1887

Abstract

A novel bacterial strain, designated Dae 13, was isolated from sediment from a freshwater lake in Daejeon, South Korea, and was characterized taxonomically by using a polyphasic approach. The isolate was Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the genus in the family but was clearly separate from established species of this genus. The 16S rRNA gene sequence similarities between strain Dae 13 and type strains of species with validly published names ranged from 91.6 to 97.5 %. The G+C content of the genomic DNA was 33.8 mol%. Chemotaxonomic data, i.e. the presence of MK-7 as the major menaquinone and iso-C, C and summed feature 3 (iso-C 2-OH and/or C 7) as the major fatty acids, supported the affiliation of strain Dae 13 to the genus . However, the results of physiological and biochemical tests allowed phenotypic differentiation of the isolate with respect to species with validly published names. Therefore, strain Dae 13 represents a novel species within the genus , for which the name sp. nov. is proposed. The type strain is Dae 13 (=KCTC 12637=LMG 23489).

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2009-01-01
2019-10-16
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References

  1. Buck, J. D. ( 1982; ). Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44, 992–993.
    [Google Scholar]
  2. 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]
  3. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  4. 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]
  5. 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]
  6. Hwang, C. Y., Choi, D. H. & Cho, B. C. ( 2006; ). Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 56, 1831–1836.[CrossRef]
    [Google Scholar]
  7. 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]
  8. Kimura, M. ( 1983; ). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  9. 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]
  10. 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]
  11. Moore, D. D. & Dowhan, D. ( 1995; ). Preparation and analysis of DNA. In Current Protocols in Molecular Biology, pp. 2–11. Edited by F. W. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith & K. Struhl. New York: Wiley.
  12. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  13. Sasser, M. ( 1990; ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  14. Shivaji, S., Chaturvedi, P., Reddy, G. S. N. & Suresh, K. ( 2005; ). Pedobacter himalayensis sp. nov., from the Hamta glacier located in the Himalayan mountain ranges of India. Int J Syst Evol Microbiol 55, 1083–1088.[CrossRef]
    [Google Scholar]
  15. 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]
  16. Steyn, P. L., Segers, P., Vancanneyt, M., Sandra, P., Kersters, K. & Joubert, J. J. ( 1998; ). Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. Proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 48, 165–177.[CrossRef]
    [Google Scholar]
  17. 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]
  18. Ten, L. N., Liu, Q.-M., Im, W.-T., Lee, M., Yang, D.-C. & Lee, S.-T. ( 2006; ). Pedobacter gingsengisoli sp. nov., a DNase-producing bacterium isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 56, 2565–2570.[CrossRef]
    [Google Scholar]
  19. 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]
  20. Vanparys, B., Heylen, K., Lebbe, L. & De Vos, P. ( 2005; ). Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum. Int J Syst Evol Microbiol 55, 1315–1318.[CrossRef]
    [Google Scholar]
  21. Yoon, J.-H., Lee, M.-H., Kang, S.-J., Park, S.-Y. & Oh, T.-K. ( 2006; ). Pedobacter sandarakinus sp. nov., isolated from soil. Int J Syst Evol Microbiol 56, 1273–1277.[CrossRef]
    [Google Scholar]
  22. Yoon, J.-H., Kang, S.-J., Park, S. & Oh, T.-K. ( 2007a; ). Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov., isolated from soil. Int J Syst Evol Microbiol 57, 2089–2095.[CrossRef]
    [Google Scholar]
  23. Yoon, M.-H., Ten, L. N., Im, W.-T. & Lee, S.-T. ( 2007b; ). Pedobacter panaciterrae sp. nov., isolated from soil in South Korea. Int J Syst Evol Microbiol 57, 381–386.[CrossRef]
    [Google Scholar]
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