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Volume 59, Issue 3

sp. nov., isolated from soil of a ginseng field in South Korea Free

Abstract

A Gram-negative, aerobic, yellow-pigmented, non-spore-forming, motile, rod-shaped bacterium, designated strain Gsoil 3046, was isolated from soil from a ginseng field in Pocheon Province, South Korea, and was characterized taxonomically by using a polyphasic approach. A comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil 3046 belongs to the family in the . The greatest sequence similarity was found with respect to KCTC 12359 (97.7 %), IAM 15069 (97.4 %), DSM 6220 (96.7 %), LMG 19981 (96.2 %) and DSM 16549 (96.0 %). The phylogenetic distances from other recognized species within the family , including KACC 11405, were greater than 4.0 % (i.e. the sequence similarities were less than 96.0 %). DNA–DNA hybridization experiments showed that the levels of DNA–DNA relatedness between strain Gsoil 3046 and its phylogenetically closest neighbours were below 25 %. The G+C content of the genomic DNA was 66.6 mol%. In addition, the presence of ubiquinone Q-8 as the predominant respiratory quinone, iso-C 9, iso-C, iso-C and iso-C as the major cellular fatty acids and iso-C 3-OH and iso-C 3-OH as the major hydroxy fatty acids supported the affiliation of strain Gsoil 3046 to the genus . On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 3046 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is Gsoil 3046 (=KCTC 12599=DSM 18387).

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2009-03-01
2023-04-01
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References

  1. An, D.-S., Im, W.-T., Yang, H.-C., Yang, D.-C. & Lee, S.-T.(2005).Dyella koreensis sp. nov., a β-glucosidase-producing bacterium. Int J Syst Evol Microbiol 55, 1625–1628.[CrossRef] [Google Scholar]
  2. Atlas, R. M.(1993).Handbook of Microbiological Media. Edited by L. C. Parks. Boca Raton, FL: CRC Press.
  3. Buck, J. D.(1982). Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44, 992–993. [Google Scholar]
  4. 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, 224–229.[CrossRef] [Google Scholar]
  5. Felsenstein, J.(1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef] [Google Scholar]
  6. 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]
  7. 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]
  8. 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]
  9. Im, W.-T., Jung, H.-M., Cui, Y.-S., Liu, Q.-M., Zhang, S.-L. & Lee, S.-T.(2005). Cultivation of the three hundreds of bacterial species from the soil of the ginseng field and mining the novel lineage bacteria. In Proceedings of the International Meeting of the Federation of Korean Microbiological Societies, abstract A035, p. 169. Seoul: Federation of Korean Microbiological Societies.
  10. Kim, M. K., Im, W.-T., Ohta, H., Lee, M. & Lee, S.-T.(2005).Sphingopyxis granuli sp. nov., a β-glucosidase-producing bacterium in the family Sphingomonadaceae in α-4 subclass of the Proteobacteria. J Microbiol 43, 152–157. [Google Scholar]
  11. Kim, B.-Y., Weon, H.-Y., Lee, K.-H., Seok, S.-J., Kwon, S.-W., Go, S.-J. & Stackebrandt, E.(2006).Dyella yeojuensis sp. nov., isolated from greenhouse soil in Korea. Int J Syst Evol Microbiol 56, 2079–2082.[CrossRef] [Google Scholar]
  12. Kimura, M.(1983).The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  13. Kouker, G. & Jaeger, K.-E.(1987). Specific and sensitive plate assay for bacterial lipases. Appl Environ Microbiol 53, 211–213. [Google Scholar]
  14. Kumar, S., Tamura, K. & Nei, M.(2004).mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef] [Google Scholar]
  15. Mergaert, J., Cnockaert, M. C. & Swings, J.(2002).Fulvimonas soli gen. nov., sp. nov., a γ-proteobacterium isolated from soil after enrichment on acetylated starch plastic. Int J Syst Evol Microbiol 52, 1285–1289.[CrossRef] [Google Scholar]
  16. 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]
  17. Moore, D. D. & Dowhan, D.(1995). Preparation and analysis of DNA. In Current Protocols in Molecular Biology, pp. 2–11. Edited by F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith & K. Struhl. New York: Wiley.
  18. Nalin, R., Simonet, P., Vogel, T. M. & Normand, P.(1999).Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium. Int J Syst Bacteriol 49, 19–23.[CrossRef] [Google Scholar]
  19. Saitou, N. & Nei, M.(1987). The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  20. Sasser, M.(1990).Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  21. Stackebrandt, E. & Goebel, B. M.(1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846–849.[CrossRef] [Google Scholar]
  22. Swings, J., De Ley, J. & Gillis, M.(1984). Genus III. Frateuria Swings, Gillis, Kersters, De Vos, Gosselé and De Ley, 1980, 547VP. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 210–213. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
  23. 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, 375–382.[CrossRef] [Google Scholar]
  24. Ten, L. N., Baek, S.-H., Im, W.-T., Liu, Q.-M., Aslam, Z. & Lee, S.-T.(2006).Bacillus panaciterrae sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 56, 2861–2866.[CrossRef] [Google Scholar]
  25. 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.[CrossRef] [Google Scholar]
  26. 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, 463–464.[CrossRef] [Google Scholar]
  27. Xie, C. H. & Yokota, A.(2005).Dyella japonica gen. nov., sp. nov., a γ-proteobacterium isolated from soil. Int J Syst Evol Microbiol 55, 753–756.[CrossRef] [Google Scholar]
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Dyella ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea
Int J Syst Evol Microbiol 59, 460 (2009); https://doi.org/10.1099/ijs.0.64514-0
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