1887

Abstract

A novel Gram-stain-negative, rod-shaped bacterial strain, designated KX27, was isolated from deep-sea sediment of the Okinawa Trough and characterized on the basis of a polyphasic taxonomic approach. The phenotypic features of strain KX27 were similar to those of members of the genus . Strain KX27 exhibited highest 16S rRNA gene sequence similarity (98.37 %) to JCM 14937. Levels of gene sequence similarity between strain KX27 and its closest genetic neighbours were lower than 90 %, the species cut-off value for . The DNA–DNA hybridization value between strain KX27 and JCM 14937 (54 %) was lower than the accepted species threshold. The predominant cellular fatty acids of strain KX27 were summed feature 3 (C 7 and/or C 6), C 8, summed feature 8 (C 7 and/or C 6) and iso-C. The major polar lipids of strain KX27 were phosphatidylethanolamine and phosphatidylglycerol. On the basis of combined phenotypic, chemotaxonomic and phylogenetic analysis, strain KX27 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is KX27 (=KCTC 42807=CGMCC 1.15339).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001450
2016-12-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/12/4947.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001450&mimeType=html&fmt=ahah

References

  1. Anzai Y., Kim H., Park J. Y., Wakabayashi H., Oyaizu H. 2000; Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 50:1563–1589 [View Article][PubMed]
    [Google Scholar]
  2. Bernardet J. F., Nakagawa Y., Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes 2002; Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070 [View Article][PubMed]
    [Google Scholar]
  3. Bowman J. P., McCammon S. A., Nichols D. S., Skerratt J. H., Rea S. M., Nichols P. D., McMeekin T. A. 1997; Shewanella gelidimarina sp. nov. and Shewanella frigidimarina sp. nov., novel Antarctic species with the ability to produce eicosapentaenoic acid (20:5ω3) and grow anaerobically by dissimilatory Fe(III) reduction. Int J Syst Bacteriol 47:1040–1047 [View Article][PubMed]
    [Google Scholar]
  4. Dai X., Shi X., Gao X., Liu J., Zhang X. H. 2014; Roseivivax marinus sp. nov., isolated from deep water. Int J Syst Evol Microbiol 64:2540–2544 [View Article][PubMed]
    [Google Scholar]
  5. Doetsch R. N. 1981; Determinative methods of light microscopy. In Manual of Methods for General Bacteriology pp. 21–33 Edited by Gerdhart P., Murray R. G. E., Costilow R. N., Nester E. W., Wood W. A., Krieg N. R., Phillips G. B. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  6. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [View Article][PubMed]
    [Google Scholar]
  7. Frank J. A., Reich C. I., Sharma S., Weisbaum J. S., Wilson B. A., Olsen G. J. 2008; Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 74:2461–2470 [View Article][PubMed]
    [Google Scholar]
  8. Huang J., Sun B., Zhang X. 2010; Shewanella xiamenensis sp. nov., isolated from coastal sea sediment. Int J Syst Evol Microbiol 60:1585–1589 [View Article][PubMed]
    [Google Scholar]
  9. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 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]
  10. Kim M., Oh H. S., Park S. C., Chun J. 2014; Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351 [View Article][PubMed]
    [Google Scholar]
  11. Kimura M. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 [View Article][PubMed]
    [Google Scholar]
  12. Kobayashi T., Koide O., Mori K., Shimamura S., Matsuura T., Miura T., Takaki Y., Morono Y., Nunoura T. et al. 2008; Phylogenetic and enzymatic diversity of deep subseafloor aerobic microorganisms in organics- and methane-rich sediments off Shimokita Peninsula. Extremophiles 12:519–527 [View Article][PubMed]
    [Google Scholar]
  13. Komagata K., Suzuki K. 1987; Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207 [CrossRef]
    [Google Scholar]
  14. Liu C., Shao Z. 2005; Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. Int J Syst Evol Microbiol 55:1181–1186 [View Article][PubMed]
    [Google Scholar]
  15. MacDonell M. T., Colwell R. R. 1985; Phylogeny of the Vibrionaceae, and recommendation for two new genera, Listonella and Shewanella . Syst Appl Microbiol 6:171–182 [View Article]
    [Google Scholar]
  16. Mesbah M., Premachandran U., Whitman W. B. 1989; Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167 [View Article]
    [Google Scholar]
  17. 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]
  18. Park H. Y., Jeon C. O. 2013; Shewanella aestuarii sp. nov., a marine bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 63:4683–4690 [View Article][PubMed]
    [Google Scholar]
  19. Park S. C., Baik K. S., Kim M. S., Kim D., Seong C. N. 2009; Shewanella marina sp. nov., isolated from seawater. Int J Syst Evol Microbiol 59:1888–1894 [View Article][PubMed]
    [Google Scholar]
  20. Romanenko L. A., Tanaka N., Uchino M., Kalinovskaya N. I., Mikhailov V. V. 2008; Diversity and antagonistic activity of sea ice bacteria isolated from the sea of Japan. Microbes Environ 23:209–214 [View Article][PubMed]
    [Google Scholar]
  21. Sasser M. 1990 Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids MIDI Technical Note 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  22. 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 [View Article][PubMed]
    [Google Scholar]
  23. Satomi M., Vogel B. F., Gram L., Venkateswaran K. 2006; Shewanella hafniensis sp. nov. and Shewanella morhuae sp. nov., isolated from marine fish of the Baltic Sea. Int J Syst Evol Microbiol 56:243–249 [View Article][PubMed]
    [Google Scholar]
  24. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  25. Tindall B. J., Rosselló-Móra R., Busse H. J., Ludwig W., Kämpfer P. 2010; Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266 [View Article][PubMed]
    [Google Scholar]
  26. Toffin L., Bidault A., Pignet P., Tindall B. J., Slobodkin A., Kato C., Prieur D. 2004; Shewanella profunda sp. nov., isolated from deep marine sediment of the Nankai Trough. Int J Syst Evol Microbiol 54:1943–1949 [View Article][PubMed]
    [Google Scholar]
  27. Tollefson J. 2014; China plunges into ocean research. Nature 506:276 [View Article][PubMed]
    [Google Scholar]
  28. Venkateswaran K., Moser D. P., Dollhopf M. E., Lies D. P., Saffarini D. A., MacGregor B. J., Ringelberg D. B., White D. C., Nishijima M. et al. 1999; Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol 49:705–724 [View Article][PubMed]
    [Google Scholar]
  29. Wang D., Wang Y., Huang H., Lin J., Xiao D., Kan B. 2013; Identification of tetrodotoxin-producing Shewanella spp. from feces of food poisoning patients and food samples. Gut Pathog 5:1–4 [View Article][PubMed]
    [Google Scholar]
  30. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I, Moore L. H., Moore W. E. C., Murray R. G. E. et al. 1987; International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [CrossRef]
    [Google Scholar]
  31. Xiao X., Wang P., Zeng X., Bartlett D. H., Wang F. 2007; Shewanella psychrophila sp. nov. and Shewanella piezotolerans sp. nov., isolated from west Pacific deep-sea sediment. Int J Syst Evol Microbiol 57:60–65 [View Article][PubMed]
    [Google Scholar]
  32. Xu M., Guo J., Cen Y., Zhong X., Cao W., Sun G. 2005; Shewanella decolorationis sp. nov., a dye-decolorizing bacterium isolated from activated sludge of a waste-water treatment plant. Int J Syst Evol Microbiol 55:363–368 [View Article][PubMed]
    [Google Scholar]
  33. Yamamoto S., Harayama S. 1995; PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61:1104–1109[PubMed]
    [Google Scholar]
  34. Yoon J. H., Park S., Jung Y. T., Lee J. S. 2012; Shewanella seohaensis sp. nov., isolated from a tidal flat sediment. Antonie van Leeuwenhoek 102:149–156 [View Article][PubMed]
    [Google Scholar]
  35. 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 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001450
Loading
/content/journal/ijsem/10.1099/ijsem.0.001450
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
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