1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 65, Issue Pt_9

sp. nov., a marine bacterium isolated from cold-seep sediment Free

Abstract

A novel marine bacterial strain designated JAMH 011 was isolated from the cold-seep sediment in Sagami Bay, Japan. Cells were Gram-stain-negative, rod-shaped, non-spore-forming, aerobic chemo-organotrophs and motile by means of a single polar flagellum. Growth occurred at temperatures below 31 °C, with the optimum at 25 °C. The major respiratory quinone was Q-10. The predominant fatty acid was Cω7. On the basis of 16S rRNA gene sequence analysis, the isolated strain was closely affiliated with members of the genus in the class , and the 16S rRNA gene sequence similarity of the novel isolate with the type strain of the closest related species, WM35, was 98.1  %. The DNA G+C content of the novel strain was 57.3 mol%. The hybridization values for DNA–DNA relatedness between strain JAMH 011 and reference strains belonging to the genus were less than 9.4 ± 0.7  %. Based on differences in taxonomic characteristics, the isolated strain represents a novel species of the genus for which the name sp. nov. is proposed. The type strain is JAMH 011 ( = JCM 30583 = DSM 29734)

  • Published Online:
© 2015 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.000333
2015-09-01
2024-04-16
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/9/2786.html?itemId=/content/journal/ijsem/10.1099/ijs.0.000333&mimeType=html&fmt=ahah

References

  1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. ( 1990;). Basic local alignment search tool. J Mol Biol 215 403–410 [View Article] [PubMed] .
     [Google Scholar]
  2. Barrow G. I., Feltham R. K. A. ), ( 1993). Cowan and Steel's Manual for the Identification of Medical Bacteria , 3rd edn. Cambridge: Cambridge University Press; [View Article].
     [Google Scholar]
  3. Baumann L., Baumann P., Mandel M., Allen R.D. ( 1972;). Taxonomy of aerobic marine eubacteria. J Bacteriol 110 402–429 [PubMed].
     [Google Scholar]
  4. Chen M.-H., Sheu S.-Y., Chen C.A., Wang J.-T., Chen W.-M. ( 2011;). Shimia isoporae sp. nov., isolated from the reef-building coral Isopora palifera . Int J Syst Evol Microbiol 61 823–827 [View Article] [PubMed] .
     [Google Scholar]
  5. Choi D.H., Cho B.C. ( 2006;). Shimia marina gen. nov., sp. nov., a novel bacterium of the Roseobacter clade isolated from biofilm in a coastal fish farm. Int J Syst Evol Microbiol 56 1869–1873 [View Article] [PubMed] .
     [Google Scholar]
  6. Ezaki T., Hashimoto Y., Yabuuchi E. ( 1989;). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39 224–229 [View Article].
     [Google Scholar]
  7. Felsenstein J. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 368–376 [View Article] [PubMed] .
     [Google Scholar]
  8. Fitch W.M. ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20 406–416 [View Article].
     [Google Scholar]
  9. Hameed A., Shahina M., Lin S.-Y., Lai W.-A., Hsu Y.-H., Liu Y.-C., Huang Y.-M., Young C.-C. ( 2013;). Shimia biformata sp. nov., isolated from surface seawater, and emended description of the genus Shimia Choi and Cho 2006. Int J Syst Evol Microbiol 63 4533–4539 [View Article] [PubMed] .
     [Google Scholar]
  10. Hugh R., Leifson E. ( 1953;). The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various Gram negative bacteria. J Bacteriol 66 24–26 [PubMed].
     [Google Scholar]
  11. Hyun D.-W., Kim M.-S., Shin N.-R., Kim J.Y., Kim P.S., Whon T.W., Yun J.-H., Bae J.-W. ( 2013;). Shimia haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai . Int J Syst Evol Microbiol 63 4248–4253 [View Article] [PubMed] .
     [Google Scholar]
  12. Jukes T.H., Cantor C.R. ( 1969;). Evolution of protein molecules. . In Mammalian Protein Metabolism vol. 3, pp. 21–132. Edited by Munro H. N. New York: Academic Press; [View Article].
     [Google Scholar]
  13. Kim O.-S., Cho Y.-J., Lee K., Yoon S.-H., Kim M., Na H., Park S.-C., Jeon Y.S., Lee J.-H., other authors. ( 2012;). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62 716–721 [View Article] [PubMed] .
     [Google Scholar]
  14. Komagata K., Suzuki K. ( 1987;). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19 161–207 [View Article].
     [Google Scholar]
  15. Lane D.J. ( 1991;). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–148. Edited by Stackebrandt E., Goodfellow M. New York: Wiley;.
     [Google Scholar]
  16. MIDI ( 1999). Sherlock, Microbial Identification System, Operating Manual version 3.0 Newark, DE: MIDI, Inc;.
     [Google Scholar]
  17. Minnikin D.E., O'Donnell A.G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J.H. ( 1984;). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2 233–241 [View Article].
     [Google Scholar]
  18. Miyazaki M., Nogi Y., Usami R., Horikoshi K. ( 2006;). Shewanella surugensis sp. nov., Shewanella kaireitica sp. nov. and Shewanella abyssi sp. nov., isolated from deep-sea sediments of Suruga Bay, Japan. Int J Syst Evol Microbiol 56 1607–1613 [View Article] [PubMed] .
     [Google Scholar]
  19. Saito H., Miura K.I. ( 1963;). Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 72 619–629 [View Article] [PubMed] .
     [Google Scholar]
  20. Saitou N., Nei M. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 406–425 [PubMed].
     [Google Scholar]
  21. Stackebrandt E., Ebers J. ( 2006;). Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33 152–155.
     [Google Scholar]
  22. Tamaoka J., Komagata K. ( 1984;). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25 125–128 [View Article].
     [Google Scholar]
  23. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28 2731–2739 [View Article] [PubMed] .
     [Google Scholar]
  24. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. ( 1997;). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25 4876–4882 [View Article] [PubMed] .
     [Google Scholar]
  25. Uchida H., Hamana K., Miyazaki M., Yoshida T., Nogi Y. ( 2012;). Parasphingopyxis lamellibrachiae gen. nov., sp. nov., isolated from a marine annelid worm. Int J Syst Evol Microbiol 62 2224–2228 [View Article] [PubMed] .
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.000333
Loading
Shimia sagamensis sp. nov., a marine bacterium isolated from cold-seep sediment
Int J Syst Evol Microbiol 65, 2786 (2015); https://doi.org/10.1099/ijs.0.000333
/content/journal/ijsem/10.1099/ijs.0.000333
/content/journal/ijsem/10.1099/ijs.0.000333
Loading

Data & Media loading...

Supplements

Supplementary Data

PDF

Most cited 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