A phylogenetic analysis of microbial communities associated with methane hydrate containing marine fluids and sediments in the Cascadia margin (ODP site 892B)

FEMS Microbiology Letters

Volumn 177, Issue 1, 1999, Pages 101-108

  Bidle, Kelly A ^a   Kastner, Miriam ^b   Bartlett, Douglas H ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b GEOSCIENCES RESEARCH DIVISION   (United States)

Author keywords

Crenarchaeota; Gas hydrate; rDNA sequencing; Sulfate reducer

Indexed keywords

METHANE; RIBOSOME DNA; SULFATE;

ARTICLE; CRENARCHAEOTA; DNA SEQUENCE; GAS; MARINE ENVIRONMENT; METHANOBACTERIUM; METHANOTROPHIC BACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEDIMENT;

CRENARCHAEOTA;

EID: 0032774189     PISSN: 03781097     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1097(99)00297-9     Document Type: Article

References (32)

1. Kvenvolden, K.A. (1998) A primer on the geological occurrence of gas hydrate. In : Gas Hydrates : Relevance to World Margin Stability and Climate Change (Henriet, J.-P. and Mienert, J., Eds.), pp. 39-80. The Geological Society, London.
2. Hyndman, R.D. (1992) 'Ice' beneath the deep sea: studies of methane hydrate layers beneath the continental slope off Vancouver Island. Geosc. Can. 19, 21-26.
3. Alperin, M.J. and Reeburgh, W.S. (1985) Inhibition experiments on anaerobic methane oxidation. Appl. Environ. Microbiol. 50, 940-945.
4. Cragg, B.A., Parkes, R.J., Fry, J.C., Weightman, A.J., Rochelle, P.A. and Maxwell, J.R. (1996) Bacterial populations and processes in sediments containing gas hydrates (ODP leg 146: Cascadia margin). Earth Planet. Sci. Lett. 139, 497-507.
5. Hoehler, T.M., Alperin, M.J., Albert, D.B. and Martens, C.S. (1994) Field and laboratory studies of methane oxidation in an anoxic marine sediment : evidence for a methanogen-sulfate reducer consortium. Global Biogeochem. Cycles 8, 451-463.
6. Iversen, N. and Jorgenssen, B. B. (1985) Anaerobic methane oxidation rates at the sulfate-methane transition in marine sediments from Kattegat and Skagerrak (Denmark). Limnol. Oceanogr. 30, 944-955.
7. Masuzawa, T., Handa, N., Kitagawa, H. and Kusakabe, M. (1992) Sulfate reduction using methane in sediments beneath a bathyal 'cold seep' giant clam community off Hatsushima Island, Sagami Bay, Japan. Earth Planet. Sci. Lett. 110, 39-50.
8. Sassen, R., MacDonald, I.R., Guinaso Jr., N.L., Joye, S., Requejo, A.G., Sweet, S.T., Alcala-Herrera, J., DeFreitas, D.A. and Schink, D.R. (1998) Bacterial methane oxidation in sea-floor gas hydrate: significance to life in extreme environments. Geology 26, 851-854.
9. Schink, B. (1997) Energetics of syntrophic cooperation in methanogenic degradation. Microbiol. Mol. Biol. Rev. 61, 262-280.
10. Davis, J.B. and Yarbrough, H.E. (1966) Anaerobic oxidation of hydrocarbons by Desulfovibrio desulfuricans. Chem. Geol. 1, 137-144.
11. Zehnder, A.J.B. and Brock, T.J. (1979) Methane formation and methane oxidation by methanogenic bacteria. J. Bacteriol. 137, 420-432.
12. Kulm, L.D., Duess, E., Moore, J.C., Carson, B., Lewis, B.T., Ritger, S.D., Kadko, D.C., Thornburg, T.M., Embley, R.W., Rugh, W.D., Massoth, G.J., Langseth, M.G., Cochrane, G.R. and Scamman, R.L. (1986) Oregon subduction zone: venting, fauna, and carbonates. Science 231, 561-566.
13. Zehnder, A.J.B. and Brock, T.D. (1980) Anaerobic methane oxidation : occurrence and ecology. Appl. Environ. Microbiol. 39, 194-204.
14. Kastner, M., Sample, J.C., Whiticar, M.J., Hovland, M., Cragg, B.A. and Parkes, J.R. (1995) Relation between pore fluid chemistry and gas hydrates associated with bottom-simulating reflectors at the Cascadia margin, sites 889 and 892. In: Proc. Ocean Drilling Prog, Scientific Results, Leg 146 (Part 1) (Carson, B., Westbrook, G.K., Musgrave, R.J. and Suess, E., Eds.), pp. 175-187. College Station, TX.
15. Westbrook, G.K., Carson, B. and Musgrave, R.J. (1994) In: Proc. Ocean Drilling Prog. Initial Results, Leg 146. College Station, TX.
16. Kastner, M., Kvenvolden, K. and Lorenson, T.D. (1998) Chemistry, isotope composition, and origin of a methane-hydrogen sulfide hydrate at the Cascadia subduction zone. Earth Planet. Sci. Lett. 156, 173-183.
17. Barnes, S.P., Bradbrook, S.D., Cragg, B.A., Marchesi, J.R., Weightman, A.J., Fry, J.C. and Parkes, R.J. (1998) Isolation of sulfate-reducing bacteria from deep sediment layers of the Pacific Ocean. Geomicrobiol. J. 15, 67-83.
18. Hugenholtz, P., Goebel, B.M. and Pace, N.R. (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180, 4765-4774.
19. Zhou, J., Bruns, M.A. and Tiedje, J.M. (1996) DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62, 316-322.
20. Somerville, C.C., Knight, I.T., Straube, W.L. and Colwell, R.R. (1989) Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Appl. Environ. Microbiol. 55, 548-554.
21. DeLong, E.F. (1992) Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89, 5685-5689.
22. Amann, R.I., Stromley, J., Devereux, R., Key, R. and Stahl, D.A. (1992) Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms. Appl. Environ. Microbiol. 58, 614-623.
23. Hales, B.A., Edwards, C., Ritchie, D.A., Hall, G., Pickup, R.W. and 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.
24. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
25. Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
26. Kastner, M., Paytan, A., Volmer, M., Ransom, B., Bartlett, D., Bidle, K., Jannasch, H., Carson, B. and Jaeger, J. (1998) Methane advection, methane hydrate formation and possibly dissociation, at the Cascadia margin, off central Oregon. Trans. Am. Geophys. Union V 79, 419.
27. Stumm, W. and Morgan, J.J. (1981) Aquatic Chemistry, John Wiley and Sons, New York.
28. Gray, J.P. and Herwig, R.P. (1996) Phylogenetic analysis of the bacterial communities in marine sediments. Appl. Environ. Microbiol. 62, 4049-4059.
29. Rochelle, P.A., Cragg, B.A., Fry, J.C., Parkes, R.J. and Weightman, A.J. (1994) Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis. FEMS Microbiol. Ecol. 15, 215-226.
30. Finster, K., Liesack, W. and Thamdrup, B. (1998) Elemental sulfur and thiosulfate disproportionation by Desulfocapsa sulfoexigens sp. nov., a new anaerobic bacterium isolated from marine surface sediment. Appl. Environ. Microbiol. 64, 119-125.
31. Massana, R., Murray, A.E., Preston, C.M. and DeLong, E.F. (1997) Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara channel. Appl. Environ. Microbiol. 63, 50-56.
32. Davis, E.E., Becker, K., Wang, K. and Carson, B. (1995) Long-term observations of pressure and temperature in hole 892B, Cascadia Accretionary Prism. In: Proc. Ocean Drilling Prog., Scientific Results, Leg 146 (Part 1) (Carson, B., Westbrook, G.K., Musgrave, R.J. and Suess, E., Eds.), pp. 299-312. College Station, TX.