1887

Abstract

Strain T5-04, a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from soil of a ginseng field in South Korea and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain T5-04 belongs to the -4 subgroup of the , and the highest degrees of sequence similarity determined were to IFO 10564 (97·5 %), JSS26 (97·1 %), IFO 15500 (96·7 %) and IFO 15498 (96·6 %). Chemotaxonomic data revealed that strain T5-04 possesses ubiquinone Q-10 predominantly, C as the predominant fatty acid and sphingoglycolipids, all of which corroborate its assignment to the genus . The results of DNA–DNA hybridization and physiological and biochemical tests clearly demonstrated that strain T5-04 represents a distinct species. Based on polyphasic evidence, T5-04 (=KCTC 12210=NBRC 100801=IAM 15213) should be classified as the type strain of a novel species, for which the name sp. nov. is proposed.

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2006-04-01
2019-10-20
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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. Busse, H.-J., Denner, E. B. M., Buczolits, S., Salkinoja-Salonen, M., Bennasar, A. & Kämpfer, P. ( 2003; ). Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air- and dustborne and antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas. Int J Syst Evol Microbiol 53, 1253–1260.[CrossRef]
    [Google Scholar]
  3. Cappuccino, J. G. & Sherman, N. ( 2002; ). Microbiology: a Laboratory Manual, 6th edn. San Francisco: Pearson Education, Inc. and Benjamin Cummings.
  4. Collins, M. D. & Jones, D. ( 1981; ). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 45, 316–354.
    [Google Scholar]
  5. 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]
  6. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  7. Fitch, W. M. ( 1972; ). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406–416.
    [Google Scholar]
  8. Fujii, K., Satomi, M., Morita, N., Motomura, T., Tanaka, T. & Kikuchi, S. ( 2003; ). Novosphingobium tardaugens sp. nov., an oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo. Int J Syst Evol Microbiol 53, 47–52.[CrossRef]
    [Google Scholar]
  9. Godoy, F., Vancanneyt, M., Martínez, M., Steinbüchel, A., Swings, J. & Rehm, B. H. A. ( 2003; ). Sphingopyxis chilensis sp. nov., a chlorophenol-degrading bacterium that accumulates polyhydroxyalkanoate, and transfer of Sphingomonas alaskensis to Sphingopyxis alaskensis comb. nov. Int J Syst Evol Microbiol 53, 473–477.[CrossRef]
    [Google Scholar]
  10. 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]
  11. Kämpfer, P., Witzenberger, R., Denner, E. B. M., Busse, H.-J. & Neef, A. ( 2002; ). Sphingopyxis witflariensis sp. nov. isolated from activated sludge. Int J Syst Evol Microbiol 52, 2029–2034.[CrossRef]
    [Google Scholar]
  12. 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]
  13. Kimura, M. ( 1983; ). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  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. Lee, J.-S., Shin, Y. K., Yoon, J.-H., Takeuchi, M., Pyun, Y.-R. & Park, Y.-H. ( 2001; ). Sphingomonas aquatilis sp. nov., Sphingomonas koreensis sp. nov. and Sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water. Int J Syst Evol Microbiol 51, 1491–1498.
    [Google Scholar]
  16. Li, Y., Kawamura, Y., Fujiwara, N., Naka, T., Liu, H., Huang, X., Kobayashi, K. & Ezaki, T. ( 2004; ). Sphingomonas yabuuchiae sp. nov. and Brevundimonas nasdae sp. nov., isolated from the Russian space laboratory Mir. Int J Syst Evol Microbiol 54, 819–825.[CrossRef]
    [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.[CrossRef]
    [Google Scholar]
  18. MIDI ( 1999; ). Sherlock Microbial Identification System Operating Manual, version 3.0. Newark, DE: MIDI, Inc.
  19. Rivas, R., Abril, A., Trujillo, M. E. & Velázquez, E. ( 2004; ). Sphingomonas phyllosphaerae sp. nov., from the phyllosphere of Acacia caven in Argentina. Int J Syst Evol Microbiol 54, 2147–2150.[CrossRef]
    [Google Scholar]
  20. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  21. Shin, Y. K., Lee, J.-S., Chun, C. O., Kim, H.-J. & Park, Y.-H. ( 1996; ). Isoprenoid quinone profiles of the Leclercia adecarboxylata KCTC 1036T. J Microbiol Biotechnol 6, 68–69.
    [Google Scholar]
  22. Sohn, J. H., Kwon, K. K., Kang, J.-H., Jung, H.-B. & Kim, S.-J. ( 2004; ). Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int J Syst Evol Microbiol 54, 1483–1487.[CrossRef]
    [Google Scholar]
  23. 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]
  24. Takeuchi, M., Sakane, T., Yanagi, M., Yamasato, K., Hamana, K. & Yokota, A. ( 1995; ). Taxonomic study of bacteria isolated from plants: proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov. Int J Syst Bacteriol 45, 334–341.[CrossRef]
    [Google Scholar]
  25. Takeuchi, M., Hamana, K. & Hiraishi, A. ( 2001; ). Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 51, 1405–1417.
    [Google Scholar]
  26. 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]
  27. Tiirola, M. A., Busse, H.-J., Kämpfer, P. & Männistö, M. K. ( 2005; ). Novosphingobium lentum sp. nov., a psychrotolerant bacterium from a polychlorophenol bioremediation process. Int J Syst Evol Microbiol 55, 583–588.[CrossRef]
    [Google Scholar]
  28. Ushiba, Y., Takahara, Y. & Ohta, H. ( 2003; ). Sphingobium amiense sp. nov., a novel nonylphenol-degrading bacterium isolated from a river sediment. Int J Syst Evol Microbiol 53, 2045–2048.[CrossRef]
    [Google Scholar]
  29. Yabuuchi, E., Yano, I., Oyaizu, H., Hashimoto, Y., Ezaki, T. & Yamamoto, H. ( 1990; ). Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol Immunol 34, 99–119.[CrossRef]
    [Google Scholar]
  30. Yabuuchi, E., Kosako, Y., Fujiwara, N., Naka, T., Matsunaga, I., Ogura, H. & Kobayashi, K. ( 2002; ). Emendation of the genus Sphingomonas Yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastomonas ursincola. Int J Syst Evol Microbiol 52, 1485–1496.[CrossRef]
    [Google Scholar]
  31. Yoon, J.-H. & Oh, T.-K. ( 2005; ). Sphingopyxis flavimaris sp. nov., isolated from sea water of the Yellow Sea in Korea. Int J Syst Evol Microbiol 55, 369–373.[CrossRef]
    [Google Scholar]
  32. Yoon, J.-H., Lee, C.-H., Yeo, S.-H. & Oh, T.-K. ( 2005; ). Sphingopyxis baekryungensis sp. nov., an orange-pigmented bacterium isolated from sea water of the Yellow Sea in Korea. Int J Syst Evol Microbiol 55, 1223–1227.[CrossRef]
    [Google Scholar]
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