Shewanella profunda sp. nov., isolated from deep marine sediment of the Nankai Trough

International Journal of Systematic and Evolutionary Microbiology

Volumn 54, Issue 6, 2004, Pages 1943-1949

  Toffin, Laurent ^a,b   Bidault, Adeline ^a   Pignet, Patricia ^c   Tindall, Brian J ^d   Slobodkin, Alexander ^e   Kato, Chiaki ^b   Prieur, Daniel ^a  

^a UNIVERSITÉ DE BRETAGNE OCCIDENTALE   (France)

^b JAPAN AGENCY FOR MARINE EARTH SCIENCE AND TECHNOLOGY   (Japan)

^c IFREMER   (France)

^d LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^e RUSSIAN ACADEMY OF SCIENCES   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CITRIC ACID; CYSTINE; CYTOSINE; FATTY ACID; FERRIC ION; FUMARIC ACID; GLUTAMIC ACID; GUANINE; LACTIC ACID; NITRATE; OXYGEN; PEPTONE; PYRUVIC ACID; RNA 16S; SUCCINIC ACID;

ANAEROBIC BACTERIUM; ARTICLE; BACTERIAL FLAGELLUM; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATION; CARBON SOURCE; CONTROLLED STUDY; ENERGY; GRAM NEGATIVE BACTERIUM; GRAM NEGATIVE FACULTATIVELY ANAEROBIC RODS; GROWTH RATE; HYDROSTATIC PRESSURE; JAPAN; MARINE ENVIRONMENT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PRIORITY JOURNAL; RNA SEQUENCE; SEDIMENT; SEQUENCE HOMOLOGY; SHEWANELLA; SHEWANELLA BALTICA; SHEWANELLA ONEIDENSIS; SHEWANELLA PROFUNDA; SHEWANELLA PUTREFACIENS;

ANAEROBIOSIS; BASE COMPOSITION; CYSTINE; DNA, BACTERIAL; DNA, RIBOSOMAL; FATTY ACIDS; FERRIC COMPOUNDS; FLAGELLA; FUMARATES; GENES, RRNA; GEOLOGIC SEDIMENTS; HYDROSTATIC PRESSURE; JAPAN; MOLECULAR SEQUENCE DATA; NITRATES; NUCLEIC ACID HYBRIDIZATION; ORGANIC CHEMICALS; OXYGEN; PACIFIC OCEAN; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SHEWANELLA; TEMPERATURE; WATER MICROBIOLOGY;

BACTERIA (MICROORGANISMS); GAMMAPROTEOBACTERIA; SHEWANELLA BALTICA; SHEWANELLA ONEIDENSIS; SHEWANELLA PROFUNDA; SHEWANELLA PUTREFACIENS;

EID: 9744242717     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.03007-0     Document Type: Article

References (47)

1. Akagawa-Matsushita, M., Itoh, T., Katayama, Y., Kuraishi, H. & Yamasato, K. (1992). Isoprenoid quinone composition of some marine Alteromonas, Marinomonas, Deleya, Pseudomonas and Shewanella species. J Gen Microbiol 138, 2275-2281.
2. Bale, S. J., Goodman, K., Rochelle, P. A., Marchesi, J. R., Fry, J. C., Weightman, A. J. & Parkes, R. J. (1997). Desulfovibrio profundus sp. nov., a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea. Int J Syst Bacteriol 47, 515-521.
3. Bozal, N., Montes, M. J., Tudela, E., Jiménez, F. & Guinea, J. (2002). Shewanella frigidimarina and Shewanella livingstonensis sp. nov. isolated from Antarctic coastal areas. Int J Syst Evol Microbiol 52, 195-205.
4. Brettar, I. & Höfle, M. G. (1993). Nitrous oxide producing heterotrophic bacteria from the water column of the central Baltic: abundance and molecular identification. Mar Ecol Prog Ser 94, 253-265.
5. Brettar, I., Christen, R. & Höfle, M. G. (2002). Shewanella denitrificans sp. nov., a vigorously denitrifying bacterium isolated from the oxic-anoxic interface of the Gotland Deep in the central Baltic Sea. Int J Syst Evol Microbiol 52, 2211-2217.
6. Cragg, B. A., Bale, S. J. & Parkes, R. J. (1992a). A novel method for the transport and long-term storage of cultures and samples in an anaerobic atmosphere. Lett Appl Microbiol 15, 125-128.
7. Cragg, B. A., Harvey, F. M., Fry, J. C., Herbert, R. A. & Parkes, R. J. (1992b). Bacterial biomass and activity in the deep sediment layers of the Japan Sea, Hole 798B. In Proceedings of the Ocean Drilling Program, Scientific Results, Leg 128, pp. 761-776. College Station, TX: Texas A&M University.
8. DeLong, E. F., Franks, D. G. & Yayanos, A. A. (1997). Evolutionary relationships of cultivated psychrophilic and barophilic deep-sea bacteria. Appl Environ Microbiol 63, 2105-2108.
9. Erauso, G., Charbonnier, F., Barbeyron, T., Forterre, P. & Prieur, D. (1992). Preliminary characterization of a hyperthermophilic archaebacterium with a plasmid, isolated from a North Fiji Basin hydrothermal vent. C R Acad Sci Ser III Sci Vie 314, 387-393.
10. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
11. Ghosh, D., Bal, B., Kashyap, V. K. & Pal, S. (2003). Molecular phylogenetic exploration of bacterial diversity in a Bakreshwar (India) hot spring and culture of Shewanella-related thermophiles. Appl Environ Microbiol 69, 4332-4336.
12. Ivanova, E. P., Sawabe, T., Hayashi, K., Gorshkova, N. M., Zhukova, N. V., Nedashkovskaya, O. I., Mikhailov, V. V., Nicolau, D. V. & Christen, R. (2003). Shewanella fidelis sp. nov., isolated from sediments and sea water. Int J Syst Evol Microbiol 53, 577-582.
13. Jensen, M. J., Tebo, B. M., Baumann, P., Mandel, M. & Nealson, K. H. (1980). Characterization of Alteromonas hanedai (sp. nov.), a nonfermentative luminous species of marine origin. Curr Microbiol 3, 311-315.
14. Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21-132. Edited by H. N. Munro. New York: Academic Press.
15. Kato, C. & Nogi, Y. (2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiol Ecol 35, 223-230.
16. Kato, C., Sato, T. & Horikoshi, K. (1995). Isolation and properties of barophilic and barotolerant bacteria from deep-sea mud samples. Biodivers Conserv 4, 1-9.
17. Koroleff, F. (1969). Direct determination of ammonia in natural waters as indophenol blue. In Information on Techniques and Methods for Seawater Analysis, pp. 19-22. Charlottenlund, Denmark: International Council for the Exploration of the Sea.
18. Lake, J. A. (1987). A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol Biol Evol 4, 167-191.
19. Leonardo, M. R., Moser, D. P., Barbieri, E., Brantner, C. A., MacGregor, B. J., Paster, B. J., Stackebrandt E. & Nealson, K. H. (1999). Shewanella pealeana sp. nov., a member of the microbial community associated with the accessory nidamental gland of the squid Loligo pealei. Int J Syst Bacteriol 49, 1341-1351.
20. Lucas, S., Toffin, L., Zivanovic, Y., Charlier, D., Moussard, H., Forterre, P., Prieur, D. & Erauso, G. (2002). Construction of a shuttle vector for, and spheroplast transformation of, the hyperthermophilic archaeon Pyrococcus abyssi. Appl Environ Microbiol 68, 5528-5536.
21. Ludwig, W., Strunk, O., Westram, R. & 29 other authors (2004). ARB: a software environment for sequence data. Nucleic Acids Res 32, 1363-1371.
22. MacDonell, M. T. & Colwell, R. R. (1985). Phylogeny of the Vibrionaceae, and recommendation for two new genera, Listonella and Shewanella. Syst Appl Bacteriol 6, 171-182.
23. Maidak, B. L., Cole, J. R., Lilburn, T. G. & 7 other authors (2001). The RDP-II (Ribosomal Database Project). Nucleic Acids Res 29, 173-174.
24. Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. M. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034-1039.
25. Marteinsson, V. T., Watrin, L., Prieur, D., Caprais, J. C., Raguénès, G. & Erauso, G. (1995). Phenotypic characterization, DNA similarities, and protein profiles of twenty sulfur-metabolizing hyperthermophilic anaerobic archaea isolated from hydrothermal vents in the south-western Pacific Ocean. Int J Syst Bacteriol 45, 623-632.
26. Mikucki, J. A., Liu, Y., Delwiche, M., Colwell, F. S. & Boone, D. R. (2003). Isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of Methanoculleus submarinus sp. nov. Appl Environ Microbiol 69 3311-3316.
27. Moore, E. R. B., Arnscheidt, A., Krüger, A., Strömpl, C. & Mau, M. (1995). Simplified protocols for the preparation of genomic DNA from bacterial cultures. In Molecular Microbial Ecology Manual, Supplement 4, pp. 1.6.1.1-1.6.1.15. Edited by A. D. L. Akkermans, J. D. van Elsas & F. J. de Bruijn. Dordrecht: Kluwer.
28. Moore, G. F., Taira, A., Klaus, A. & 23 other authors (2001). Deformation and fluid flow processes in the Nankai Trough accretionary prism sites 1173-1178. In Proceedings of the Ocean Drilling Program, Initial Reports, vol. 190. College Station, TX: Texas A&M University.
29. Moser, D. P. & Nealson, K. H. (1996). Growth of the facultative anaerobe Shewanella putrefaciens by elemental sulfur reduction. Appl Environ Microbiol 62, 2100-2105.
30. Myers, C. R. & Nealson, K. H. (1988). Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science 240, 1319-1321.
31. Myers, C. R. & Nealson, K. H. (1990). Respiration-linked proton translocation coupled to anaerobic reduction of manganese (IV) and iron(III) in Shewanella putrefaciens MR-1. J Bacteriol 172, 6232-6238.
32. Nogi, Y., Kato, C. & Horikoshi, K. (1998). Taxonomic studies of deep-sea barophilic Shewanella strains and description of Shewanella violacea sp. nov. Arch Microbiol 170, 331-338.
33. Parkes, R. J., Cragg, B. A., Bale, S. J., Goodman, K. & Fry, J. C. (1995). A combined ecological and physiological approach to studying sulphate reduction within deep marine sediment layers. J Microbiol Methods 23, 235-249.
34. Pfennig, N., Widdel, F. & Trüper, H. G. (1981). The dissimilatory sulfate-reducing bacteria. In The Prokaryotes, pp. 926-940. Edited by M. P. Starr, H. Stolp, H. G. Trüper, A. Balows & H. G. Schlegel. New York: Springer.
35. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
36. Satomi, M., Oikawa, H. & Yano, Y. (2003). Shewanella marinintestina sp. nov., Shewanella schlegeliana sp. nov. and Shewanella sairae sp. nov., novel eicosapentaenoic-acid-producing marine bacteria isolated from sea-animal intestines. Int J Syst Evol Microbiol 53, 491-499.
37. Semple, K. M. & Westlake, D. W. S. (1987). Characterization of iron-reducing Alteromonas putrefaciens strains from oil field fluids. Can J Microbiol 33, 366-371.
38. Slobodkin, A. I., Tourova, T. P., Kuznetsov, B. B., Kostrikina, N. A., Chernyh, N. A. & Bonch-Osmolovskaya, E. A. (1999 . Thermoanaerobacter siderophilus sp. nov., a novel dissimilatory Fe(III)-reducing, anaerobic, thermophilic bacterium. Int J Syst Bacteriol 49, 1471-1478.
39. Solorzano, L. (1969). Determination of ammonia in natural waters by the phenol-hypochlorite method. Limnol Oceanogr 14, 799-801.
40. Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846-849.
41. Tindall, B. J. (1990a). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13, 128-130.
42. Tindall, B. J. (1990b). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66, 199-202.
43. Venkateswaran, K., Dollhopf, M. E., Aller, R., Stackebrandt, E. & Nealson, K. H. (1998). Shewanella amazonensis sp. nov., a novel metal-reducing facultative anaerobe from Amazonian shelf muds. Int J Syst Bacteriol 48, 965-972.
44. Venkateswaran, K., Moser, D. P., Dollhopf, M. E. & 10 other authors (1999). Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol 49, 705-724.
45. Wery, N., Moricet, J.-M., Cueff, V., Jean, J., Pignet, P., Lesongeur, F., Cambon-Bonavita, M.-A. & Barbier, G. (2001). Caloranaerobacter azorensis gen. nov., sp. nov., an anaerobic thermophilic bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 51, 1789-1796.
46. Widdel, F. & Bak, F. (1992). Gram-negative mesophilic sulfate-reducing bacteria. In The Prokaryotes, 2nd edn, pp. 3352-3378. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York: Springer.
47. Ziemke, F., Höfle, M. G., Lalucat, J. & Rosselló-Mora, R. (1998). Reclassification of Shewanella putrefaciens Owen's genomic group II as Shewanella baltica sp. nov. Int J Syst Bacteriol 48, 179-186.