1887

Abstract

A Gram-staining-positive, non-motile, aerobic, non-spore-forming and short rod-shaped bacterial strain, PAMC 26527, was isolated from biofilm formed in coastal seawater of the Norwegian Sea. Analysis of the 16S rRNA gene sequence of strain PAMC 26527 revealed a clear affiliation with the genus . Based on phylogenetic analysis, strain PAMC 26527 showed the closest phylogenetic relationship with YC6903 with 16S rRNA gene sequence similarity of 96.3 %. Strain PAMC 26527 grew in the presence of 0–5.0 % sea salts. The optimum temperature and pH for growth were 20 °C and pH 7.5. The major cellular fatty acids of strain PAMC 26527 were iso-C, Cω8 and Cω9 and the major isoprenoid quinone was MK-8(H). Cell-wall analysis showed that strain PAMC 26527 contained -diaminopimelic acid. The genomic DNA G+C content was 69.3 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain PAMC 26527 could be clearly distinguished from recognized members of the genus . Thus, strain PAMC 26527 should be classified as representing a novel species in the genus , for which the name sp. nov. is proposed. The type strain is PAMC 26527 ( = KCTC 29158 = JCM 18743).

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2013-10-01
2019-10-15
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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 and psi-blast: a new generation of protein database search programs. . Nucleic Acids Res 25:, 3389–3402. [CrossRef][PubMed]
    [Google Scholar]
  2. Anzai Y., Kudo Y., Oyaizu H.. ( 1997;). The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. . Int J Syst Bacteriol 47:, 249–251. [CrossRef][PubMed]
    [Google Scholar]
  3. Bhadra B., Roy P., Chakraborty R.. ( 2005;). Serratia ureilytica sp. nov., a novel urea-utilizing species. . Int J Syst Evol Microbiol 55:, 2155–2158. [CrossRef][PubMed]
    [Google Scholar]
  4. Busse H.-J., Schumann P.. ( 1999;). Polyamine profiles within genera of the class Actinobacteria with ll-diaminopimelic acid in the peptidoglycan. . Int J Syst Bacteriol 49:, 179–184. [CrossRef][PubMed]
    [Google Scholar]
  5. Cappuccino J. G., Sherman N.. ( 2002;). Microbiology: a Laboratory Manual, , 6th edn.. Menlo Park, CA:: Benjamin/Cummings;.
    [Google Scholar]
  6. Cho Y., Jang G. I., Cho B. C.. ( 2013;). Nocardioides marinquilinus sp. nov., isolated from coastal seawater. . Int J Syst Evol Microbiol 63:, 2594–2599. [CrossRef][PubMed]
    [Google Scholar]
  7. Choi D. H., Kim H. M., Noh J.-H., Cho B. C.. ( 2007;). Nocardioides marinus sp. nov.. Int J Syst Evol Microbiol 57:, 775–779. [CrossRef][PubMed]
    [Google Scholar]
  8. Cole J. R., Chai B., Farris R. J., Wang Q., Kulam-Syed-Mohideen A. S., McGarrell D. M., Bandela A. M., Cardenas E., Garrity G. M., Tiedje J. M.. ( 2007;). The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. . Nucleic Acids Res 35: (Database issue), D169–D172. [CrossRef][PubMed]
    [Google Scholar]
  9. Collins M. D.. ( 1985;). Analysis of isoprenoid quinones. . Methods Microbiol 18:, 329–366. [CrossRef]
    [Google Scholar]
  10. Collins M. D., Cockcroft S., Wallbanks S.. ( 1994;). Phylogenetic analysis of a new ll-diaminopimelic acid-containing coryneform bacterium from herbage, Nocardioides plantarum sp. nov.. Int J Syst Bacteriol 44:, 523–526. [CrossRef][PubMed]
    [Google Scholar]
  11. Enger Ø., Nygaard H., Solberg M., Schei G., Nielsen J., Dundas I.. ( 1987;). Characterization of Alteromonas denitrificans sp. nov.. Int J Syst Bacteriol 37:, 416–421. [CrossRef]
    [Google Scholar]
  12. Englen M. D., Kelley L. C.. ( 2000;). A rapid DNA isolation procedure for the identification of Campylobacter jejuni by the polymerase chain reaction. . Lett Appl Microbiol 31:, 421–426. [CrossRef][PubMed]
    [Google Scholar]
  13. Felsenstein J.. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368–376. [CrossRef][PubMed]
    [Google Scholar]
  14. 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]
  15. Høvik Hansen G. H., Sørheim R.. ( 1991;). Improved method for phenotypical characterization of marine bacteria. . J Microbiol Methods 13:, 231–241. [CrossRef]
    [Google Scholar]
  16. Holt J. G., Krieg N. R., Sneath P. H. A., Staley J. T., Williams S. T.. ( 1994;). Nocardioform actinomycetes. . In Shorter Bergey's Manual of Determinative Bacteriology, pp. 625–650. Edited by Hensyl W. R... Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  17. Hwang C. Y., Cho B. C.. ( 2006;). Flectobacillus lacus sp. nov., isolated from a highly eutrophic pond in Korea. . Int J Syst Evol Microbiol 56:, 1197–1201. [CrossRef][PubMed]
    [Google Scholar]
  18. Hwang C. Y., Choi D. H., Cho B. C.. ( 2006;). Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter. . Int J Syst Evol Microbiol 56:, 1831–1836. [CrossRef][PubMed]
    [Google Scholar]
  19. Jeon Y. S., Chung H., Park S., Hur I., Lee J. H., Chun J.. ( 2005;). jphydit: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences. . Bioinformatics 21:, 3171–3173. [CrossRef][PubMed]
    [Google Scholar]
  20. 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;.
    [Google Scholar]
  21. Kim H. M., Choi D. H., Hwang C. Y., Cho B. C.. ( 2008;). Nocardioides salarius sp. nov., isolated from seawater enriched with zooplankton. . Int J Syst Evol Microbiol 58:, 2056–2064. [CrossRef][PubMed]
    [Google Scholar]
  22. Kim K. H., Roh S. W., Chang H. W., Nam Y. D., Yoon J. H., Jeon C. O., Oh H. M., Bae J. W.. ( 2009;). Nocardioides basaltis sp. nov., isolated from black beach sand. . Int J Syst Evol Microbiol 59:, 42–47. [CrossRef][PubMed]
    [Google Scholar]
  23. 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]
  24. Komagata K., Suzuki K.. ( 1987;). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19:, 161–206. [CrossRef]
    [Google Scholar]
  25. Lane D. J.. ( 1991;). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by Stackebrandt E., Goodfellow M... Chichester:: Wiley;.
    [Google Scholar]
  26. Lee S. D.. ( 2007;). Nocardioides furvisabuli sp. nov., isolated from black sand. . Int J Syst Evol Microbiol 57:, 35–39. [CrossRef][PubMed]
    [Google Scholar]
  27. Lee D. W., Hyun C. G., Lee S. D.. ( 2007;). Nocardioides marinisabuli sp. nov., a novel actinobacterium isolated from beach sand. . Int J Syst Evol Microbiol 57:, 2960–2963. [CrossRef][PubMed]
    [Google Scholar]
  28. Lee S. D., Lee D. W., Kim J. S.. ( 2008;). Nocardioides hwasunensis sp. nov.. Int J Syst Evol Microbiol 58:, 278–281. [CrossRef][PubMed]
    [Google Scholar]
  29. Lee S. H., Liu Q. M., Lee S. T., Kim S. C., Im W. T.. ( 2012;). Nocardioides ginsengagri sp. nov., isolated from the soil of a ginseng field. . Int J Syst Evol Microbiol 62:, 591–595. [CrossRef][PubMed]
    [Google Scholar]
  30. Marmur J.. ( 1961;). A procedure for the isolation of deoxyribonucleic acid from microorganisms. . J Mol Biol 3:, 208–218. [CrossRef]
    [Google Scholar]
  31. 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. [CrossRef]
    [Google Scholar]
  32. 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]
  33. Park S. C., Baik K. S., Kim M. S., Chun J., Seong C. N.. ( 2008;). Nocardioides dokdonensis sp. nov., an actinomycete isolated from sand sediment. . Int J Syst Evol Microbiol 58:, 2619–2623. [CrossRef][PubMed]
    [Google Scholar]
  34. Posada D., Crandall K. A.. ( 1998;). modeltest: testing the model of DNA substitution. . Bioinformatics 14:, 817–818. [CrossRef][PubMed]
    [Google Scholar]
  35. Prauser H.. ( 1976;). Nocardioides, a new genus of the order Actinomycetales. . Int J Syst Bacteriol 26:, 58–65. [CrossRef]
    [Google Scholar]
  36. 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]
  37. Scheidle M., Dittrich B., Klinger J., Ikeda H., Klee D., Büchs J.. ( 2011;). Controlling pH in shake flasks using polymer-based controlled-release discs with pre-determined release kinetics. . BMC Biotechnol 11:, 25. [CrossRef][PubMed]
    [Google Scholar]
  38. Smibert R. M., Krieg N. R.. ( 1994;). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, 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]
  39. Song G. C., Yasir M., Bibi F., Chung E. J., Jeon C. O., Chung Y. R.. ( 2011;). Nocardioides caricicola sp. nov., an endophytic bacterium isolated from a halophyte, Carex scabrifolia Steud.. Int J Syst Evol Microbiol 61:, 105–109. [CrossRef][PubMed]
    [Google Scholar]
  40. Staneck J. L., Roberts G. D.. ( 1974;). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. . Appl Microbiol 28:, 226–231.[PubMed]
    [Google Scholar]
  41. Suzuki M., Nakagawa Y., Harayama S., Yamamoto S.. ( 2001;). Phylogenetic analysis and taxonomic study of marine Cytophaga-like bacteria: proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov.. Int J Syst Evol Microbiol 51:, 1639–1652. [CrossRef][PubMed]
    [Google Scholar]
  42. Swofford D. L.. ( 1998;). paup* – Phylogenetic analysis using parsimony, version 4. . Sunderland, MA:: Sinauer;.
  43. 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]
  44. Tóth E. M., Kéki Z., Homonnay Z. G., Borsodi A. K., Márialigeti K., Schumann P.. ( 2008;). Nocardioides daphniae sp. nov., isolated from Daphnia cucullata (Crustacea: Cladocera). . Int J Syst Evol Microbiol 58:, 78–83. [CrossRef][PubMed]
    [Google Scholar]
  45. Yi H., Chun J.. ( 2004a;). Nocardioides aestuarii sp. nov., isolated from tidal flat sediment. . Int J Syst Evol Microbiol 54:, 2151–2154. [CrossRef][PubMed]
    [Google Scholar]
  46. Yi H., Chun J.. ( 2004b;). Nocardioides ganghwensis sp. nov., isolated from tidal flat sediment. . Int J Syst Evol Microbiol 54:, 1295–1299. [CrossRef][PubMed]
    [Google Scholar]
  47. Yoon J.-H., Rhee S.-K., Lee J.-S., Park Y.-H., Lee S.-T.. ( 1997;). Nocardioides pyridinolyticus sp. nov., a pyridine-degrading bacterium isolated from the oxic zone of an oil shale column. . Int J Syst Bacteriol 47:, 933–938. [CrossRef][PubMed]
    [Google Scholar]
  48. Yoon J.-H., Cho Y. G., Lee S. T., Suzuki K. I., Nakase T., Park Y. H.. ( 1999;). Nocardioides nitrophenolicus sp. nov., a p-nitrophenol-degrading bacterium. . Int J Syst Bacteriol 49:, 675–680. [CrossRef][PubMed]
    [Google Scholar]
  49. Yoon J.-H., Kim I.-G., Kang K. H., Oh T.-K., Park Y.-H.. ( 2004;). Nocardioides aquiterrae sp. nov., isolated from groundwater in Korea. . Int J Syst Evol Microbiol 54:, 71–75. [CrossRef][PubMed]
    [Google Scholar]
  50. Yoon J.-H., Lee C. H., Oh T. K.. ( 2006;). Nocardioides lentus sp. nov., isolated from an alkaline soil. . Int J Syst Evol Microbiol 56:, 271–275. [CrossRef][PubMed]
    [Google Scholar]
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