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Abstract

A Gram-staining-negative, oxidase- and catalase-positive, non-motile, aerobic and rod-shaped bacterium producing white colonies, PAMC 20958, was isolated from a marine sediment of the Arctic. PAMC 20958 grew at 10–27 °C (optimally at 21 °C), at pH 5.5–9.5 (optimally at pH 7.0–7.5) and in the presence of 0.5–7.5 % (w/v) (optimally at 2.0 %) NaCl. PAMC 20958 showed 97.5 % 16S rRNA gene sequence similarity with KCTC 32362 and formed a robust phylogenetic clade with this species. The average nucleotide identity value between strain PAMC 20958 and KCTC 32362 was 79.7 % and the genome-to-genome distance was 13.0 % on average. The genomic DNA G+C content calculated from the genome sequence was 53.2 mol%. The major fatty acids were Cω7 and/or Cω6. The major respiratory isoprenoid quinone was ubiquinone-10 (Q-10) and major polar lipids were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. On the basis of phylogenetic analysis and genotypic and phenotypic data obtained in this study, it is concluded that strain PAMC 20958 ( = KCTC 42129 = JCM 30530) represents the type strain of a novel species of the genus for which the name sp. nov. is proposed.

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2015-11-01
2019-10-19
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References

  1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J.. ( 1997;). Gapped blast psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402 [CrossRef] [PubMed].
    [Google Scholar]
  2. Auch A. F., von Jan M., Klenk H.-P., Göker M.. ( 2010;). Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2: 117–134 [CrossRef] [PubMed].
    [Google Scholar]
  3. Cho J.-C., Giovannoni S. J.. ( 2004;). Cultivation and growth characteristics of a diverse group of oligotrophic marine Gammaproteobacteria. Appl Environ Microbiol 70: 432–440 [CrossRef] [PubMed].
    [Google Scholar]
  4. Choo Y.-J., Lee K., Song J., Cho J.-C.. ( 2007;). Puniceicoccus vermicola gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam. nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum ‘Verrucomicrobia’. Int J Syst Evol Microbiol 57: 532–537 [CrossRef] [PubMed].
    [Google Scholar]
  5. Cole J. R., Wang Q., Fish J. A., Chai B., McGarrell D. M., Sun Y., Brown C. T., Porras-Alfaro A., Kuske C. R., Tiedje J. M.. ( 2014;). Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42: (D1), D633–D642 [CrossRef] [PubMed].
    [Google Scholar]
  6. Felsenstein J.. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368–376 [CrossRef] [PubMed].
    [Google Scholar]
  7. 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]
  8. Giovannoni S., Rappé M.. ( 2000;). Evolution, diversity and molecular ecology of marine prokaryotes. . In Microbial Ecology of the Oceans, pp. 47–84. Edited by Kirchman D. L.. New York: Wiley;.
    [Google Scholar]
  9. Gordon R. E., Barnett D. A., Handerhan J. E., Pang C. H. -N.. ( 1974;). Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24: 54–63 [CrossRef].
    [Google Scholar]
  10. 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]
  11. Jorgensen J. H., Turnidge J. D., Washington J. A.. ( 1999;). Antibacterial susceptibility tests: dilution and disk diffusion methods. . In Manual of Clinical Microbiology, pp. 1526–1543. Edited by Murray P. R., Baron E. J., Pfaller M. A., Tenover F. C., Yolken R. H.. Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  12. 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; [CrossRef].
    [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 [CrossRef] [PubMed].
    [Google Scholar]
  14. Kim Y.-O., Park S., Kim H., Park D. S., Nam B. H., Kim D. G., Yoon J. H.. ( 2014;). Halocynthiibacter namhaensis gen. nov., sp. nov., a novel alphaproteobacterium isolated from sea squirt Halocynthia roretzi. Antonie van Leeuwenhoek 105: 881–889 [CrossRef] [PubMed].
    [Google Scholar]
  15. Komagata K., Suzuki K.. ( 1987;). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19: 161–207 [CrossRef].
    [Google Scholar]
  16. Liu K., Zong R., Li Q., Fu Y., Xu Y., Wang Y., Jiao N.. ( 2012;). Oceaniovalibus guishaninsula gen. nov., sp. nov., a marine bacterium of the family Rhodobacteraceae. Curr Microbiol 64: 385–391 [CrossRef] [PubMed].
    [Google Scholar]
  17. Lyman J., Fleming R. H.. ( 1940;). Composition of sea water. J Mar Res 3: 134–146.
    [Google Scholar]
  18. 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 [CrossRef].
    [Google Scholar]
  19. 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] [PubMed].
    [Google Scholar]
  20. Rosselló-Mora R., Amann R.. ( 2001;). The species concept for prokaryotes. FEMS Microbiol Rev 25: 39–67 [CrossRef] [PubMed].
    [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.
    [Google Scholar]
  22. Smibert R. M., Krieg N. R.. ( 1994;). Phenotypic characteristics. . In Methods for General and Molecular Biology, pp. 607–654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R.. Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  23. 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 [CrossRef] [PubMed].
    [Google Scholar]
  24. 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, pp. 330–393. Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R.. Washington, DC: American Society for Microbiology; [CrossRef].
    [Google Scholar]
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