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. 1997 Dec;63(12):4729–4733. doi: 10.1128/aem.63.12.4729-4733.1997

Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh.

M A Munson 1, D B Nedwell 1, T M Embley 1
PMCID: PMC168796  PMID: 9406392

Abstract

The Archaea present in salt marsh sediment samples from a tidal creek and from an adjacent area of vegetative marshland, both of which showed active methanogenesis and sulfate reduction, were sampled by using 16S rRNA gene libraries created with Archaea-specific primers. None of the sequences were the same as reference sequences from cultured taxa, although some were closely related to sequences from methanogens previously isolated from marine sediments. A wide range of Euryarchaeota sequences were recovered, but no sequences from Methanococcus, Methanobacterium, or the Crenarchaeota were recovered. Clusters of closely related sequences were common and generally contained sequences from both sites, suggesting that some related organisms were present in both samples. Recovery of sequences closely related to those of methanogens such as Methanococcoides and Methanolobus, which can use substrates other than hydrogen, provides support for published hypotheses that such methanogens are probably important in sulfate-rich sediments and identifies some likely candidates. Sequences closely related to those of methanogens such as Methanoculleus and Methanogenium, which are capable of using hydrogen, were also discovered, in agreement with previous inhibitor and process measurements suggesting that these taxa are present at low levels of activity. More surprisingly, we recovered a variety of sequences closely related to those from different halophilic Archaea and a cluster of divergent sequences specifically related to the marine group II archaeal sequences recently shown by PCR and probing to have a cosmopolitan distribution in marine samples.

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Selected References

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  1. Abram J. W., Nedwell D. B. Hydrogen as a substrate for methanogenesis and sulphate reduction in anaerobic saltmarsh sediment. Arch Microbiol. 1978 Apr 27;117(1):93–97. doi: 10.1007/BF00689357. [DOI] [PubMed] [Google Scholar]
  2. Abram J. W., Nedwell D. B. Inhibition of methanogenesis by sulphate reducing bacteria competing for transferred hydrogen. Arch Microbiol. 1978 Apr 27;117(1):89–92. doi: 10.1007/BF00689356. [DOI] [PubMed] [Google Scholar]
  3. Banat I. M., Lindström E. B., Nedwell D. B., Balba M. T. Evidence for coexistence of two distinct functional groups of sulfate-reducing bacteria in salt marsh sediment. Appl Environ Microbiol. 1981 Dec;42(6):985–992. doi: 10.1128/aem.42.6.985-992.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. DeLong E. F. Archaea in coastal marine environments. Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5685–5689. doi: 10.1073/pnas.89.12.5685. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. DeLong E. F., Wu K. Y., Prézelin B. B., Jovine R. V. High abundance of Archaea in Antarctic marine picoplankton. Nature. 1994 Oct 20;371(6499):695–697. doi: 10.1038/371695a0. [DOI] [PubMed] [Google Scholar]
  6. Don R. H., Cox P. T., Wainwright B. J., Baker K., Mattick J. S. 'Touchdown' PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res. 1991 Jul 25;19(14):4008–4008. doi: 10.1093/nar/19.14.4008. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Embley T. M., Finlay B. J., Thomas R. H., Dyal P. L. The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont. J Gen Microbiol. 1992 Jul;138(7):1479–1487. doi: 10.1099/00221287-138-7-1479. [DOI] [PubMed] [Google Scholar]
  8. Embley T. M. The linear PCR reaction: a simple and robust method for sequencing amplified rRNA genes. Lett Appl Microbiol. 1991 Sep;13(3):171–174. doi: 10.1111/j.1472-765x.1991.tb00600.x. [DOI] [PubMed] [Google Scholar]
  9. Franklin M. J., Wiebe W. J., Whitman W. B. Populations of methanogenic bacteria in a georgia salt marsh. Appl Environ Microbiol. 1988 May;54(5):1151–1157. doi: 10.1128/aem.54.5.1151-1157.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Fuhrman J. A., McCallum K., Davis A. A. Novel major archaebacterial group from marine plankton. Nature. 1992 Mar 12;356(6365):148–149. doi: 10.1038/356148a0. [DOI] [PubMed] [Google Scholar]
  11. Giovannoni S. J., Britschgi T. B., Moyer C. L., Field K. G. Genetic diversity in Sargasso Sea bacterioplankton. Nature. 1990 May 3;345(6270):60–63. doi: 10.1038/345060a0. [DOI] [PubMed] [Google Scholar]
  12. Gottschal J. C. Some reflections on microbial competitiveness among heterotrophic bacteria. Antonie Van Leeuwenhoek. 1985;51(5-6):473–494. doi: 10.1007/BF00404494. [DOI] [PubMed] [Google Scholar]
  13. Holben William E., Jansson Janet K., Chelm Barry K., Tiedje James M. DNA Probe Method for the Detection of Specific Microorganisms in the Soil Bacterial Community. Appl Environ Microbiol. 1988 Mar;54(3):703–711. doi: 10.1128/aem.54.3.703-711.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Jones W. J., Nagle D. P., Jr, Whitman W. B. Methanogens and the diversity of archaebacteria. Microbiol Rev. 1987 Mar;51(1):135–177. doi: 10.1128/mr.51.1.135-177.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kusukawa N., Uemori T., Asada K., Kato I. Rapid and reliable protocol for direct sequencing of material amplified by the polymerase chain reaction. Biotechniques. 1990 Jul;9(1):66-8, 70, 72. [PubMed] [Google Scholar]
  16. Maidak B. L., Larsen N., McCaughey M. J., Overbeek R., Olsen G. J., Fogel K., Blandy J., Woese C. R. The Ribosomal Database Project. Nucleic Acids Res. 1994 Sep;22(17):3485–3487. doi: 10.1093/nar/22.17.3485. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Martens C. S., Berner R. A. Methane production in the interstitial waters of sulfate-depleted marine sediments. Science. 1974 Sep 27;185(4157):1167–1169. doi: 10.1126/science.185.4157.1167. [DOI] [PubMed] [Google Scholar]
  18. McInerney J. O., Wilkinson M., Patching J. W., Embley T. M., Powell R. Recovery and phylogenetic analysis of novel archaeal rRNA sequences from a deep-sea deposit feeder. Appl Environ Microbiol. 1995 Apr;61(4):1646–1648. doi: 10.1128/aem.61.4.1646-1648.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Moré M. I., Herrick J. B., Silva M. C., Ghiorse W. C., Madsen E. L. Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl Environ Microbiol. 1994 May;60(5):1572–1580. doi: 10.1128/aem.60.5.1572-1580.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Rodriguez-Valera F., Ruiz-Berraquero F., Ramos-Cormenzana A. Isolation of extreme halophiles from seawater. Appl Environ Microbiol. 1979 Jul;38(1):164–165. doi: 10.1128/aem.38.1.164-165.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
  22. Schmidt T. M., DeLong E. F., Pace N. R. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol. 1991 Jul;173(14):4371–4378. doi: 10.1128/jb.173.14.4371-4378.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Selenska S., Klingmüller W. DNA recovery and direct detection of Tn5 sequences from soil. Lett Appl Microbiol. 1991 Jul;13(1):21–24. doi: 10.1111/j.1472-765x.1991.tb00559.x. [DOI] [PubMed] [Google Scholar]
  24. Senior E., Lindström E. B., Banat I. M., Nedwell D. B. Sulfate reduction and methanogenesis in the sediment of a saltmarsh on the East coast of the United kingdom. Appl Environ Microbiol. 1982 May;43(5):987–996. doi: 10.1128/aem.43.5.987-996.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Sowers K. R., Baron S. F., Ferry J. G. Methanosarcina acetivorans sp. nov., an Acetotrophic Methane-Producing Bacterium Isolated from Marine Sediments. Appl Environ Microbiol. 1984 May;47(5):971–978. doi: 10.1128/aem.47.5.971-978.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Tsai Y. L., Olson B. H. Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol. 1991 Apr;57(4):1070–1074. doi: 10.1128/aem.57.4.1070-1074.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Winfrey M. R., Ward D. M. Substrates for sulfate reduction and methane production in intertidal sediments. Appl Environ Microbiol. 1983 Jan;45(1):193–199. doi: 10.1128/aem.45.1.193-199.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Winfrey M. R., Zeikus J. G. Effect of sulfate on carbon and electron flow during microbial methanogenesis in freshwater sediments. Appl Environ Microbiol. 1977 Feb;33(2):275–281. doi: 10.1128/aem.33.2.275-281.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]

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