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Abstract

A Gram-positive, rod-shaped, non-spore-forming bacterium (Gsoil 1124) was isolated from soil of a ginseng field of Pocheon province in South Korea, and was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 1124 was shown to belong to the family and related to (98.2 % 16S rRNA gene sequence similarity), (98.1 %), (97.7 %) and (97.5 %). The sequence similarity with any other species with validly published names within the genus was less than 94.5 %. Strain Gsoil 1124 was characterized chemotaxonomically as having -2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H) as the predominant menaquinone and iso-C, C, C, and C 9 as the major fatty acids. The G+C content of the genomic DNA was 70.2 mol%. The chemotaxonomic properties and phenotypic characteristics supported the affiliation of strain Gsoil 1124 to the genus . The results of physiological and biochemical tests, and the low level of DNA–DNA relatedness allowed genotypic differentiation of strain Gsoil 1124 from recognized species. Therefore, strain Gsoil 1124 is considered to represent a novel species, for which the name sp. nov. is proposed, with the type strain Gsoil 1124 (=KCTC 19135=CCUG 52478=DSM 17921).

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2009-12-01
2020-01-17
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References

  1. Atlas, R. M. ( 1993; ). Handbook of Microbiological Media. Edited by L. C. Parks. Boca Raton, FL: CRC Press.
  2. Ausubel, F. W., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. & Struhl, K. ( 1995; ). Current Protocols in Molecular Biology. In Preparation and Analysis of DNA. New York: Wiley.
  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. Cappuccino, J. G. & Sherman, N. ( 2002; ). Microbiology: a Laboratory Manual, 6th edn. Menlo Park, CA: Benjamin/Cummings.
  5. Chou, J.-H., Cho, N.-T., Arun, A. B., Young, C.-C. & Chen, W.-M. ( 2008; ). Nocardioides fonticola sp. nov., a novel actinomycete isolated from spring water. Int J Syst Evol Microbiol 58, 1864–1868.[CrossRef]
    [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, 2292–2296.[CrossRef]
    [Google Scholar]
  7. Dastager, S. G., Lee, J.-C., Ju, Y.-J., Park, D.-J. & Kim, C.-J. ( 2009; ). Nocardioides sediminis sp. nov., isolated from a sediment sample. Int J Syst Evol Microbiol 59, 280–284.[CrossRef]
    [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, 224–229.[CrossRef]
    [Google Scholar]
  9. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  10. 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]
  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, 95–98.
    [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, 457–469.[CrossRef]
    [Google Scholar]
  13. 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 soil of a 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.
  14. 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, 2056–2064.[CrossRef]
    [Google Scholar]
  15. 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, 42–47.[CrossRef]
    [Google Scholar]
  16. Kimura, M. ( 1983; ). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  17. Komagata, K. & Suzuki, K. ( 1987; ). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161–207.
    [Google Scholar]
  18. Kouker, G. & Jaeger, K.-E. ( 1987; ). Specific and sensitive plate assay for bacterial lipase. Appl Environ Microbiol 53, 211–213.
    [Google Scholar]
  19. 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]
  20. Lee, D -S., Lee, D. W. & Kim, J.-S. ( 2008; ). Norcardioides hwasunensis sp. nov. Int J Syst Bacteriol 58, 278–281.[CrossRef]
    [Google Scholar]
  21. 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]
  22. Prauser, H. ( 1976; ). Nocardioides, a new genus of the order Actinomycetales. Int J Syst Bacteriol 26, 58–65.[CrossRef]
    [Google Scholar]
  23. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  24. Sasser, M. ( 1990; ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  25. 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]
  26. Suzuki, K. & Komagata, K. ( 1983; ). Pimelobacter gen. nov., a new genus of coryneform bacteria with LL-diaminopimelic acid in the cell wall. J Gen Appl Microbiol 29, 59–71.[CrossRef]
    [Google Scholar]
  27. 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]
  28. Ten, L. N., Jung, H.-M., Yoo, S.-A., Im, W.-T. & Lee, S.-T. ( 2008; ). Lysobacter daecheongensis sp. nov., isolated from sediment of stream near the Daechung dam in South Korea. J Microbiol 46, 519–524.[CrossRef]
    [Google Scholar]
  29. 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]
  30. 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, 78–83.[CrossRef]
    [Google Scholar]
  31. Tschech, A. & Pfennig, N. ( 1984; ). Growth yield increase linked to caffeate reduction in Acetobacterium woodii. Arch Microbiol 137, 163–167.[CrossRef]
    [Google Scholar]
  32. 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]
  33. Widdel, F. & Bak, F. ( 1992; ). Gram-negative mesophilic sulfate reducing bacteria. In The Prokaryotes, 2nd edn, pp. 3352–3378. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York: Springer.
  34. Widdel, F., Kohring, G. & Mayer, F. ( 1983; ). Studies in dissimilatory sulfate-reducing bacteria that decompose fatty acids. III. Characterization of the filamentous gliding Desulfonema limicola gen. nov., sp. nov. and Desulfonema magnum sp. nov. Arch Microbiol 134, 286–294.[CrossRef]
    [Google Scholar]
  35. Yoon, J.-H., Kang, S.-J., Lee, M.-H. & Oh, T.-K. ( 2008; ). Nocardioides hankookensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 58, 434–437.[CrossRef]
    [Google Scholar]
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