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).

Funding
This study was supported by the:
  • National Research Foundation of Korea (NRF) (Award 2011-0012369)
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2013-10-01
2024-03-28
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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, 33893402. [View Article] [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, 249251. [View Article] [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, 21552158. [View Article] [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, 179184. [View Article] [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, 25942599. [View Article] [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, 775779. [View Article] [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), D169D172. [View Article] [PubMed]
    [Google Scholar]
  9. Collins M. D. ( 1985 ). Analysis of isoprenoid quinones. . Methods Microbiol 18, 329366. [View Article]
    [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, 523526. [View Article] [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, 416421. [View Article]
    [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, 421426. [View Article] [PubMed]
    [Google Scholar]
  13. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  14. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [View Article]
    [Google Scholar]
  15. Høvik Hansen G. H., Sørheim R. ( 1991 ). Improved method for phenotypical characterization of marine bacteria. . J Microbiol Methods 13, 231241. [View Article]
    [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. 625650. 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, 11971201. [View Article] [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, 18311836. [View Article] [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, 31713173. [View Article] [PubMed]
    [Google Scholar]
  20. Jukes T. H., Cantor C. R. ( 1969 ). Evolution of protein molecules. . In Mammalian Protein Metabolism, pp. 21132. 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, 20562064. [View Article] [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, 4247. [View Article] [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, 716721. [View Article] [PubMed]
    [Google Scholar]
  24. Komagata K., Suzuki K. ( 1987 ). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19, 161206. [View Article]
    [Google Scholar]
  25. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115175. 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, 3539. [View Article] [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, 29602963. [View Article] [PubMed]
    [Google Scholar]
  28. Lee S. D., Lee D. W., Kim J. S. ( 2008 ). Nocardioides hwasunensis sp. nov.. Int J Syst Evol Microbiol 58, 278281. [View Article] [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, 591595. [View Article] [PubMed]
    [Google Scholar]
  30. Marmur J. ( 1961 ). A procedure for the isolation of deoxyribonucleic acid from microorganisms. . J Mol Biol 3, 208218. [View Article]
    [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, 159167. [View Article]
    [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, 233241. [View Article]
    [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, 26192623. [View Article] [PubMed]
    [Google Scholar]
  34. Posada D., Crandall K. A. ( 1998 ). modeltest: testing the model of DNA substitution. . Bioinformatics 14, 817818. [View Article] [PubMed]
    [Google Scholar]
  35. Prauser H. ( 1976 ). Nocardioides, a new genus of the order Actinomycetales . . Int J Syst Bacteriol 26, 5865. [View Article]
    [Google Scholar]
  36. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[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. [View Article] [PubMed]
    [Google Scholar]
  38. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. 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, 105109. [View Article] [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, 226231.[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, 16391652. [View Article] [PubMed]
    [Google Scholar]
  42. Swofford D. L. ( 1998 ). paup* – Phylogenetic analysis using parsimony, version 4. . Sunderland, MA:: Sinauer;.
    [Google Scholar]
  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, 27312739. [View Article] [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, 7883. [View Article] [PubMed]
    [Google Scholar]
  45. Yi H., Chun J. ( 2004a ). Nocardioides aestuarii sp. nov., isolated from tidal flat sediment. . Int J Syst Evol Microbiol 54, 21512154. [View Article] [PubMed]
    [Google Scholar]
  46. Yi H., Chun J. ( 2004b ). Nocardioides ganghwensis sp. nov., isolated from tidal flat sediment. . Int J Syst Evol Microbiol 54, 12951299. [View Article] [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, 933938. [View Article] [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, 675680. [View Article] [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, 7175. [View Article] [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, 271275. [View Article] [PubMed]
    [Google Scholar]
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