1986; Microbiology of landfill. Identification of methanogenic bacteria and their enumeration. Inst Chem Eng Symp Ser 96:331–341
     [Google Scholar]
  14. Fielding E. R, Archer D. B, Conway de Macario E., Macario A. J. L. 1988; Isolation and characterization of methanogenic bacteria from landfills. Appl Environ Microbiol 54:835–836
     [Google Scholar]
  15. Finlay B. J., Fenchel T. 1991; An anaerobic protozoon, with symbiotic methanogens, living in municipal landfill material. FEMS Microbiol Ecol 85:169–180
     [Google Scholar]
  16. Gorris L. G, De Kok T. M, Kroon B. M, Van der Drfit C., Vogels G. D. 1988; Relationship between methanogenic cofactor content and maximum specific methanogenic activity of anaerobic granular sludges. Appl Environ Microbiol 54:1126–1130
     [Google Scholar]
  17. Grosskopf R, Janssen P. H., Liesack W. 1998; Diversity and structure of the methanogenic community in anoxic rice paddy soil microorganisms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl Environ Microbiol 64:960–969
     [Google Scholar]
  18. Grotenhuis J. T, Smit M, Plugge C. M, Xu Y. S, van Lammeren A. A, Stams A. J., Zehnder A. J. 1991; Bacteriological composition and structure of granular sludge adapted to different substrates. Appl Environ Microbiol 57:1942–1949
     [Google Scholar]
  19. Gupta R. S. 1998; Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria and eukaryotes. Microbiol Mol Biol Rev 62:1435–1491
     [Google Scholar]
  20. Hales B. A, Edwards C, Ritchie D. A, Hall G, Pickup R. W., Saunders J. R. 1996; Isolation and identification of methanogen-specific DNA from blanket bog peat by PCR amplification and sequence analysis. Appl Environ Microbiol 62:668–675
     [Google Scholar]
  21. Innis M. A., Gelfand D. H. 1990; Optimization of PCRs. In PCR Protocols: a Guide to Methods and Applications pp 3–12 Edited by Innis M. A., Gelfand D. H., Sninisky J. J., White T. J. San Diego: Academic Press;
     [Google Scholar]
  22. Ladapo J. A., Barlaz M. A. 1997; Isolation and characterization of refuse methanogens. J Appl Microbiol 82:751–758
     [Google Scholar]
  23. Lloyd D, Thomas K. L, Hayes A, Hill B, Hales B. A, Edwards C, Saunders J. R, Ritchie D. A., Upton M. 1998; Micro-ecology of peat: minimally invasive analysis using confocal laser scanning microscopy, membrane inlet mass spectrometry and PCR amplification of methanogen-specific gene sequences. FEMS Microbiol Ecol 25:179–188
     [Google Scholar]
  24. Lueders T, Chin K.-J, Conrad R., Friedrich M. 2001; Molecular analyses of methyl-coenzyme M reductase alpha-subunit ( mcrA ) gene in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environ Microbiol 3:194–204
     [Google Scholar]
  25. Luton P. E. 1996 A study of landfill methanogens PhD Thesis Liverpool John Moores University;
     [Google Scholar]
  26. Maule A, Luton P., Sharp R. 1994 A Microbiological and Chemical Study of the Brogborough Test Cells Oxfordshire, UK: Energy Technology Support Unit, Department of Trade and Industry;
     [Google Scholar]
  27. Moré M. I, Herrick J. B, Silva M. C, Ghiorse W. C., Madsen E. L. 1994; Quantitative cell lysis of indigenous microorganisms and rapid extraction of DNA from sediment. Appl Environ Microbiol 60:1572–1580
     [Google Scholar]
  28. Mori K, Yamamoto H, Kamagata Y, Hatsu M., Takamizawa K. 2000; Methanocalculus pumilus sp. nov., a heavy-metal-tolerant methanogen isolated from a waste-disposal site. Int J Syst Evol Microbiol 50:1723–1729
     [Google Scholar]
  29. Nercessian D, Upton M, Lloyd D., Edwards C. 1999; Phylogenetic analysis of peat bog methanogen populations. FEMS Microbiol Lett 173:425–429
     [Google Scholar]
  30. Ohkuma M, Noda S, Horikoshi K., Kudo T. 1995; Phylogeny of symbiotic methanogens in the gut of the termite Reticulitermes speratus . FEMS Microbiol Lett 134:45–50
     [Google Scholar]
  31. Page R. D. M. 1996; treeview: an application to display phylogenetic trees on personal computers. Comput Applic Biosci 12:357–358
     [Google Scholar]
  32. Peck M. W., Archer D. B. 1989; Methods for the quantification of methanogenic bacteria. Int Ind Biotechnol 9:5–12
     [Google Scholar]
  33. Polz M. F., Cavanaugh C. M. 1998; Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64:3724–3730
     [Google Scholar]
  34. Reeve J. N, Nolling J, Morgan R. M., Smith D. R. 1997; Methanogenesis: genes, genomes and who’s on first?. J Bacteriol 179:5975–5986
     [Google Scholar]
  35. Reysenbach A. L, Giver L. J, Wickham G. S., Pace N. R. 1992; Differential amplification of rRNA genes by polymerase chain reaction. Appl Environ Microbiol 58:3417–3418
     [Google Scholar]
  36. Sambrook J, Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
     [Google Scholar]
  37. Springer E, Sachs M. S, Woese C. R., Boone D. R. 1995; Partial gene sequences for the A subunit of methyl-coenzyme M reductase ( mcrI ) as a phylogenetic tool for the family Methanosarcinaceae . Int J Syst Bacteriol 45:554–559
     [Google Scholar]
  38. Suzuki M. T., Giovannoni S. J. 1996; Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625–630
     [Google Scholar]
  39. Thauer R. K. 1998; Biochemistry of methanogenesis: a tribute to Marjory Stephenson. 1998 Marjory Stephenson Prize Lecture. Microbiology 144:2377–2406
     [Google Scholar]
  40. Wasserfallen A, Nolling J, Pfister P, Reeve J., deMacario E. C. 2000; Phylogenetic analysis of 18 thermophilic Methanobacterium isolates supports the proposals to create a new genus, Methanothermobacter gen. nov., and to reclassify several isolates in three species, Methanothermobacter thermautotrophicus comb.nov., Methanothermobacter wolfeii comb. nov. and Methanothermobacter marburgensis sp. nov. Int J Syst Evol Microbiol 50:43–53
     [Google Scholar]
  41. Weil C. F, Cram D. S, Sherf B. A., Reeve J. N. 1988; Structure and comparative analysis of the genes encoding component C of methyl coenzyme M reductase in the extremely thermophilic archaebacterium Methanothermus fervidus . J Bacteriol 170:4718–4726
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-148-11-3521
Loading
The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfillbbThe GenBank accession numbers for the mcrA sequences reported in this paper are AF414034–AF414051 (see Fig. 2) and AF414007–AF414033 (environmental isolates in Fig. 3).
Microbiology 148, 3521 (2002); https://doi.org/10.1099/00221287-148-11-3521
/content/journal/micro/10.1099/00221287-148-11-3521
/content/journal/micro/10.1099/00221287-148-11-3521
Loading

Data & Media loading...

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error