1887

Abstract

A Gram-stain-negative, rod-shaped and motile strain, designated PAMC 27536, was isolated from deep-sea sediment in the East Sea, Korea. Analysis of the 16S rRNA gene sequence of the strain showed an affiliation with the genus . Phylogenetic analyses revealed that strain PAMC 27536 was related most closely to CL-YJ9 with a 16S rRNA gene sequence similarity of 98.5 % and to other members of the genus (94.0–91.7 %). Genomic relatedness analyses between strain PAMC 27536 and KCCM 42386 gave an average nucleotide identity of 85.6 % and an estimated DNA–DNA hybridization of 24.6 % using the genome-to-genome distance calculator, indicating that they represent genomically distinct species. Cells of strain PAMC 27536 grew optimally at 25–30 °C and pH 7.0–7.5 in the presence of 3 % (w/v) sea salts. The major cellular fatty acids were Cω6 and/or Cω7, Cω6 and/or Cω7, and C. The major isoprenoid quinone was Q-8. The genomic DNA G+C content was 56.1–57.2 mol%. Based on the phylogenetic, chemotaxonomic, genomic and phenotypic data presented, a novel species with the name sp. nov. is proposed, with PAMC 27536 ( = KCCM 43095 = JCM 30410) as the type strain.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000918
2016-03-01
2021-08-06
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/3/1561.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000918&mimeType=html&fmt=ahah

References

  1. Alfaro-Espinoza G., Ullrich M. S. 2014; Marinobacterium mangrovicola sp. nov., a marine nitrogen-fixing bacterium isolated from mangrove roots of Rhizophora mangle . Int J Syst Evol Microbiol 64:3988–3993 [View Article][PubMed]
    [Google Scholar]
  2. 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]
  3. 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 [View Article][PubMed]
    [Google Scholar]
  4. Baumann P., Bowditch R. D., Baumann L., Beaman B. 1983; Taxonomy of marine Pseudomonas species: P. stanieri sp. nov., P. perfectomarina sp. nov., nom. rev., P. nautica; and P. doudorofii . Int J Syst Bacteriol 33:857–865 [View Article]
    [Google Scholar]
  5. Bowditch R. D., Baumann L., Baumann P. 1984; Description of Oceanospirillum kriegii sp. nov. and O. jannaschii sp. nov. and assignment of two species of Alteromonas to this genus as O. commune comb. nov. and O. vagum comb. nov. Curr Microbiol 10:221–229 [View Article]
    [Google Scholar]
  6. Bruns A., Rohde M., Berthe-Corti L. 2001; Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 51:1997–2006 [View Article][PubMed]
    [Google Scholar]
  7. Cappuccino J. G., Sherman N. 2002 Microbiology: a Laboratory Manual, 6th edn. Menlo Park, CA: Benjamin/Cummings;
    [Google Scholar]
  8. Chang H.-W., Nam Y.-D., Kwon H.-Y., Park J. R., Lee J.-S., Yoon J.-H., An K.-G., Bae J.-W. 2007; Marinobacterium halophilum sp. nov., a marine bacterium isolated from the Yellow Sea. Int J Syst Evol Microbiol 57:77–80 [View Article][PubMed]
    [Google Scholar]
  9. Chimetto L. A., Cleenwerck I., Brocchi M., Willems A., De Vos P., Thompson F. L. 2011; Marinobacterium coralli sp. nov., isolated from mucus of coral (Mussismilia hispida). Int J Syst Evol Microbiol 61:60–64 [View Article][PubMed]
    [Google Scholar]
  10. 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 [View Article][PubMed]
    [Google Scholar]
  11. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [View Article][PubMed]
    [Google Scholar]
  12. González J. M., Mayer F., Moran M. A., Hodson R. E., Whitman W. B. 1997; Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., two marine bacteria from a lignin-rich pulp mill waste enrichment community. Int J Syst Bacteriol 47:369–376 [View Article][PubMed]
    [Google Scholar]
  13. 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]
  14. Hansen G. H., Sørheim R. 1991; Improved method for phenotypical characterization of marine bacteria. J Microbiol Methods 13:231–241 [View Article]
    [Google Scholar]
  15. Huo Y.-Y., Xu X.-W., Cao Y., Wang C.-S., Zhu X.-F., Oren A., Wu M. 2009; Marinobacterium nitratireducens sp. nov. and Marinobacterium sediminicola sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 59:1173–1178 [View Article][PubMed]
    [Google Scholar]
  16. Hwang C. Y., Cho B. C. 2008; Cohaesibacter gelatinilyticus gen. nov., sp. nov., a marine bacterium that forms a distinct branch in the order Rhizobiales, and proposal of Cohaesibacteraceae fam. nov. Int J Syst Evol Microbiol 58:267–277 [View Article][PubMed]
    [Google Scholar]
  17. Hwang C. Y., Kim M. H., Bae G. D., Zhang G. I., Kim Y. H., Cho B. C. 2009; Muricauda olearia sp. nov., isolated from crude-oil-contaminated seawater, and emended description of the genus Muricauda . Int J Syst Evol Microbiol 59:1856–1861 [View Article][PubMed]
    [Google Scholar]
  18. Hwang C. Y., Lee I., Cho Y., Lee Y. M., Baek K., Jung Y.-J., Yang Y. Y., Lee T., Rhee T. S., Lee H. K. 2015; Rhodococcus aerolatus sp. nov., isolated from subarctic rainwater. Int J Syst Evol Microbiol 65:465–471 [View Article][PubMed]
    [Google Scholar]
  19. Jukes T. H., Cantor C. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism vol. 3 pp 21–132Edited by Munro H. N. New York: Academic Press; [CrossRef]
    [Google Scholar]
  20. Kim H., Choo Y.-J., Song J., Lee J.-S., Lee K. C., Cho J.-C. 2007; Marinobacterium litorale sp. nov. in the order Oceanospirillales . Int J Syst Evol Microbiol 57:1659–1662 [View Article][PubMed]
    [Google Scholar]
  21. Kim Y.-G., Jin Y.-A., Hwang C. Y., Cho B. C. 2008; Marinobacterium rhizophilum sp. nov., isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica . Int J Syst Evol Microbiol 58:164–167 [View Article][PubMed]
    [Google Scholar]
  22. Kim H., Oh H.-M., Yang S.-J., Lee J.-S., Hong J.-S., Cho J.-C. 2009a; Marinobacterium marisflavi sp. nov., isolated from a costal seawater. Curr Microbiol 58:511–515 [View Article][PubMed]
    [Google Scholar]
  23. Kim S.-J., Park S.-J., Yoon D.-N., Park B.-J., Choi B.-R., Lee D.-H., Roh Y., Rhee S.-K. 2009b; Marinobacterium maritimum sp. nov., a marine bacterium isolated from Arctic sediment. Int J Syst Evol Microbiol 59:3030–3034 [View Article][PubMed]
    [Google Scholar]
  24. Kim J. M., Lee S. H., Jung J. Y., Jeon C. O. 2010; Marinobacterium lutimaris sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 60:1828–1831 [View Article][PubMed]
    [Google Scholar]
  25. 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]
  26. 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][PubMed]
    [Google Scholar]
  27. Rosselló-Mora R., Amann R. 2001; The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67 [View Article][PubMed]
    [Google Scholar]
  28. Rzhetsky A., Nei M. 1992; A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 9:945–967
    [Google Scholar]
  29. 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]
  30. Satomi M., Kimura B., Hamada T., Harayama S., Fujii T. 2002; Phylogenetic study of the genus Oceanospirillum based on 16S rRNA and gyrB genes: emended description of the genus Oceanospirillum, description of Pseudospirillum gen. nov., Oceanobacter gen. nov. and Terasakiella gen. nov. and transfer of Oceanospirillum jannaschii and Pseudomonas stanieri to Marinobacterium as Marinobacterium jannaschii comb. nov. and Marinobacterium stanieri comb. nov. Int J Syst Evol Microbiol 52:739–747[PubMed]
    [Google Scholar]
  31. Smibert R. M., Krieg N. R. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology pp 607–654Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  32. 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]
  33. 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]
  34. Witthoff S., Mühlroth A., Marienhagen J., Bott M. 2013; C1 metabolism in Corynebacterium glutamicum: an endogenous pathway for oxidation of methanol to carbon dioxide. Appl Environ Microbiol 79:6974–6983 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000918
Loading
/content/journal/ijsem/10.1099/ijsem.0.000918
Loading

Data & Media loading...

Supplements

Supplementary Data

PDF

Most cited this month 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