1887

Abstract

A novel bacterial strain, YC6899, was isolated from the root of growing on a tidal flat of Namhae Island, Korea. Cells were Gram-reaction-negative, rod-shaped, non-motile, slightly halophilic and heterotrophic. Strain YC6899 grew optimally at a salinity of 2–4 %, at 25–37 °C and at pH 6.5–8.0. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that strain YC6899 was closely related to YIM D10 (96.1 % similarity) and RS.Sph.026 (95.9 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown aminolipids, an unknown aminophospholipid, an unknown aminoglycolipid, unknown glycolipids and unknown lipids. The major fatty acids of strain YC6899 were C cyclo ω8 and Cω7. The G+C content of the genomic DNA was 61.3 mol%. Strain YC6899 contained ubiquinone-10 (Q-10) as the major respiratory quinone system. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YC6899 represents a novel species within the genus , for which the name sp. nov. is proposed. The type strain is YC6899 ( = KACC 14912 = NBRC 107845).

Funding
This study was supported by the:
  • Brain Korea (BK)
  • Ministry of Education, Science and Technology, Korea
  • Ministry of Food, Agriculture, Forestry and Fisheries (Award 808015-3)
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2013-10-01
2024-04-24
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References

  1. Atlas R. M. ( 1993 ). Handbook of Microbiological Media. Edited by Parks L. C. . Boca Raton, FL:: CRC Press;.
    [Google Scholar]
  2. Bernardet J. F., Nakagawa Y., Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes ( 2002 ). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. . Int J Syst Evol Microbiol 52, 10491070. [View Article] [PubMed]
    [Google Scholar]
  3. Bibi F., Yasir M., Song G. C., Lee S. Y., Chung Y. R. ( 2012 ). Diversity and characterization of endophytic bacteria associated with tidal flat plants and their antagonistic effects on oomycetous plant pathogens. . Plant Pathol J 28, 2031. [View Article]
    [Google Scholar]
  4. Cappuccino J. G., Sherman N. ( 2002 ). Microbiology: a Laboratory Manual, , 6th edn.. Menlo Park, CA:: Benjamin/Cummings;.
    [Google Scholar]
  5. Chung B. S., Aslam Z., Kim S. W., Kim G. G., Kang H. S., Ahn J. W., Chung Y. R. ( 2008 ). A bacterial endophyte, Pseudomonas brassicacearum YC5480 isolated from the root of Artemisia sp. producing antifungal and phytotoxic compounds. . Plant Pathol J 24, 461468. [View Article]
    [Google Scholar]
  6. Dittmer J. C., Lester R. L. ( 1964 ). A simple, specific spray for the detection of phospholipids on thin-layer chromatograms. . J Lipid Res 5, 126127.[PubMed]
    [Google Scholar]
  7. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  8. Fitch W. M. ( 1972 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [View Article]
    [Google Scholar]
  9. Gerhardt P., Murray R. G. M., Wood W. A., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  10. Gonzalez J. M., Saiz-Jimenez C. ( 2002 ). A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. . Environ Microbiol 4, 770773. [View Article] [PubMed]
    [Google Scholar]
  11. Hall T. A. ( 1999 ). BioEdit: a user-friendly biological sequencealignment editor and analysis program for Windows 95/98/NT. . Nucleic Acids Symp Ser 41, 9598.
    [Google Scholar]
  12. Hendricks C. W., Doyle J. D., Hugley B. ( 1995 ). A new solid medium for enumerating cellulose-utilizing bacteria in soil. . Appl Environ Microbiol 61, 20162019. [View Article] [PubMed]
    [Google Scholar]
  13. Jacin H., Mishkin A. R. ( 1965 ). Separation of carbohydrates on borate impregnated silica gel G plates. . J Chromatogr A 18, 170173. [View Article] [PubMed]
    [Google Scholar]
  14. Kim H., Choo Y. J., Cho J. C. ( 2007 ). Litoricolaceae fam. nov., to include Litoricola lipolytica gen. nov., sp. nov., a marine bacterium belonging to the order Oceanospirillales . . Int J Syst Evol Microbiol 57, 17931798. [View Article] [PubMed]
    [Google Scholar]
  15. Kim O. S., Cho Y. J., Lee K. H., Yoon S. H., Kim M. C., Na H. S., 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]
  16. Komagata K., Suzuki K. ( 1987 ). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19, 161207. [View Article]
    [Google Scholar]
  17. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115175. Edited by Stackebrandt E., Goodfellow M. . New York:: Wiley;.
    [Google Scholar]
  18. Lányí B. ( 1987 ). Classical and rapid identification methods for medically important bacteria. . Methods Microbiol 19, 167. [View Article]
    [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. . J Microbiol Methods 2, 233241. [View Article]
    [Google Scholar]
  21. Ross H. N. M., Grant W. D., Harris J. E. ( 1985 ). Lipids in archaebacterial taxonomy. . In Chemical Methods in Bacterial Systematics, pp. 289300. Edited by Goodfellow M., Minnikin D. E. . London:: Academic Press;.
    [Google Scholar]
  22. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  23. Shieh W. Y., Chen Y. W., Chaw S. M., Chiu H. H. ( 2003 ). Vibrio ruber sp. nov., a red, facultatively anaerobic, marine bacterium isolated from sea water. . Int J Syst Evol Microbiol 53, 479484. [View Article] [PubMed]
    [Google Scholar]
  24. 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]
  25. 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]
  26. Ten L. N., Im W. T., Kim M. K., Kang M. S., Lee S. T. ( 2004 ). Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates. . J Microbiol Methods 56, 375382. [View Article] [PubMed]
    [Google Scholar]
  27. 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]
  28. Wang Y. X., Liu J. H., Chen Y. G., Zhang X. X., Wang Z. G., Chen Y., Tian S. P., Hu B., Cui X. L. ( 2010 ). Amorphus orientalis sp. nov., an exopolysaccharide-producing bacterium isolated from salt mine sediment. . Int J Syst Evol Microbiol 60, 17501754. [View Article] [PubMed]
    [Google Scholar]
  29. Zeevi Ben Yosef D., Ben-Dov E., Kushmaro A. ( 2008 ). Amorphus coralli gen. nov., sp. nov., a marine bacterium isolated from coral mucus, belonging to the order Rhizobiales . . Int J Syst Evol Microbiol 58, 27042709. [View Article] [PubMed]
    [Google Scholar]
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