1887

Abstract

A novel piezotolerant, mesophilic, facultatively anaerobic, organotrophic, polarly flagellated bacterium (strain LT13a) was isolated from a deep sediment layer in the Nankai Trough (Leg 190, Ocean Drilling Program) off the coast of Japan. This organism used a wide range of organic substrates as sole carbon and energy sources: pyruvate, glutamate, succinate, fumarate, lactate, citrate, peptone and tryptone. Oxygen, nitrate, fumarate, ferric iron and cystine were used as electron acceptors. Maximal growth rates were observed at a hydrostatic pressure of 10 MPa. Hydrostatic pressure for growth was in the range 0·1–50 MPa. Predominant cellular fatty acids were 16 : 17, 15 : 0 iso, 16 : 0 and 13 : 0 iso. The G+C content of the DNA was 44·9 mol%. On the basis of 16S rRNA gene sequences, strain LT13a was shown to belong to the -, being closely related to (98 %), (97 %) and (96 %). Levels of DNA homology between strain LT13a and , and were <20 %, indicating that strain LT13a represents a novel species. Genetic evidence and phenotypic characteristics showed that isolate LT13a constitutes a novel species of the genus . Because of the deep origin of the strain, the name sp. nov. is proposed, with LT13a (=DSM 15900=JCM 12080) as the type strain.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.03007-0
2004-11-01
2020-11-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/54/6/ijs541943.html?itemId=/content/journal/ijsem/10.1099/ijs.0.03007-0&mimeType=html&fmt=ahah

References

  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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;
    [Google Scholar]
  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
    [Google Scholar]
  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
    [Google Scholar]
  10. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  14. Jukes T. H., Cantor C. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism pp  21–132 Edited by Munro H. N. New York: Academic Press;
    [Google Scholar]
  15. Kato C., Nogi Y. 2001; Correlation between phylogenetic structure and function: examples from deep-sea Shewanella . FEMS Microbiol Ecol 35:223–230 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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;
    [Google Scholar]
  18. Lake J. A. 1987; A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol Biol Evol 4:167–191
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  21. Ludwig W., Strunk O., Westram R. 29 other authors 2004; arb: a software environment for sequence data. Nucleic Acids Res 32:1363–1371 [CrossRef]
    [Google Scholar]
  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
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 southwestern Pacific Ocean. Int J Syst Bacteriol 45:623–632 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 Akkermans A. D. L., van Elsas J. D., de Bruijn F. J. Dordrecht: Kluwer;
    [Google Scholar]
  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;
    [Google Scholar]
  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
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  34. Pfennig N., Widdel F., Trüper H. G. 1981; The dissimilatory sulfate-reducing bacteria. In The Prokaryotes pp  926–940 Edited by Starr M. P., Stolp H., Trüper H. G., Balows A., Schlegel H. G. New York: Springer;
    [Google Scholar]
  35. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  39. Solorzano L. 1969; Determination of ammonia in natural waters by the phenol-hypochlorite method. Limnol Oceanogr 14:799–801 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  41. Tindall B. J. 1990a; A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130 [CrossRef]
    [Google Scholar]
  42. Tindall B. J. 1990b; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66:199–202 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  46. Widdel F., Bak F. 1992; Gram-negative mesophilic sulfate-reducing bacteria. In The Prokaryotes , 2nd edn. pp  3352–3378 Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K. H. New York: Springer;
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.03007-0
Loading
/content/journal/ijsem/10.1099/ijs.0.03007-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error