Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 63, Issue Pt_3

sp. nov., isolated from soil of a ginseng field, and emended descriptions of the genus and of Free

Abstract

A Gram-negative bacterium, designated DCY13, was isolated from soil of a ginseng field in South Korea. Comparative analysis of 16S rRNA gene sequences showed that strain DCY13 shared the highest sequence similarity (95.0 %) with NBRC 103935 and 87.6–91.4 % sequence similarity with other members of the family . Cells were non-spore-forming rods, catalase- and oxidase-positive, motile by gliding and facultatively anaerobic. The only respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids were iso-C 3-OH, iso-C and iso-C G. The GC content of the genomic DNA was 47.5±1.0 mol%. In addition to phosphatidylethanolamine, the major polar lipids were two unidentified aminophospholipids, one unidentified aminolipid and three unidentified polar lipids. The major cell-wall sugars were ribose, xylose and galactose. It is proposed that strain DCY13 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is DCY13 ( = KCTC 12833  = JCM 15794  = DSM 22335). Emended descriptions of the genus and of are also proposed.

  • Published Online:
Funding
This study was supported by the:
  • Next-Generation BioGreen 21 Program (SSAC) (Award PJ008204)
© 2013 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.038554-0
2013-03-01
2025-03-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/3/905.html?itemId=/content/journal/ijsem/10.1099/ijs.0.038554-0&mimeType=html&fmt=ahah

References

  1. An D. S., Lee H. G., Im W. T., Liu Q. M., Lee S. T. ( 2007 ). Segetibacter koreensis gen. nov., sp. nov., a novel member of the phylum Bacteroidetes, isolated from the soil of a ginseng field in South Korea. . Int J Syst Evol Microbiol 57, 1828–1833. [View Article] [PubMed]
    [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, 1049–1070. [View Article] [PubMed]
    [Google Scholar]
  3. Bligh E. G., Dyer W. J. ( 1959 ). A rapid method of total lipid extraction and purification. . Can J Biochem Physiol 37, 911–917. [View Article] [PubMed]
    [Google Scholar]
  4. Buck J. D. ( 1982 ). Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. . Appl Environ Microbiol 44, 992–993.[PubMed]
    [Google Scholar]
  5. Choi D. H., Zhang G. I., Noh J. H., Kim W. S., Cho B. C. ( 2009 ). Gracilimonas tropica gen. nov., sp. nov., isolated from a Synechococcus culture. . Int J Syst Evol Microbiol 9, 1167–1172.[PubMed] [CrossRef]
    [Google Scholar]
  6. 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, 95–98.
     [Google Scholar]
  7. 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, 457–469. [CrossRef]
    [Google Scholar]
  8. Kämpfer P., Young C.-C., Sridhar K. R., Arun A. B., Lai W. A., Shen F. T., Rekha P. D. ( 2006 ). Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arvensicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov.. Int J Syst Evol Microbiol 56, 2223–2228. [View Article] [PubMed]
    [Google Scholar]
  9. Kämpfer P., Lodders N., Falsen E. ( 2011 ). Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov. . Int J Syst Evol Microbiol 61, 518–523.[PubMed] [CrossRef]
    [Google Scholar]
  10. Kasana R. C., Salwan R., Dhar H., Dutt S., Gulati A. ( 2008 ). A rapid and easy method for the detection of microbial cellulases on agar plates using Gram’s iodine. . Curr Microbiol 57, 503–507. [View Article] [PubMed]
    [Google Scholar]
  11. Kim B. Y., Weon H. Y., Yoo S. H., Hong S. B., Kwon S. W., Stackebrandt E., Go S. J. ( 2007 ). Niabella aurantiaca gen. nov., sp. nov., isolated from a greenhouse soil in Korea. . Int J Syst Evol Microbiol 57, 538–541. [View Article] [PubMed]
    [Google Scholar]
  12. Kimura M. ( 1983 ). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  13. Kumar S., Tamura K., Jakobsen I. B., Nei M. ( 2001 ). mega2: molecular evolutionary genetics analysis software. . Bioinformatics 17, 1244–1245. [View Article] [PubMed]
    [Google Scholar]
  14. Lee H.-G., An D.-S., Im W.-T., Liu Q.-M., Na J.-R., Cho D. H., Jin C. W., Lee S.-T., Yang D. C. ( 2007 ). Chitinophaga ginsengisegetis sp. nov. and Chitinophaga ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea. . Int J Syst Evol Microbiol 57, 1396–1401. [View Article] [PubMed]
    [Google Scholar]
  15. Lim J. H., Baek S.-H., Lee S.-T. ( 2009 ). Ferruginibacter alkalilentus gen. nov., sp. nov. and Ferruginibacter lapsinanis sp. nov., novel members of the family ‘Chitinophagaceae’ in the phylum Bacteroidetes, isolated from freshwater sediment. . Int J Syst Evol Microbiol 59, 2394–2399. [View Article] [PubMed]
    [Google Scholar]
  16. Mellmann A., Cloud J., Maier T., Keckevoet U., Ramminger I., Iwen P., Dunn J., Hall G., Wilson D. & other authors ( 2008 ). Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in comparison to 16S rRNA gene sequencing for species identification of nonfermenting bacteria. . J Clin Microbiol 46, 1946–1954. [View Article] [PubMed]
    [Google Scholar]
  17. 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. [View Article]
    [Google Scholar]
  18. Prescott L. M., Harley J. P. ( 2001 ). Laboratory Exercises in Microbiology, , 5th edn.. New York:: McGraw-Hill;.
     [Google Scholar]
  19. Qu J. H., Yuan H. L. ( 2008 ). Sediminibacterium salmoneum gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment of a eutrophic reservoir. . Int J Syst Evol Microbiol 58, 2191–2194. [View Article] [PubMed]
    [Google Scholar]
  20. Qu J.-H., Yuan H.-L., Yang J.-S., Li H.-F., Chen N. ( 2009 ). Lacibacter cauensis gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from sediment of a eutrophic lake. . Int J Syst Evol Microbiol 59, 1153–1157. [View Article] [PubMed]
    [Google Scholar]
  21. 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]
  22. Sangkhobol V., Skerman V. B. D. ( 1981 ). Chitinophaga, a new genus of chitinolytic Myxobacteria . . Int J Syst Bacteriol 31, 285–293. [View Article]
    [Google Scholar]
  23. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc.;
  24. Shiratori H., Tagami Y., Morishita T., Kamihara Y., Beppu T., Ueda K. ( 2009 ). Filimonas lacunae gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from fresh water. . Int J Syst Evol Microbiol 59, 1137–1142. [View Article] [PubMed]
    [Google Scholar]
  25. Sly L. I., Taghavi M., Fegan M. ( 1999 ). Phylogenetic position of Chitinophaga pinensis in the Flexibacter–Bacteroides–Cytophaga phylum. . Int J Syst Bacteriol 49, 479–481. [View Article] [PubMed]
    [Google Scholar]
  26. 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]
  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, 4876–4882. [View Article] [PubMed]
    [Google Scholar]
  28. Urios L., Agogué H., Lesongeur F., Stackebrandt E., Lebaron P. ( 2006 ). Balneola vulgaris gen. nov., sp. nov., a member of the phylum Bacteroidetes from the north-western Mediterranean Sea. . Int J Syst Evol Microbiol 56, 1883–1887. [View Article] [PubMed]
    [Google Scholar]
  29. Urios L., Intertaglia L., Lesongeur F., Lebaron P. ( 2008 ). Balneola alkaliphila sp. nov., a marine bacterium isolated from the Mediterranean Sea. . Int J Syst Evol Microbiol 58, 1288–1291. [View Article] [PubMed]
    [Google Scholar]
  30. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. ( 1991 ). 16S ribosomal DNA amplification for phylogenetic study. . J Bacteriol 173, 697–703.[PubMed]
    [Google Scholar]
  31. Weon H. Y., Kim B.-Y., Yoo S.-H., Lee S.-Y., Kwon S.-W., Go S.-J., Stackebrandt E. ( 2006 ). Niastella koreensis gen. nov., sp. nov. and Niastella yeongjuensis sp. nov., novel members of the phylum Bacteroidetes, isolated from soil cultivated with Korean ginseng. . Int J Syst Evol Microbiol 56, 1777–1782. [View Article] [PubMed]
    [Google Scholar]
  32. Xie C.-H., Yokota A. ( 2006 ). Reclassification of [Flavobacterium] ferrugineum as Terrimonas ferruginea gen. nov., comb. nov., and description of Terrimonas lutea sp. nov., isolated from soil. . Int J Syst Evol Microbiol 56, 1117–1121. [View Article] [PubMed]
    [Google Scholar]
  33. Yoon M.-H., Im W.-T. ( 2007 ). Flavisolibacter ginsengiterrae gen. nov., sp. nov. and Flavisolibacter ginsengisoli sp. nov., isolated from ginseng cultivating soil. . Int J Syst Evol Microbiol 57, 1834–1839. [View Article] [PubMed]
    [Google Scholar]
  34. Zhang K., Tang Y., Zhang L., Dai J., Wang Y., Luo X., Liu M., Luo G., Fang C. ( 2009 ). Parasegetibacter luojiensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from a forest soil. . Int J Syst Evol Microbiol 59, 3058–3062. [View Article] [PubMed]
    [Google Scholar]
  35. Zhang N. N., Qu J. H., Yuan H. L., Sun Y. M., Yang J. S. ( 2010 ). Flavihumibacter petaseus gen. nov., sp. nov., isolated from soil of a subtropical rainforest. . Int J Syst Evol Microbiol 60, 1609–1612. [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijs.0.038554-0
Loading
Sediminibacterium ginsengisoli sp. nov., isolated from soil of a ginseng field, and emended descriptions of the genus Sediminibacterium and of Sediminibacterium salmoneum
Int J Syst Evol Microbiol 63, 905 (2013); https://doi.org/10.1099/ijs.0.038554-0
/content/journal/ijsem/10.1099/ijs.0.038554-0
/content/journal/ijsem/10.1099/ijs.0.038554-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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