Comparative Analysis of Methane-Oxidizing Archaea and Sulfate-Reducing Bacteria in Anoxic Marine Sediments

Applied and Environmental Microbiology

Volumn 67, Issue 4, 2001, Pages 1922-1934

  Orphan, V J ^a   Hinrichs, K U ^b   Ussler III, W ^a   Paull, C K ^a   Taylor, L T ^a   Sylva, S P ^b   Hayes, J M ^b   Delong, E F ^a  

^a MONTEREY BAY AQUARIUM RESEARCH INSTITUTE   (United States)

^b WOODS HOLE OCEANOGRAPHIC INSTITUTION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIPID; METHANE; RIBOSOME DNA; RNA 16S; SEA WATER; SULFATE;

ANAEROBIC GROWTH; ARCHAEBACTERIUM; ARTICLE; CLASSIFICATION; COMPARATIVE STUDY; DNA SEQUENCE; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; GRAM NEGATIVE ANAEROBIC BACTERIA; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; OXIDATION REDUCTION REACTION; PHYLOGENY; POLYMERASE CHAIN REACTION; SEDIMENT;

ANAEROBIOSIS; ARCHAEA; DNA, RIBOSOMAL; GEOLOGIC SEDIMENTS; IN SITU HYBRIDIZATION, FLUORESCENCE; LIPIDS; METHANE; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; SULFATES; SULFUR-REDUCING BACTERIA;

EID: 0035317030     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.67.4.1922-1934.2001     Document Type: Article

References (49)

1. Amann, R. I., W. Ludwig, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
2. Barry, J. P., R. E. Kochevar, and C. H. Baxter. 1997. The influence of pore-water chemistry and physiology on the distribution of vesicomyid clams at cold seeps in Monterey Bay: implications for patterns of chemosynthetic community organization. Limnol. Oceanogr. 42:318-328.
3. Bidle, K., M. Kastner, and D. H. Bartlett. 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.
4. Boetius, A., K. Ravenschlag, C. J. Schubert, D. Rickert, F. Widdel, A. Gieseke, R. Amann, B. B. Joørgensen, U. Witte, and O. Pfannkuche. 2000. Microscopic identification of a microbial consortium apparently mediating anaerobic methane oxidation above marine gas hydrate. Nature (London) 407:623-626.
5. Borowski, W., C. K. Paull, and W. Ussler. 1999. Global and local variations of interstitial sulfate gradients in deep-water, continental margin sediments: sensitivity to underlying methane and gas hydrates. Mar. Geol. 159:131-154.
6. Bowman, J., S. M. Rea, S. A. McCammon, and T. A. McMeekin. 2000. Diversity and community structure within anoxic sediment from marine salinity meromictic lakes and a coastal meromictic marine basin, Vestfold Hills, Eastern Antarctica. Environ. Microbiol. 2:227-237.
7. Burns, S. J. 1998. Carbon isotopic evidence for coupled sulfate reduction-methane oxidation in Amazon Fan sediments. Geochim. Cosmochim. Acta 62:797-804.
8. Cline, J. 1969. Spectropholometric determination of hydrogen sulphide in natural waters. Limnol. Oceanogr. 14:454-458.
9. DeLong, E. F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89:5685-5689.
10. Dowling, N. J. E., F. Widdel, and D. C. White. 1986. Phospholipid ester-linked fatty acid biomarkers of acetate-oxidizing sulphate-reducers and other sulphide-forming bacteria. J. Gen. Microbiol. 132:1815-1825.
11. Elvert, M., E. Suess, and M. J. Whiticar. 1999. Anaerobic methane oxidation associated with marine gas hydrates: superlight C-isotopes from saturated and unsaturated C20 and C25 irregular isoprenoids. Naturwissenschaften 86: 295-300.
12. Felsenstein, J. 1993. PHYLIP-Phylogeny inference package (version 3.5). Cladistics 5:164-166.
13. Franzmann, P. D., N. Springer, W. Ludwig, C. de Macario, and M. Rohde. 1992. A methanogenic bacterium from ACE Lake, Antarctica: Methanococcoides burtonii sp. nov. Syst. Appl. Microbiol. 15:573-582.
14. Gambacorta, A., A. Trincone, B. Nicolaus, and L. Lama. 1994. Unique features of lipids in Archaea. Syst. Appl. Microbiol. 16:518-527.
15. Glöckner, F., B. Fuchs, and R. Amann. 1999. Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl. Environ. Microbiol. 65:3721-3726.
16. Gray, J. P., and R. P. Herwig. 1996. Phylogenetic analysis of bacterial communities in marine sediments. Appl. Environ. Microbiol. 62:4049-4059.
17. Hansen, L. B., K. Finster, H. Fossing, and N. Iversen. 1998. Anaerobic methane oxidation in sulfate depleted sediments: effects of sulfate and molybdate additions. Aquat. Microb. Ecol. 14:195-204.
18. Hinrichs, K.-U., J. M. Hayes, S. P. Sylva, P. G. Brewer, and E. F. DeLong. 1999. Methane-consuming archaebacteria in marine sediments. Nature (London) 398:802-805.
19. Hinrichs, K.-U., R. E. Summons, V. J. Orphan, S. P. Sylva, and J. M. Hayes. 2000. Molecular and isotopic analysis of anaerobic methane-oxidizing communities in marine sediments. Org. Geochem. 31:1685-1701.
20. 1 compounds. Kluwer Academic Publishers Dordrecht, The Netherlands.
21. Hoehler, T. M., M. J. Alperin, D. B. Albert, and C. S. Martens. 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.
22. Huber, R., T. Wilharm, D. Huber, A. Trincone, S. Burggraf, R. Rachel, I. Rockinger, H. Fricke, and K. O. Stetter. 1992. Aquifex pyrophilus gen. nov., sp. nov., represents a novel group of marine hyperthermophilic hydrogenoxidizing bacteria. Syst. Appl. Microbiol. 15:340-351.
23. Iversen, N., and B. B. Jørgensen. 1985. Anaerobic methane oxidation rates at the sulfate-methane transition in marine sediments from Kattegat and Skagerrak (Denmark). Limnol. Oceanogr. 30:944-955.
24. Kaneda, T. 1991. Iso- and anteiso-fatty acids in bacteria: biosynthesis, function, and taxonomic significance. Microbiol. Rev. 55:288-302.
25. Langworthy, T. A., G. Holzer, J. G. Zeikus, and T. G. Tornabene. 1983. Iso- and anteiso-branched glycerol diethers of thermophilic anaerobe Thermodesulfotobacterium commune. Syst. Appl. Microbiol. 4:1-17.
26. Li, L., C. Kato, and K. Horikoshi. 1999. Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench. Mar. Biotechnol. 1:391-400.
27. 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 Acid Res. 22:3485-3487.
28. Martens, C. S., and R. A. Berner. 1977. Interstitial water chemistry of anoxic Long Island Sound sediments. 1. Dissolved gases. Limnol. Oceanogr. 22:10-25.
29. Munson, M. A., D. B. Nedwell, and T. M. Embley. 1997. Phylogenetic diversity of archaea in sediment samples from a coastal salt marsh. Appl. Environ. Microbiol. 63:4729-4733.
30. Pancost, R. D., J. S. Sinninghe Damste, S. de Lint, M. J. E. C. van der Maarel, J. C. Gottschal, and The Medinaut Shipboard Scientific Party, 2000. Biomarker evidence for widespread anaerobic methane oxidation in Mediterranean sediments by a consortium of methanogenic archaea and bacteria. Appl. Environ. Microbiol. 66:1126-1132.
31. Phelps, C., L. Kerkhof, and L. Young. 1998. Molecular characterization of a sulfate-reducing consortium which mineralizes benzene. FEMS Microb. Ecol. 27:269-279.
32. Ravenschlag, K., K. Sahm, C. Knoblauch, B. Jørgensen, and R. Amann. 2000. Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine Arctic sediments. Appl. Environ. Microbiol. 66: 3592-3602.
33. Ravenschlag, K., K. Sahm, J. Pernthaler, and R. Amann. 1999. High bacterial diversity in permanently cold marine sediments. Appl. Environ. Microbiol. 65:3982-3989.
34. Reeburgh, W. S. 1967. An improved interstitial water sampler. Limnol. Oceanogr. 12:163-165.
35. 1 compounds. Proceedings of the 7th International Symposium. American Society for Microbiology. Washington, D.C.
36. Santegoeds, C. M., L. R. Damgaard, G. Hesselink, J. Zopfi, P. Lens, G. Muyzer, and D. de Beer. 1999. Distribution of sulfate-reducing and methanogenic bacteria in anaerobic aggregates determined by microsensor and molecular analyses. Appl. Environ. Microbiol. 65:4618-4629.
37. Sekiguchi, Y., Y. Kamagata, K. Nakamura, A. Ohashi, and H. Harada. 1999. Fluorescence in situ hybridization using 16S rRNA-targeted oligonucleotides reveals localization of methanogens and selected uncultured bacteria in mesophilic and thermophilic sludge granules. Appl. Environ. Microbiol. 65: 1280-1288.
38. Suzuki, M., and S. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
39. Takai, K., and K. Horikoshi. 1999. Genetic diversity of Archaea in deep-sea hydrothermal vent environments. Genetics 152:1285-1297.
40. Taylor, J., and R. J. Parkes. 1983. The cellular fatty acids of the sulphate-reducing bacteria, Desulfobacter sp., Desulfobulbus sp., and Desulvovibrio desulfuricans. J. Gen. Microbiol. 129:3303-3309.
41. Thiel, V., J. Peckmann, H. H. Richnow, U. Luth, J. Reitner, and W. Michaelis. 2001. Molecular signals for anaerobic methane oxidation in Black Sea seep carbonates and a microbial mat. Mar. Chem. 73:97-112.
42. Thiel, V., J. Peckmann, R. Seifert, P. Wehrung, J. Reitner, and W. Michaelis. 1999. Highly isotopically depleted isoprenoids: molecular markers for ancient methane venting. Geochim. Cosmochim. Acta 63:3959-3966.
43. Tyron, M. D., K. M. Brown, M. E. Torres, A. M. Trehu, J. McManus, and R. W. Collier. 1999. Measurement of transience and downward fluid flow near episodic methane gas vents, Hydrate Ridge, Cascadia. Geology 27: 1075-1078.
44. Urakawa, H., K. K. Tsukamoto, and K. Ohwada. 1999. Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis. Microbiology 145:3305-3315.
45. Valentine, D. L., and W. S. Reeburgh. 2000. New perspectives on anaerobic methane oxidation. Environ. Microbiol. 2:477-484.
46. Vetriani, C., H. W. Jannasch, B. J. MacGregor, D. A. Stahl, and A.-L. Reysenbach. 1999. Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Appl. Environ. Microbiol. 65:4375-4384.
47. Vetriani, C., A.-L. Reysenbach, and J. Dore. 1998. Recovery and phylogenetic analysis of archaeal rRNA sequences from continental shelf sediments. FEMS Microbiol. Lett. 161:83-88.
48. Wellsbury, P., K. Goodman, B. Cragg, and R. Parkes. 2000. The geomicrobiology of deep marine sediments from Blake Ridge containing methane hydrate (sites 994, 995, and 997). Proc. Ocean Drill. Prog. Sci. Results 164: 379-391.
49. Zehnder, A. J. B., and T. D. Brock. 1979. Methane formation and oxidation by methanogenic bacteria. J. Bacteriol. 137:420-432.