1887

Abstract

A Gram-stain-negative, aerobic, rod-shaped bacterium, designated M41, was isolated from a surface seawater sample collected from the western Pacific Ocean. The isolate grew in medium containing 0.5–10.0 % (w/v) NaCl (optimally at 1.0–3.0 %) at 15–45 °C and pH 5.5–9.5. Positive for oxidase, catalase and nitrate reduction. The respiratory quinone is Q-10. The major fatty acids (>10 %) are iso-C, iso-Cω9 and summed feature 3 (comprising Cω7 and/or iso-C 2-OH). The major polar lipids are phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid, and three unidentified glycolipids.The genomic DNA G+C content is 56.3 mol %. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M41should be assigned to the genus . The 16S rRNA gene sequence similarities between the isolate and the type strains of species of the genus with validly published names were in the range 96.2– 98.6 %. Strain M41 exhibited average nucleotide identity (ANI) values of 81.7 and 72.3 % with respect to S3-22 and JCM 12864, respectively. The genome-to-genome distance analysis revealed that strain M41 shared 51.4 % DNA–DNA relatedness with S3-22 and 16.3 % with JCM 12864. On the basis of phenotypic and genotypic characteristics, strain M41 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is M41 (=CGMCC 1.15304=JCM 30877). An emended description of is also provided.

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2016-06-10
2024-03-29
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References

  1. Baumann P., Baumann L., Mandel M. 1971; Taxonomy of marine bacteria: The genus Beneckea . J Bacteriol 107:268–294[PubMed]
    [Google Scholar]
  2. Dong X., Cai M. 2001 Determinative Manual for Routine Bacteriology Beijing: Scientific Press (English translation);
    [Google Scholar]
  3. Felsenstein J. 1981; Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17:368–376 [View Article][PubMed]
    [Google Scholar]
  4. 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]
  5. Goris J., Konstantinidis K. T., Klappenbach J. A., Coenye T., Vandamme P., Tiedje J. M. 2007; DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91 [View Article][PubMed]
    [Google Scholar]
  6. Kamekura M., Kates M. 1988; Lipids of halophilic archaebacteria. In Halophilic Bacteria II pp. 25–54 Edited by Rodriguez-Valera F. Boca Raton, FL: CRC Press;
    [Google Scholar]
  7. 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]
    [Google Scholar]
  8. 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]
  9. Komagata K., Suzuki K.-I. 1987; Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207 [View Article]
    [Google Scholar]
  10. Kwon K. K., Lee H. S., Yang S. H., Kim S. J. 2005; Kordiimonas gwangyangensis gen. nov., sp. nov., a marine bacterium isolated from marine sediments that forms a distinct phyletic lineage (Kordiimonadales ord. nov.) in the 'Alphaproteobacteria'. Int J Syst Evol Microbiol 55:2033–2037 [View Article][PubMed]
    [Google Scholar]
  11. Lee I., Kim Y. O., Park S.-C., Chun J. 2016; OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103 [CrossRef]
    [Google Scholar]
  12. Leifson E. 1963; Determination of carbohydrate metabolism of marine bacteria. J Bacteriol 85:1183–1184
    [Google Scholar]
  13. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Buchner A., Lai T., Steppi S. et al. 2004; ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371 [View Article][PubMed]
    [Google Scholar]
  14. Marmur J. 1961; The formation of hybrid DNA molecules and their use in studies of DNA homologies. J Mol Biol 3:208–218 [View Article][PubMed]
    [Google Scholar]
  15. Math R. K., Jeong S. H., Jin H. M., Park M. S., Kim J. M., Jeon C. O. 2012; Kordiimonas aestuarii sp. nov., a marine bacterium isolated from a tidal flat. Int J Syst Evol Micr 62:3049–3054 [CrossRef]
    [Google Scholar]
  16. Meier-Kolthoff J. P., Auch A. F., Klenk H. P., Göker M. 2013; Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60 [View Article][PubMed]
    [Google Scholar]
  17. Paramasivam N., Ben-Dov E., Arotsker L., Kushmaro A. 2013; Eilatimonas milleporae gen. nov., sp. nov., a marine bacterium isolated from the hydrocoral millepora dichotoma . Int J Syst Evol Microbiol 63:1880–1884 [View Article]
    [Google Scholar]
  18. Park Y. D., Baik K. S., Yi H., Bae K. S., Chun J. 2005; Pseudoalteromonas byunsanensis sp. nov., isolated from tidal flat sediment in korea. Int J Syst Evol Microbiol 55:2519–2523 [View Article]
    [Google Scholar]
  19. Pruesse E., Quast C., Knittel K., Fuchs B. M., Ludwig W., Peplies J., Glöckner F. O. 2007; SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188–7196 [View Article][PubMed]
    [Google Scholar]
  20. Richter M., Rosselló-Móra R. 2009; Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106:19126–19131 [View Article]
    [Google Scholar]
  21. 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]
  22. 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]
  23. Teramoto M., Nishijima M. 2014; Temperatibacter marinus gen. nov., sp. nov., a mesophilic bacterium isolated from surface seawater and description of Temperatibacteraceae fam. nov. in the class Alphaproteobacteria . Int J Syst Evol Microbiol 64:3075–3080 [View Article]
    [Google Scholar]
  24. Thompson J. D., Higgins D. G., Gibson T. J. 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 [View Article]
    [Google Scholar]
  25. Tindall B. J., Sikorski J., Smibert R. A., Krieg N. R. 2007; Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology, 3rd edn. pp. 330–393 Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G., Schmidt T. M., Snyder L. R. Washington, DC: American Society of Microbiology;
    [Google Scholar]
  26. 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; Report of the Ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [CrossRef]
    [Google Scholar]
  27. Xu X.-W., Huo Y.-Y., Bai X.-D., Wang C.-S., Oren A., Li S.-Y., Wu M. 2011; Kordiimonas lacus sp. nov., isolated from a ballast water tank, and emended description of the genus Kordiimonas . Int J Syst Evol Microbiol 61:422–426 [View Article]
    [Google Scholar]
  28. Xu X.-W., Wu M., Oren A. 2014; The Family Kordiimonadaceae. In The Prokaryotes pp. 307–312 Edited by Rosenberg E., DeLong E. F., Lory S., Stackebrandt E., Thompson F. Berlin: Springer; [View Article]
    [Google Scholar]
  29. Xu X. W., Wu Y. H., Zhou Z., Wang C. S., Zhou Y. G., Zhang H. B., Wang Y., Wu M. 2007; Halomonas saccharevitans sp. nov., Halomonas arcissp. nov. and Halomonas subterranea sp. nov., halophilic bacteria isolated from hypersaline environments of China. Int J Syst Evol Microbiol 57:1619–1624 [View Article][PubMed]
    [Google Scholar]
  30. Yang S. H., Kim M. R., Seo H. S., Lee S. H., Lee J. H., Kim S.-J., Kwon K. K. 2013; Description of Kordiimonas aquimaris sp. nov., isolated from seawater, and emended descriptions of the genus Kordiimonas Kwon et al. 2005 emend. Xu, et al. 2011 and of its existing species. Int J Syst Evol Microbiol 63:298–302 [View Article]
    [Google Scholar]
  31. Yarza P., Richter M., Peplies J., Euzeby J., Amann R., Schleifer K.-H., Ludwig W., Glöckner F. O., Rosselló-Móra R. 2008; The all-species living tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250 [View Article]
    [Google Scholar]
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