1887

Abstract

A Gram-negative, aerobic, non-motile, non-spore-forming rod, designated DC-3, was isolated from activated sludge of a wastewater treatment plant in China. Comparative 16S rRNA gene sequence analysis showed that strain DC-3 belonged to the family and formed a lineage within the genus . Strain DC-3 shared the highest 16S rRNA gene sequence similarity with KIS28-6 (97.1 %) and A3 (97.1 %). The G+C content of the genomic DNA was 71.5 mol%. The major respiratory quinone was Q-8 and the major fatty acids were iso-Cω9c (31.6 %), iso-C (12.6 %), iso-C (21.3 %), iso-C (13.1 %) and iso-C 3-OH (6.5 %), which supported the affiliation of strain DC-3 with the genus . DNA–DNA relatedness between strain DC-3 and its closest phylogenetic neighbours was <30 %. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain DC-3 from the recognized species of the genus . On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DC-3 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is DC-3 ( = CCTCC AB 2011179  = KACC 16511). The description of the genus is also emended.

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 30970099)
  • Natural Science Foundation of Jiangsu Province, China (Award BK2011066)
  • Fundamental Research Funds for the Central Universities (Award KYZ201122)
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2013-04-01
2024-04-19
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References

  1. Bernardet J.-F., Nakagawa Y., Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes ( 2002 ). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. . Int J Syst Evol Microbiol 52, 10491070. [View Article] [PubMed]
    [Google Scholar]
  2. Buck J. D. ( 1982 ). Nonstaining (KOH) method for determination of gram reactions of marine bacteria. . Appl Environ Microbiol 44, 992993.[PubMed]
    [Google Scholar]
  3. Chun J., Lee J.-H., Jung Y., Kim M., Kim S., Kim B. K., Lim Y.-W. ( 2007 ). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. . Int J Syst Evol Microbiol 57, 22592261. [View Article] [PubMed]
    [Google Scholar]
  4. Collins M. D., Jones D. ( 1980 ). Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2,4-diaminobutyric acid. . J Appl Bacteriol 48, 459470. [View Article]
    [Google Scholar]
  5. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. ( 1977 ). Distribution of menaquinones in actinomycetes and corynebacteria. . J Gen Microbiol 100, 221230. [View Article] [PubMed]
    [Google Scholar]
  6. Cunha S., Tiago I., Luísa Pires A., da Costa M. S., Veríssimo A. ( 2006 ). Dokdonella fugitiva sp. nov., a Gammaproteobacterium isolated from potting soil. . Syst Appl Microbiol 29, 191196. [View Article] [PubMed]
    [Google Scholar]
  7. 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, 224229. [View Article]
    [Google Scholar]
  8. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  9. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  10. 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]
  11. Lane D. L. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115175. Edited by Stackebrandt E. R., Goodfellow M. . Chichester, UK:: Wiley;.
    [Google Scholar]
  12. Mandel M., Marmur J. ( 1968 ). Use of ultraviolet absorbance-temperature profile for determining the guanine plus cytosine content of DNA. . Methods Enzymol 12, 195206. [View Article]
    [Google Scholar]
  13. 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]
  14. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  15. Sambrook J., Russell D. W. ( 2001 ). Molecular Cloning: a Laboratory Manual, , 3rd edn.. Cold Spring Harbor, NY:: Cold Spring Harbor Laboratory;.
    [Google Scholar]
  16. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  17. 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]
  18. Suzuki T., Yamasato K. ( 1994 ). Phylogeny of spore-forming lactic acid bacteria based on 16S rRNA gene sequences. . FEMS Microbiol Lett 115, 1317. [View Article] [PubMed]
    [Google Scholar]
  19. Tamaoka J., Katayama-Fujimura Y., Kuraishi H. ( 1983 ). Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. . J Appl Bacteriol 54, 3136. [View Article]
    [Google Scholar]
  20. 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]
  21. Ten L. N., Jung H.-M., Im W.-T., Oh H. W., Yang D.-C., Yoo S.-A., Lee S.-T. ( 2009 ). Dokdonella ginsengisoli sp. nov., isolated from soil from a ginseng field, and emended description of the genus Dokdonella . . Int J Syst Evol Microbiol 59, 19471952. [View Article] [PubMed]
    [Google Scholar]
  22. 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, 48764882. [View Article] [PubMed]
    [Google Scholar]
  23. 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, 463464. [View Article]
    [Google Scholar]
  24. Yoo S.-H., Weon H.-Y., Anandham R., Kim B.-Y., Hong S.-B., Jeon Y.-A., Koo B.-S., Kwon S.-W. ( 2009 ). Dokdonella soli sp. nov., a gammaproteobacterium isolated from soil. . Int J Syst Evol Microbiol 59, 19651968. [View Article] [PubMed]
    [Google Scholar]
  25. Yoon J.-H., Kang S.-J., Oh T.-K. ( 2006 ). Dokdonella koreensis gen. nov., sp. nov., isolated from soil. . Int J Syst Evol Microbiol 56, 145150. [View Article] [PubMed]
    [Google Scholar]
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