Phylogenetic Diversity of Dissimilatory Sulfite Reductase Genes from Deep-sea Cold Seep Sediment

Marine Biotechnology

Volumn 5, Issue 5, 2003, Pages 458-468

  Fukuba, Tatsuhiro ^a   Ogawa, Mari ^b   Fujii, Teruo ^a   Naganuma, Takeshi ^b  

^a INSTITUTE OF INDUSTRIAL SCIENCE   (Japan)

^b HIROSHIMA UNIVERSITY   (Japan)

Author keywords

Methane seep; Sagami Sea Knoll; Sulfate reduction; Sulfate reducing prokaryotes

Indexed keywords

OXIDOREDUCTASE; PRIMER DNA;

PHYLOGENETICS;

AMINO ACID SEQUENCE; ARTICLE; COMPARATIVE STUDY; DELTAPROTEOBACTERIA; DNA BASE COMPOSITION; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEA; SEDIMENT; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BASE COMPOSITION; BASE SEQUENCE; DELTAPROTEOBACTERIA; DNA PRIMERS; GEOLOGIC SEDIMENTS; MOLECULAR SEQUENCE DATA; OCEANS AND SEAS; OXIDOREDUCTASES ACTING ON SULFUR GROUP DONORS; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; VARIATION (GENETICS);

ALVINELLA; ALVINELLA POMPEJANA; ARCHAEA; BACTERIA (MICROORGANISMS); NEGIBACTERIA; PROKARYOTA; PROTEOBACTERIA;

EID: 0348226759     PISSN: 14362228     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10126-002-0091-0     Document Type: Article

References (37)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990). Basic local alignment search tool. J Mol Biol 215:403-410.
2. Barry, J.P., Kochevar, R.E., and Baxter, C.H. (1997). The influence of pore-water chemistry and physiology on the distribution of vescomyid clams at cold seeps in Montrey Bay: implication for patterns of chemosynthetic community organization. Limnol Oceanogr 42:318-328.
3. Boetius, A., Ravenschlag, K., Schubert, C.J., Rickert, D., Widdel, F., Gieseke, A., Amann, R., Jørgensen, B.B., Witte, U., and Pfannkuche, O. (2000). A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407: 623-626.
4. Bridge, T.A.M., White, C., and Gadd, G.M. (1999). Extracellular metal-binding activity of the sulphate-reducing bacterium Desulfococcus multivorans. Microbiology 145:2987-2995.
5. Brock, T.D., Madigan, M.T., Martinko, J.M., and Parker, J. (1997). Biology of microorganisms, 8th ed. Englewood Cliffs, N.J.: Prentice Hall.
6. Brysch, K., Schneider, C., Fuchs, G., and Widdel, F. (1987). Lithoautotrophic growth of sulfate-reducing bacteria, and description of Desulfobacterium autotrophicum gen. nov., sp. nov. Arch Microbiol 148:264-274.
7. Campbell, B.J., Jeanthon, C., Kostka, S.E., Luther, G.W., and Cary, S.C. (2001). Growth and phylogenetic properties of novel bacteria belonging to the epsilon subdivision of the Proteobacteria enriched from Alvinella pompejana and deep-sea hydrothermal vents. Appl Environ Microbiol 67:4566-4572.
8. Cary, S.C., Shank, T., and Stein, J. (1998). Worms bask in extreme temperatures. Nature 391:545-546.
9. Cottrell, M.T., and Cary, S.C. (1999). Diversity of dissimilatory bisulfite reductase genes of bacteria associated with the deep-sea hydrothermal vent polychaete annelid Alvinella pompejana. Appl Environ Microbiol 65:1127-1132.
10. Devereux, R., Delaney, M., Widdel, F., and Stahl, D.A. (1989). Natural relationships among sulfate-reducing eubacteria. J Bacteriol 171:6689-6695.
11. Elsaied, H., and Naganuma, T. (2001). Phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) large subunit genes of deep-sea microorganisms. Appl Environ Microbiol 67:1751-1765.
12. Elvert, M., Suess, E., Greinert, J., and Whiticar, M.J. (2000). Archaea mediating anaerobic methane oxidation in deep-sea sediments at cold seeps of the eastern Aleutian subduction zone. Organic Geochem 31:1175-1187.
13. Fisher, C.R. (1990). Chemoautotrophic and methanotrophic symbioses in marine invertebrates. Rev Aquat Sci 2:399-436.
14. 4 and trace metal concentrations associated with high heat flow at the Calyptogena community off Hatsuhima Island, Sagami Bay, Japan: preliminary report of Tansei Maru KT-88-1 cruise Leg-1. Geochem J 22:215-230.
15. Hashimoto, J., Ohta, S., Tanaka, T., Hotta, H., Matsuzawa, S., and Sakai, H. (1989). Deep sea communities dominated by the giant clam Calyptogena soyoae, along the slope of foot of Hatsushima Island, Sagami Bay, central Japan. Palaeogeogr Palaeoclimatol Palaeoecol 71:179-192.
16. Hattori, M., Kanie, Y, Okada, H., and Arima, M. (1992). Geology of Sagami Knoll Okinoyama Bank Chain, Sagami Bay, central Japan. JAMSTEC Deep Sea Res 8:185-192 (in Japanese with English abstract).
17. Hattori, M., Kanie, Y, Hashimoto, J., and Fujikura, K. (1993). Geological settings, mode of life and morphology of genus Calyptogena along the subduction zone of the Sagami and Suruga Troughs, central Japan. JAMSTEC Deep Sea Res 9:237-251 (in Japanese with English abstract).
18. Hinrichs, K.-U., Hayes, J.M., Sylva, S.P., Brewer, P.G., and DeLong, E.F. (1999). Methane-consuming archaebacteria in marine sediments. Nature 398:802-805.
19. Hinrichs, K.-U., Summons, R.E., Orphan, V., Sylva, S.P., and Hayes, J.M. (2000). Molecular and isotopic analysis of anaerobic methane-oxidizing communities in marine sediments. Organic Geochem 31:1685-1701.
20. Jørgensen, B.B. (1982). Mineralization of organic matter in the sea bed-the role of sulphate reduction. Nature 296:643-645.
21. Karkhoff-Schweizer, R.R., Huber, D.P.W., and Voordouw, G. (1995). Conservation of the genes for dissimilatory sulfite reductase from Desulfovibrio vulgaris and Archaeoglobus fulgidus allows their detection by PCR. Appl Environ Microbiol 61:290-296.
22. Klein, M., Friedrich, M., Roger, A.J., Hungenholz, P., Fishbain, S., Abicht, H., Blackall, L.L., Stahl, D.A., and Wagner, M. (2001). Multiple lateral gene transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. J Bacteriol 183:6028-6035.
23. Larsen, Ø., Lien, T., and Birkeland, N.-K. (1999). Dissimilatory sulfite reductase from Archaeoglobus profundus and Desulfotomaculum thermocisternum: phylogenetic and structural implications from gene sequences. Extremophiles 3:63-70.
24. Lipman, D.J., and Person, W.R. (1985). Rapid and sensitive protein similarity searches. Science 227:1435-1441.
25. Minz, D., Flax, J.L, Green, S.J., Muyzer, G., Cohen, Y, Wagner, M., Rittmann, B.E., and Stahl, D.A. (1999). Diversity of sulfate-reducing bacteria in oxic and anoxic regions of a microbial mat characterized by comparative analysis of dissimilatory sulfite reductase genes. Appl Environ Microbiol 65:4666-4671.
26. Molitor, M., Dahl, C., Molitor, I., Schafer, U., Speich, N., Huber, R., Deutzmann, R., and Truper, H.G. (1998). A dissimilatory sirohaem-sulfite- reductase-type protein from the hyperthermophilic archaeon Pyrobaculum islandicum. Microbiology 144:529-541.
27. Odom J.M., and Peck, H.D. Jr. (1984). Hydrogenase, electron transfer proteins, and energy coupling in the sulfate-reducing bacteria Desulfovibrio. Annu Rev Microbiol 38:551-592.
28. Pancost, R.D., Damste, J.S.S., De Lint, S., van der Maarel, M.J.E.C., Gottschal, J.C., 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.
29. Ravenschlag, K., Sahm, K., Knoblauch, C., Jørgensen, B.B., and Amann, R. (2000). Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine arctic sediment. Appl Environ Microbiol 66:3592-3602.
30. Saitou, N., and Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic tree. Mol Biol Evol 4:406-425.
31. Sambrook, J., and Russel, D.W. (2001). Molecular Cloning: A Laboratory Manual, 3rd ed. Cold Spring Harbor, N.Y.: Spring Harbor Laboratory Press.
32. Schauder, R., Preuss, A., Jetten, M., Etten, M., and Fuchs, G. (1989). Oxidation and reductive acetyl coenzyme A/carbon monoxide dehydrogenase pathway in Desulfobacterium autotrophicum. Arch Microbiol 151:84-89.
33. Schedel, M., Vanselow, M., and Truper, H.G. (1979). Siroheme sulfite reductase isolated from Chromatium vinosum: purification and investigation of some of its molecular and catalytic properties. Arch Microbiol 121:29-36.
34. Thompson, J.D., Higgins, D.G., and Gibson, T.G. (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.
35. Thomsen, T.R., Finster, K., and Ramsing, N.B. (2001) Biogeochemical and molecular signatures of anaerobic methane oxidation in a marine sediment. Appl Environ Microbiol 67:1646-1656.
36. Tsai, Y.-L., and Olson, B.H. (1992). Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Appl Environ Microbiol 58:754-757.
37. Wagner, M., Roger, A.J., Flax, J.T., Brusseau, G.A., and Stahl, C.A. (1998). Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J Bacterial 180:2975-2982.