1887

Abstract

A Gram-reaction-positive, aerobic, coccus- to rod-shaped, non-motile, non-spore-forming bacterium (strain UKS-03) was isolated from a sediment sample of Ungok Lake in Gochang, Republic of Korea. The taxonomic position of this bacterium was determined in an investigation based on a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain UKS-03 was shown to belong to the family and to be related most closely to Gsoil 485 (98.5 % similarity), MSL-09 (98.4 %) and ‘’ Gsoil 958 (97.3 %). Strain UKS-03 was characterized chemotaxonomically as having -2,6-diaminopimelic acid in its cell-wall peptidoglycan, MK-8(H) as the predominant menaquinone, diphosphatidylglycerol and phosphatidylglycerol as the main polar lipids, and iso-C, Cω8 and C 10-methyl as its major fatty acids. The G+C content of the genomic DNA was 71.9 mol%. Mean DNA–DNA relatedness values between strain UKS-03 and Gsoil 485, KCTC 19272 and ‘’ Gsoil 958 were 37.5 ± 7.2, 6.8 ± 0.9 and 3.1 ± 0.7 %, respectively. On the basis of the data from this polyphasic taxonomic study, strain UKS-03 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is UKS-03 ( = KACC 18304 = LMG 28591).

Funding
This study was supported by the:
  • National Institute of Biological Resources
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000657
2015-12-01
2024-10-11
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/12/4857.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000657&mimeType=html&fmt=ahah

References

  1. Ahn J. H., Lim J. M., Kim S. J., Song J., Kwon S. W., Weon H. Y. ( 2014;). Nocardioides paucivorans sp. nov. isolated from soil. J Microbiol 52 990994 [View Article] [PubMed] .
    [Google Scholar]
  2. Atlas R. M. ( 1993;). Handbook of Microbiological Media. . Edited by Parks L. C. Boca Raton, FL: CRC Press;.
    [Google Scholar]
  3. Buck J. D. ( 1982;). Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44 992993 [PubMed].
    [Google Scholar]
  4. Cappuccino J. G., Sherman N. ( 2002). Microbiology: a Laboratory Manual , 6th edn. Benjamin Cummings, CA: Pearson Education;.
    [Google Scholar]
  5. Cui Y., Woo S. G., Lee J., Sinha S., Kang M. S., Jin L., Kim K. K., Park J., Lee M., Lee S. T. ( 2013;). Nocardioides daeguensis sp. nov., a nitrate-reducing bacterium isolated from activated sludge of an industrial wastewater treatment plant. Int J Syst Evol Microbiol 63 37273732 [View Article] [PubMed] .
    [Google Scholar]
  6. Dastager S. G., Lee J. C., Ju Y. J., Park D. J., Kim C. J. ( 2008;). Nocardioides koreensis sp. nov, Nocardioides bigeumensis sp. nov. and Nocardioides agariphilus sp. nov. isolated from soil from Bigeum Island, Korea. Int J Syst Evol Microbiol 58 22922296 [View Article] [PubMed] .
    [Google Scholar]
  7. Euzéby J. P. ( 1997;). List of bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Bacteriol 47 590592 [View Article] [PubMed] .
    [Google Scholar]
  8. Ezaki T., Hashimoto Y., Yabuuchi E. ( 1989;). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39 224229 [View Article].
    [Google Scholar]
  9. Felsenstein J. ( 1985;). Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39 783791 [View Article].
    [Google Scholar]
  10. 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]
  11. Hall T. A. ( 1999;). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41 9598.
    [Google Scholar]
  12. Hiraishi A., Ueda Y., Ishihara J., Mori T. ( 1996;). Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42 457469 [View Article].
    [Google Scholar]
  13. Im W.-T., Kim S.-Y., Liu Q.-M., Yang J.-E., Lee S.-T., Yi T.-H. ( 2010;). Nocardioides ginsengisegetis sp. nov, isolated from soil of a ginseng field. J Microbiol 48 623628 [View Article] [PubMed] .
    [Google Scholar]
  14. 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]
  15. Kim J. K., Liu Q. M., Park H. Y., Kang M. S., Kim S. C., Im W. T., Yoon M. H. ( 2013;). Nocardioides panaciterrulae sp. nov, isolated from soil of a ginseng field, with ginsenoside converting activity. Antonie van Leeuwenhoek 103 13851393 [View Article] [PubMed] .
    [Google Scholar]
  16. Kimura M. ( 1983). The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; [View Article].
    [Google Scholar]
  17. Komagata K., Suzuki K. ( 1987;). Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 19 161207 [View Article].
    [Google Scholar]
  18. Lim J. M., Kim S. J., Hamada M., Ahn J. H., Weon H. Y., Suzuki K., Ahn T. Y., Kwon S. W. ( 2014;). Nocardioides daecheongensis sp. nov, isolated from soil. Int J Syst Evol Microbiol 64 41094114 [View Article] [PubMed] .
    [Google Scholar]
  19. 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]
  20. 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. Int J Microbiol Methods 2 233241 [View Article].
    [Google Scholar]
  21. Moore D. D., Dowhan D. ( 1995;). Preparation and analysis of DNA. . In Current Protocols in Molecular Biology, pp. 211. Edited by Ausubel F. W., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. New York: Wiley;.
    [Google Scholar]
  22. Prauser H. ( 1976;). Nocardioides, a new genus of the order Actinomycetales . Int J Syst Bacteriol 26 5865 [View Article].
    [Google Scholar]
  23. Saitou N., Nei M. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 406425 [PubMed].
    [Google Scholar]
  24. Sasser M. ( 1990). Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI Inc;.
    [Google Scholar]
  25. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30 27252729 [View Article] [PubMed] .
    [Google Scholar]
  26. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. ( 1997;). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25 48764882 [View Article] [PubMed] .
    [Google Scholar]
  27. 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., other authors. ( 1987;). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37 463464 [View Article].
    [Google Scholar]
  28. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. ( 1991;). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173 697703 [PubMed].
    [Google Scholar]
  29. Zhang D. F., Zhong J. M., Zhang X. M., Jiang Z., Zhou E. M., Tian X. P., Zhang S., Li W. J. ( 2014;). Nocardioides nanhaiensis sp. nov, an actinobacterium isolated from a marine sediment sample. Int J Syst Evol Microbiol 64 27182722 [View Article] [PubMed] .
    [Google Scholar]
  30. Zhi X.-Y., Li W.-J., Stackebrandt E. ( 2009;). An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 59 589608 [View Article] [PubMed] .
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.000657
Loading
/content/journal/ijsem/10.1099/ijsem.0.000657
Loading

Data & Media loading...

Supplements

Supplementary Data

PDF
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