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-C15:0, iso-C17:1ω9c and summed feature 3 (comprising C16:1ω7c and/or iso-C15:0 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 Kordiimonas . The 16S rRNA gene sequence similarities between the isolate and the type strains of species of the genus Kordiimonas 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 Kordiimonas. lacus S3-22 and Kordiimonas gwangyangensis JCM 12864, respectively. The genome-to-genome distance analysis revealed that strain M41 shared 51.4 % DNA–DNA relatedness with K. lacus S3-22 and 16.3 % with K. gwangyangensis JCM 12864. On the basis of phenotypic and genotypic characteristics, strain M41 represents a novel species of the genus Kordiimonas , for which the name Kordiimonas lipolytica sp. nov. is proposed. The type strain is M41 (=CGMCC 1.15304=JCM 30877). An emended description of Kordiimonas lacus is also provided.

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2016-06-10
2019-10-23
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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. [CrossRef] [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. [CrossRef]
    [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. [CrossRef] [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. [CrossRef]
    [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. [CrossRef] [PubMed]
    [Google Scholar]
  9. Komagata K. , Suzuki K.-I. . ( 1987;). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19: 161–207. [CrossRef]
    [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. [CrossRef] [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. [CrossRef] [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. [CrossRef] [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. [CrossRef] [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. [CrossRef]
    [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. [CrossRef]
    [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. [CrossRef] [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. [CrossRef]
    [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. [CrossRef] [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. [CrossRef]
    [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. [CrossRef]
    [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. [CrossRef]
    [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;. [CrossRef]
    [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. [CrossRef] [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. [CrossRef]
    [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. [CrossRef]
    [Google Scholar]
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