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

Applied and Environmental Microbiology

Volumn 63, Issue 12, 1997, Pages 4729-4733

  Munson, Mark A ^a,b   Nedwell, David B ^b   Embley, T Martin ^a  

^a DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^b UNIVERSITY OF ESSEX   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN; SULFATE;

PHYLOGENY; SALT MARSH; SEDIMENT; TIDAL CREEK;

ARTICLE; GENE SEQUENCE; GENETIC VARIABILITY; METHANOGENESIS; MINERALIZATION; PHYLOGENY; SEASHORE; SEDIMENT;

ARCHAEA; CRENARCHAEOTA; EURYARCHAEOTA; MARINE GROUP II; METHANOBACTERIUM; METHANOCOCCOIDES; METHANOCOCCUS; METHANOCULLEUS; METHANOGENIUM; METHANOLOBUS;

EID: 0030831861     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.63.12.4729-4733.1997     Document Type: Article

References (49)

1. Abram, J. W., and D. B. Nedwell. 1978. Hydrogen as a substrate for methanogenesis and sulfate reduction in anaerobic saltmarsh sediment. Arch. Microbiol. 117:93-97.
2. Abram, J. W., and D. B. Nedwell. 1978. Inhibition of methanogenesis by sulfate reducing bacteria competing for transferred hydrogen. Arch. Microbiol. 117:89-92.
3. Banat, I. M., E. B. Lindstrom, and D. B. Nedwell. 1981. Evidence for coexistance of two distinct functional groups of sulfate-reducing bacteria in salt marsh sediment. Appl. Environ. Microbiol. 42:985-992.
4. Banat, I. M., D. B. Nedwell, and M. T. Balba. 1983. Stimulation of methanogenesis by slurries of saltmarsh sediment after the addition of molybdate to inhibit sulfate-reducing bacteria. J. Gen. Microbiol. 129:123-129.
5. Capone, D. G., and R. P. Kiene. 1988. Comparison of microbial dynamics in marine and freshwater sediments: contrasts in anaerobic carbon catabolism. Limnol. Oceanogr. 33:725-749.
6. DeLong, E. F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89:5685-5689.
7. DeLong, E. F., K. Y. Wu, B. B. Prezelin, and R. V. M. Jovine. 1994. High abundance of Archaea in Antarctic marine picoplankton. Nature 371:695-697.
8. Don, R. H., P. T. Cox, B. J. Wainwright, K. Baker, and J. S. Mattick. 1991. "Touchdown" PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res. 19:4008.
9. Embley, T. M. 1991. The linear PCR reaction: a simple and robust method for sequencing amplified rRNA genes. Lett. Appl. Microbiol. 13:171-174.
10. Emblely, T. M., B. J. Finlay, R. H. Thomas, and P. L. Dyal. 1992 .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. 138:1479-1487.
11. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
12. Felsenstein, J. A. K. 1993. PHYLIP: phylogeny inference package. University of Washington, Seattle.
13. Franklin, M. J., W. J. Wiebe, and W. B. Whitman. 1988. Populations of methanogenic bacteria in a Georgia salt marsh. Appl. Environ. Microbiol. 54:1151-1157.
14. Fuhrman, J. A., K. McCallum, and A. A. Davis. 1992. Novel major archaebacterial group from marine plankton. Nature 356:148-149.
15. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63.
16. Good, I. J. 1953. The population frequencies of species and the estimation of population parameters. Biometrika 40:237-264.
17. Gottschal, J. C. 1985. Some reflections on microbial competiveness among heterotrophic bacteria. Antonie Leeuwenhoek 51:473-494.
18. Holben, W. E., J. K. Jansson, B. K. Chelm, and J. M. Tiedje. 1988. DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl. Environ. Microbiol. 54:703-711.
19. Jones, W. J., D. P. Nagel, and W. B. Whitman. 1987. Methanogens and the diversity of the archaebacteria. Microbiol. Rev. 51:135-177.
20. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules, p. 21-32. In H. N. Munro (ed.), Mammalian protein metabolism. Academic Press, New York, N.Y.
21. King, G. M. 1984. Utilization of hydrogen, acetate, and "noncompetitive" substrates by methanogenic bacteria in marine sediments. Geomicrobiol. J. 3:275-306.
22. Kusukawa, N., T. Uemori, K. Asada, and I. Kato. 1990. Rapid and reliable protocol for direct sequencing of material amplified using the polymerase chain reaction. BioTechniques 9:66-72.
23. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115-176. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons, Chichester, United Kingdom.
24. Mah, R. A., and D. A. Kuhn. 1984. Transfer of the type species of the genus Methanococcus to the genus Methanosarcina, naming it Methanosarcina mazei (Barker 1936) comb. nov. et emend. and conservation of the genus Methanococcus (Approved Lists 1980) with Methanococcus vannielii (Approved Lists 1980) as the type species. Int. J. Syst. Bacteriol. 34:263-265.
25. Maidak, B. L., N. Larsen, M. J. McCaughey, R. Overbeek, G. J. Olsen, K. Fogel, J. Blandy, and C. R. Woese. 1994. The ribosomal database project. Nucleic Acids Res. 22:3485-3487.
26. Martens, C. S., and R. A. Berner. 1974. Methane production in the interstitial waters of sulfate-depleted marine sediments. Science 185:1167-1169.
27. McInerney, J. O., M. Wilkinson, J. Patching, T. M. Embley, and R. Powell. 1995. Recovery and phylogenetic analysis of novel archaeal rRNA sequences from a deep-sea deposit feeder. Appl. Environ. Microbiol. 61:1646-1648.
28. More, M. I., J. B. Herrick, M. C. Silva, W. C. Ghiorse, and E. L. Madsen. 1994. Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl. Environ. Microbiol. 60:157-1580.
29. Mullins, T. D., T. B. Britschgi, R. L. Krest, and S. J. Giovannoni. 1995. Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol. Oceanogr. 40:148-158.
30. 29a. Munson, M. A., et al. Unpublished data.
31. Nedwell, D. B. 1984. The input and mineralization of organic carbon in anaerobic aquatic sediments. Adv. Microb. Ecol. 7:93-130.
32. Nedwell, D. B., and J. W. Abram. 1978. Bacterial sulfate reduction in relation to sulfur geochemistry in two contrasting areas of saltmarsh sediment. Estuar. Coast. Mar. Sci. 6:341-351.
33. Nedwell, D. B., and I. M. Banat. 1981. Hydrogen as an electron donor for sulfate-reducing bacteria in slurries of salt marsh sediment. Microb. Ecol. 7:305-313.
34. Oremland, R. S., L. M. Marsh, and S. Polcin. 1982. Methane production and simultaneous sulfate reduction in anoxic, salt marsh sediments. Nature 296: 143-145.
35. Oren, A. 1994. The ecology of extremely halophilic Archaea. FEMS Microbiol. Rev. 13:415-440.
36. Quesada, E., A. Ventosa, F. Rodriguez-Valera, and A. Ramos-Cormenzana. 1982. Types and properties of some bacteria from hypersaline soils. J. Appl. Bacteriol. 53:155-161.
37. Rodriguez-Valera, F., F. Ruiz-Berraquero, and A. Ramos-Cormenzana. 1979. Isolation of extreme halophiles from seawater. Appl. Environ. Microbiol. 38:164-165.
38. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
39. Schmidt, T. M., E. F. DeLong, and N. R. Pace. 1991. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173:4371-4378.
40. Schonheit, P., J. K. Kristjansson, and R. K. Thauer. 1982. Kinetic mechanism for the ability of sulfate reducers to out-compete methanogens for acetate. Arch. Microbiol. 132:285-288.
41. Selenska, S., and W. Klingmüller. 1991. DNA recovery and direct detection of Tn5 sequences from soil. Lett. Appl. Microbiol. 13:21-24.
42. Senior, E., E. B. Lindstrom, I. Banat, and D. B. Nedwell. 1982. Sulfate reduction and methanogenesis in the sediment of a saltmarsh on the east coast of the United Kingdom. Appl. Environ. Microbiol. 43:987-996.
43. Sowers, K. R., S. F. Baron, and J. G. Ferry. 1984. Mathanosarcina acetivorans sp. nov., an acetotrophic methane-producing bacterium isolated from marine sediments. Appl. Environ. Microbiol. 47:971-978.
44. Stackebrandt, E., and B. M. Goebel. 1994. Taxonomic note: a place for DNA:DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. System. Bacteriol. 44:846-849.
45. Tsai, Y.-L., and B. H. Olson. 1991. Rapid method for direct extraction of DNA from soil and sediments. Appl. Environ. Microbiol. 57:1070-1074.
46. Wagner, A., N. Blackstone, P. Cartwright, M. Dick, B. Misof, P. Snow, G. P. Wagner, J. Bartels, M. Murtha, and J. Pendleton. 1994. Surveys of gene families using polymerase chain reaction: PCR selection and PCR drift. Syst. Biol. 43:250-261.
47. Whitman, W. B., T. L. Bowen, and D. R. Boone. 1991. The methanogenic bacteria, p. 717-768. In A. Balows et al. (ed.), The prokaryotes. Springer-Verlag, New York, N.Y.
48. Winfrey, M. R., and D. M. Ward. 1983. Substrates for sulfate reduction and methane production in intertidal sediments. Appl. Environ. Microbiol. 45: 193-199.
49. Winfrey, M. R., and J. G. Zeikus. 1977. Effect of sulfate on carbon and electron flow during microbial methanogenesis in freshwater sediments. Appl. Environ. Microbiol. 33:275-281.