1887

Abstract

A halo- and organo-sensitive oligotrophic bacterium, designated strain SY-6, was isolated from humus forest soil at Gyeryong mountain in Korea. Cells of the strain were Gram-negative, strictly aerobic, non-motile rods and the strain formed yellow-pigmented colonies on 100-fold-diluted nutrient broth. Strain SY-6 grew at pH 6.0–7.0 (optimal growth at pH 7.0), at 10–37 °C (optimal growth at 28 °C) and at salinities of 0–0.5 % (w/v) NaCl, growing optimally at 0.01 % (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain SY-6 was shown to belong to the genus and showed the closest phylogenetic similarity to B2-7 (96.7 %). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. The predominant ubiquinone and polyamine were Q-10 and -homospermidine, respectively. The major fatty acids were Cω7 and C. The DNA G+C content of the novel isolate was 65.3 mol%. On the basis of the evidence from this polyphasic study, strain SY-6 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SY-6 ( = KACC 12948 = NBRC 105508).

Funding
This study was supported by the:
  • Regional SubGenBank Support Program of the Rural Development Administration, Republic of Korea
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2014-05-01
2021-10-21
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References

  1. An D. S., Liu Q.-M., Lee H. G., Jung M. S., Kim S. C., Lee S. T., Im W. T. ( 2013 ). Sphingomonas ginsengisoli sp. nov. and Sphingomonas sediminicola sp. nov.. Int J Syst Evol Microbiol 63, 496501. [View Article] [PubMed]
    [Google Scholar]
  2. Anzai Y., Kim H., Park J. Y., Wakabayashi H., Oyaizu H. ( 2000 ). Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. . Int J Syst Evol Microbiol 50, 15631589. [View Article] [PubMed]
    [Google Scholar]
  3. Busse H.-J., Auling G. ( 1988 ). Polyamine pattern as chemotaxonomic marker within the Proteobacteria . . Syst Appl Microbiol 11, 18. [View Article]
    [Google Scholar]
  4. Busse H.-J., Bunka S., Hensel A., Lubitz W. ( 1997 ). Discrimination of members of the family Pasteurellaceae based on polyamine patterns. . Int J Syst Bacteriol 47, 698708. [View Article]
    [Google Scholar]
  5. Busse H.-J., Kämpfer P., Denner E. B. M. ( 1999 ). Chemotaxonomic characterisation of Sphingomonas . . J Ind Microbiol Biotechnol 23, 242251. [View Article] [PubMed]
    [Google Scholar]
  6. Busse H.-J., Denner E. B., 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, 12531260. [View Article] [PubMed]
    [Google Scholar]
  7. Chen H., Jogler M., Tindall B. J., Klenk H. P., Rohde M., Busse H.-J., Overmann J. ( 2013 ). Sphingomonas starnbergensis sp. nov., isolated from a prealpine freshwater lake. . Int J Syst Evol Microbiol 63, 10171023. [View Article] [PubMed]
    [Google Scholar]
  8. Collins M. D., Jones D. ( 1981 ). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. . Microbiol Rev 45, 316354.[PubMed]
    [Google Scholar]
  9. DeLong E. F. ( 1992 ). Archaea in coastal marine environments. . Proc Natl Acad Sci U S A 89, 56855689. [View Article] [PubMed]
    [Google Scholar]
  10. Euzéby J. P. ( 2013 ). Genus Sphingomonas . . In List of Prokaryotic Names with Standing in Nomenclature. http://www.bacterio.net/sphingomonas.html.
    [Google Scholar]
  11. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  12. Felsenstein J. ( 1985 ). Confidence limit on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  13. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [View Article]
    [Google Scholar]
  14. Geueke B., Busse H.-J., Fleischmann T., Kämpfer P., Kohler H. P. E. ( 2007 ). Description of Sphingosinicella xenopeptidilytica sp. nov., a β-peptide-degrading species, and emended descriptions of the genus Sphingosinicella and the species Sphingosinicella microcystinivorans . . Int J Syst Evol Microbiol 57, 107113. [View Article] [PubMed]
    [Google Scholar]
  15. Kawahara K., Kuraishi H., Zähringer U. ( 1999 ). Chemical structure and function of glycosphingolipids of Sphingomonas spp and their distribution among members of the α-4 subclass of Proteobacteria . . J Ind Microbiol Biotechnol 23, 408413. [View Article] [PubMed]
    [Google Scholar]
  16. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. & other authors ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [View Article] [PubMed]
    [Google Scholar]
  17. Kimura M. ( 1980 ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16, 111120. [View Article] [PubMed]
    [Google Scholar]
  18. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A. & other authors ( 2007 ). clustal w and clustal x version 2.0. . Bioinformatics 23, 29472948. [View Article] [PubMed]
    [Google Scholar]
  19. Lee K. B., Liu C. T., Anzai Y., Kim H., Aono T., Oyaizu H. ( 2005 ). The hierarchical system of the ‘Alphaproteobacteria’: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov.. Int J Syst Evol Microbiol 55, 19071919. [View Article] [PubMed]
    [Google Scholar]
  20. Luo Y. R., Tian Y., Huang X., Kwon K., Yang S. H., Seo H. S., Kim S. J., Zheng T. L. ( 2012 ). Sphingomonas polyaromaticivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from an oil port water sample. . Int J Syst Evol Microbiol 62, 12231227. [View Article] [PubMed]
    [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, 159167. [View Article]
    [Google Scholar]
  22. Minnikin D. E., O’Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H. ( 1984 ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2, 233241. [View Article]
    [Google Scholar]
  23. Murray R. G. E., Doetsch R. N., Robinow F. ( 1994 ). Determinative and cytological light microscopy. . In Methods for General and Molecular Bacteriology, pp. 2141. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  24. Niharika N., Jindal S., Kaur J., Lal R. ( 2012 ). Sphingomonas indica sp. nov., isolated from hexachlorocyclohexane (HCH)-contaminated soil. . Int J Syst Evol Microbiol 62, 29973002. [View Article] [PubMed]
    [Google Scholar]
  25. Rosselló-Mora R., Amann R. ( 2001 ). The species concept for prokaryotes. . FEMS Microbiol Rev 25, 3967. [View Article] [PubMed]
    [Google Scholar]
  26. Saito H., Miura K. ( 1963 ). Preparation of transforming deoxyribonucleic acid by phenol treatment. . Biochim Biophys Acta 72, 619629. [View Article] [PubMed]
    [Google Scholar]
  27. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  28. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  29. Stackebrandt E., Ebers J. ( 2006 ). Taxonomic parameters revisited: tarnished gold standards. . Microbiol Today 33, 152155.
    [Google Scholar]
  30. 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, 846849. [View Article]
    [Google Scholar]
  31. Stackebrandt E., Frederiksen W., Garrity G. M., Grimont P. A. D., Kämpfer P., Maiden M. C. J., Nesme X., Rosselló-Mora R., Swings J. & other authors ( 2002 ). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. . Int J Syst Evol Microbiol 52, 10431047. [View Article] [PubMed]
    [Google Scholar]
  32. Stolz A., Busse H.-J., Kämpfer P. ( 2007 ). Pseudomonas knackmussii sp. nov.. Int J Syst Evol Microbiol 57, 572576. [View Article] [PubMed]
    [Google Scholar]
  33. 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, 14051417.[PubMed]
    [Google Scholar]
  34. Tamaoka J., Komagata K. ( 1984 ). Determination of DNA base composition by reverse-phase high-performance liquid chromatography. . FEMS Microbiol Lett 25, 125128. [View Article]
    [Google Scholar]
  35. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011 ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28, 27312739. [View Article] [PubMed]
    [Google Scholar]
  36. 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, 99119. [View Article] [PubMed]
    [Google Scholar]
  37. Yabuuchi E., Kosako Y., Naka T., Suzuki S., Yano I. ( 1999 ). Proposal of Sphingomonas suberifaciens (van Bruggen, Jochimsen and Brown 1990) comb. nov., Sphingomonas natatoria (Sly 1985) comb. nov., Sphingomonas ursincola (Yurkov et al. 1997) comb. nov., and emendation of the genus Sphingomonas . . Microbiol Immunol 43, 339349. [View Article] [PubMed]
    [Google Scholar]
  38. 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, 14851496. [View Article] [PubMed]
    [Google Scholar]
  39. Zhang Y. Q., Chen Y. G., Li W. J., Tian X. P., Xu L. H., Jiang C. L. ( 2005 ). Sphingomonas yunnanensis sp. nov., a novel Gram-negative bacterium from a contaminated plate. . Int J Syst Evol Microbiol 55, 23612364. [View Article] [PubMed]
    [Google Scholar]
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