1887

Abstract

A Gram-negative, rod-shaped, motile bacterium was isolated from the soil of a ginseng field in Daejeon, South Korea, and characterized in order to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequence analysis revealed that strain DCY34 belonged to the family , and the highest degree of sequence similarity was found with W-50 (97.1 %), Gsoil 250 (97.0 %), S37 (96.9 %), IFO 15033 (96.8 %), RB2256 (96.7 %) and JSS54 (96.7 %). Chemotaxonomic data revealed that strain DCY34 possessed ubiquinone Q-10 as the predominant respiratory lipoquinone, which is common to members of the genus . The predominant fatty acids were C 7 (27.5 %), summed feature 4 (C 7 and/or C iso 2-OH; 18.6 %), C (15.6 %) and summed feature 8 (C 6 and/or unknown 18.864; 15.4 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and an unknown polar lipid. The results of physiological and biochemical tests clearly demonstrated that strain DCY34 represented a separate species and supported its affiliation to the genus . Based on these data, the new isolate represents a novel species, for which the name sp. nov. is proposed. The type strain is DCY34 (=KCTC 22112=JCM 14844).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.019414-0
2010-10-01
2024-12-12
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/60/10/2358.html?itemId=/content/journal/ijsem/10.1099/ijs.0.019414-0&mimeType=html&fmt=ahah

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., Kämpfer P., Denner E. B. 1999; Chemotaxonomic characterisation of Sphingomonas . J Ind Microbiol Biotechnol 23:242–251 [CrossRef]
    [Google Scholar]
  3. 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]
  4. Cappuccino J. G., Sherman N. 2002 Microbiology: a Laboratory Manual, 6th edn. Menlo Park, CA: Benjamin/Cummings;
    [Google Scholar]
  5. 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]
  6. 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]
  7. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
    [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;
    [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. Lee M., Ten L. N., Lee H. W., Oh H. W., Im W. T., Lee S. T. 2008; Sphingopyxis ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 58:2342–2347 [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. Minnikin D. E., Patel P. V., Alshamaony L., Goodfellow M. 1977; Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 27:104–117 [CrossRef]
    [Google Scholar]
  18. Pal R., Bhasin V. K., Lal R. 2006; Proposal to reclassify [ Sphingomonas ] xenophaga Stolz et al. 2000 and [ Sphingomonas ] taejonensis Lee etal. 2001 as Sphingobium xenophagum comb. nov. and Sphingopyxis taejonensis comb. nov., respectively. Int J Syst Evol Microbiol 56:667–670 [CrossRef]
    [Google Scholar]
  19. Saitou N., Nei M. 1987; The neighbor-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;
    [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. 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]
  24. Tamaoka J., Komagata K. 1984; Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128 [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. 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]
  27. Vancanneyt M., Schut F., Snauwaert C., Goris J., Swings J., Gottschal J. C. 2001; Sphingomonas alaskensis sp. nov., a dominant bacterium from a marine oligotrophic environment. Int J Syst Evol Microbiol 51:73–79
    [Google Scholar]
  28. 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]
  29. 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
    [Google Scholar]
  30. 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., Sphingomonascapsulata comb. nov., and two genospecies of the genus Sphingomonas . Microbiol Immunol 34:99–119 [CrossRef]
    [Google Scholar]
  31. 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]
/content/journal/ijsem/10.1099/ijs.0.019414-0
Loading
/content/journal/ijsem/10.1099/ijs.0.019414-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

PDF
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