1887

Abstract

A Gram-stain-negative, non-motile, pale yellow, rod-shaped bacterial strain, YW14, was isolated from soil and its taxonomic position was investigated by a polyphasic study. Strain YW14 did not form nodules on three different legumes, and the and genes were not detected by PCR. Strain YW14 contained Q-10 as the predominant ubiquinone. The major cellular fatty acid was Cω7. Phylogenetic analyses based on 16S rRNA gene sequences and seven housekeeping gene sequences (, and ) showed that strain YW14 belonged to the genus . Strain YW14 showed 16S rRNA gene sequence similarity of 93.4–97.3 % to the type strains of recognized species of the genus . DNA–DNA relatedness between strain YW14 and the type strains of IS123 and CCBAU 71623 was 19.6–25.7 %, indicating that strain YW14 was distinct from them genetically. Strain YW14 could also be differentiated from these phylogenetically related species of the genus by various phenotypic properties. On the basis of phenotypic properties, phylogenetic distinctiveness and genetic data, strain YW14 is considered to represent a novel species of the genus , for which the name Rhizobium sp. nov. is proposed. The type strain is YW14 ( = KACC 17222 = CCTCC AB2013042).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31200087)
  • Ministry of Education of China (Award IRT1256)
  • Jiangsu Higher Education Institutions
  • 111 project (Award B12009)
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2014-06-01
2024-12-03
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References

  1. Chen Q., Sun L. N., Zhang X., He J., Kwon S.-W., Zhang J., Li S. P., Gu J. G. ( 2014 ). Roseomonas rhizosphaerae sp. nov., a triazophos-degrading bacterium isolated from soil. . Int J Syst Evol Microbiol doi:10.1099/ijs.0.057000-0 [Epub ahead of print]. [View Article] [PubMed]
    [Google Scholar]
  2. 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]
  3. Diange E. A., Lee S.-S. ( 2013 ). Rhizobium halotolerans sp. nov., isolated from chloroethylenes contaminated soil. . Curr Microbiol 66, 599605. [View Article] [PubMed]
    [Google Scholar]
  4. 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]
  5. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  6. 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]
  7. Frank B. ( 1889 ). Über die Pilzsymbiose der Leguminosen. . Ber Dtsch Bot Ges 7, 332346 (in German).
    [Google Scholar]
  8. 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]
  9. 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]
  10. Kimura M. ( 1983 ). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  11. Lane D. J., Pace B., Olsen G. J., Stahl D. A., Sogin M. L., Pace N. R. ( 1985 ). Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. . Proc Natl Acad Sci U S A 82, 69556959. [View Article] [PubMed]
    [Google Scholar]
  12. 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]
  13. Marmur J., Doty P. ( 1962 ). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. . J Mol Biol 5, 109118. [View Article] [PubMed]
    [Google Scholar]
  14. Martens M., Delaere M., Coopman R., De Vos P., Gillis M., Willems A. ( 2007 ). Multilocus sequence analysis of Ensifer and related taxa. . Int J Syst Evol Microbiol 57, 489503. [View Article] [PubMed]
    [Google Scholar]
  15. Peng G., Yuan Q., Li H., Zhang W., Tan Z. ( 2008 ). Rhizobium oryzae sp. nov., isolated from the wild rice Oryza alta . . Int J Syst Evol Microbiol 58, 21582163. [View Article] [PubMed]
    [Google Scholar]
  16. Poly F., Monrozier L. J., Bally R. ( 2001 ). Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. . Res Microbiol 152, 95103. [View Article] [PubMed]
    [Google Scholar]
  17. Ramana Ch. V., Parag B., Girija K. R., Ram B. R., Ramana V. V., Sasikala Ch. ( 2013 ). Rhizobium subbaraonis sp. nov., an endolithic bacterium isolated from beach sand. . Int J Syst Evol Microbiol 63, 581585. [View Article] [PubMed]
    [Google Scholar]
  18. Rivas R., Velázquez E., Willems A., Vizcaíno N., Subba-Rao N. S., Mateos P. F., Gillis M., Dazzo F. B., Martínez-Molina E. ( 2002 ). A new species of Devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L.f.) druce. . Appl Environ Microbiol 68, 52175222. [View Article] [PubMed]
    [Google Scholar]
  19. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  20. Sambrook J., Russell D. W. ( 2001 ). Molecular Cloning: a Laboratory Manual, , 3rd edn.. Cold Spring Harbor, NY:: Cold Spring Harbor Laboratory Press;.
    [Google Scholar]
  21. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI;.
    [Google Scholar]
  22. Sawaya W. N., Fawzia A., Awadhi A. ( 2000 ). Dietary intake of organophosphate pesticides in Kuwait. . Food Chem 69, 331338. [View Article]
    [Google Scholar]
  23. 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]
  24. 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]
  25. Turdahon M., Osman G., Hamdun M., Yusuf K., Abdurehim Z., Abaydulla G., Abdukerim M., Fang C., Rahman E. ( 2013 ). Rhizobium tarimense sp. nov., isolated from soil in the ancient Khiyik River. . Int J Syst Evol Microbiol 63, 24242429. [View Article] [PubMed]
    [Google Scholar]
  26. Vincent J. M. ( 1970 ). The cultivation, isolation and maintenance of rhizobia. . In A Manual for the Practical Study of the Root-Nodule Bacteria, pp. 113. Edited by Vincent J. M. . Oxford:: Blackwell Scientific;.
    [Google Scholar]
  27. 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]
  28. Wei G. H., Tan Z. Y., Zhu M. E., Wang E. T., Han S. Z., Chen W. X. ( 2003 ). Characterization of rhizobia isolated from legume species within the genera Astragalus and Lespedeza grown in the Loess Plateau of China and description of Rhizobium loessense sp. nov.. Int J Syst Evol Microbiol 53, 15751583. [View Article] [PubMed]
    [Google Scholar]
  29. Yoon J. H., Kang S. J., Yi H. S., Oh T. K., Ryu C. M. ( 2010 ). Rhizobium soli sp. nov., isolated from soil. . Int J Syst Evol Microbiol 60, 13871393. [View Article] [PubMed]
    [Google Scholar]
  30. Young J. M., Kuykendall L. D., Martínez-Romero E., Kerr A., Sawada H. ( 2001 ). A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis. . Int J Syst Evol Microbiol 51, 89103. [View Article] [PubMed]
    [Google Scholar]
  31. Zhang G. X., Ren S. Z., Xu M. Y., Zeng G. Q., Luo H. D., Chen J. L., Tan Z. Y., Sun G. P. ( 2011 ). Rhizobium borbori sp. nov., aniline-degrading bacteria isolated from activated sludge. . Int J Syst Evol Microbiol 61, 816822. [View Article] [PubMed]
    [Google Scholar]
  32. Zhang X., Li B., Wang H., Sui X., Ma X., Hong Q., Jiang R. ( 2012 ). Rhizobium petrolearium sp. nov., isolated from oil-contaminated soil. . Int J Syst Evol Microbiol 62, 18711876. [View Article] [PubMed]
    [Google Scholar]
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