1887

Abstract

A Gram-stain-negative, rod-shaped bacterial strain, H66, was isolated from the surfaces of weathered rock (purple siltstone) found in Yanting, Sichuan Province, PR China. Cells of strain H66 were motile with peritrichous flagella. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain H66 belongs to the genus . It is closely related to SO2 (98.1 %), CCBAU 01393 (98.0 %) and ALA10B2 (98.0 %). Analysis of the housekeeping genes, , and , showed low levels of sequence similarity (<92.0 %) between strain H66 and other recognized species of the genus . The predominant components of the cellular fatty acids were summed feature 8 (Cω7 and/or Cω6) and C. The G+C content of strain H66 was 60.3 mol%. Strain H66 is suggested to be a novel species of the genus based on the low levels of DNA–DNA relatedness (ranging from 14.3 % to 40.0 %) with type strains of species of the genus and on its unique phenotypic characteristics. The namehttp://dx.doi.org/10.1601/nm.1279 sp. nov. is proposed for this novel species. The type strain is H66 ( = CCTCC AB 2014007 = LMG 28229).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 41071173 and 41473075)
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2015-02-01
2024-04-16
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References

  1. Berge O., Lodhi A., Brandelet G., Santaella C., Roncato M. A., Christen R., Heulin T., Achouak W. ( 2009 ). Rhizobium alamii sp. nov., an exopolysaccharide-producing species isolated from legume and non-legume rhizospheres. . Int J Syst Evol Microbiol 59, 367372. [View Article] [PubMed]
    [Google Scholar]
  2. Bogan B. W., Sullivan W. R., Kayser K. J., Derr K. D., Aldrich H. C., Paterek J. R. ( 2003 ). Alkanindiges illinoisensis gen. nov., sp. nov., an obligately hydrocarbonoclastic, aerobic squalane-degrading bacterium isolated from oilfield soils. . Int J Syst Evol Microbiol 53, 13891395. [View Article] [PubMed]
    [Google Scholar]
  3. Chaintreuil C., Giraud E., Prin Y., Lorquin J., A., Gillis M., de Lajudie P., Dreyfus B. ( 2000 ). Photosynthetic bradyrhizobia are natural endophytes of the African wild rice Oryza breviligulata . . Appl Environ Microbiol 66, 54375447. [View Article] [PubMed]
    [Google Scholar]
  4. De Ley J., Cattoir H., Reynaerts A. ( 1970 ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12, 133142. [View Article] [PubMed]
    [Google Scholar]
  5. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  6. Frank B. ( 1889 ). Über die Pilzsymbiose der Leguminosen. . Ber Dtsch Bot Ges 7, 332346. (in German).
    [Google Scholar]
  7. Gao J. L., Sun J. G., Li Y., Wang E. T., Chen W. X. ( 1994 ). Numerical taxonomy and DNA relatedness of tropical rhizobia isolated from Hainan Province, China. . Int J Syst Evol Microbiol 44, 151158.
    [Google Scholar]
  8. García-Fraile P., Rivas R., Willems A., Peix A., Martens M., Martínez-Molina E., Mateos P. F., Velázquez E. ( 2007 ). Rhizobium cellulosilyticum sp. nov., isolated from sawdust of Populus alba . . Int J Syst Evol Microbiol 57, 844848. [View Article] [PubMed]
    [Google Scholar]
  9. Gaunt M. W., Turner S. L., Rigottier-Gois L., Lloyd-Macgilp S. A., Young J. P. W. ( 2001 ). Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. . Int J Syst Evol Microbiol 51, 20372048. [View Article] [PubMed]
    [Google Scholar]
  10. Graham P. H., Sadowsky M. J., Keyser H. H., Barnet Y. M., Bradley R. S., Cooper J. E., De Ley D. J., Jarvis B. D. W., Roslycky E. B. & other authors ( 1991 ). Proposed minimal standards for the description of new genera and species of root- and stem-nodulating bacteria. . Int J Syst Bacteriol 41, 582587. [View Article]
    [Google Scholar]
  11. Jordan D. C. ( 1984 ). Genus I. Rhizobium Frank 1889, 338AL. . In Bergey’s Manual of Systematic Bacteriology, vol. 1, pp. 235242. Edited by Krieg N. R., Holt J. G. . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  12. 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]
  13. 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]
  14. Kuykendall, L. D. , Young, J. , Martinez-Romero, E. , Kerr, A. , Sawada, H. . ( 2005 ). Genus I. Rhizobium . . In Bergey’s Manual of Systematic Bacteriology, vol. 2, pp. 325340. Ed by Garrity G. M., Brenner D. J., Krieg N. R., Staley J. R. . Springer;: US:. [View Article]
    [Google Scholar]
  15. Laguerre G., Nour S. M., Macheret V., Sanjuan J., Drouin P., Amarger N. ( 2001 ). Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts. . Microbiology 147, 981993.[PubMed]
    [Google Scholar]
  16. Lindstrom K. ( 1989 ). Rhizobium galegae, a new species of legume root nodule bacteria. . Int J Syst Bacteriol 39, 365367. [View Article]
    [Google Scholar]
  17. Lu Y. L., Chen W. F., Li Han L., Wang E. T., Chen W. X. ( 2009 ). Rhizobium alkalisoli sp. nov., isolated from Caragana intermedia growing in saline-alkaline soils in the north of China. . Int J Syst Evol Microbiol 59, 30063011. [View Article] [PubMed]
    [Google Scholar]
  18. 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]
  19. 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]
  20. Martens M., Dawyndt P., Coopman R., Gillis M., De Vos P., Willems A. ( 2008 ). Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium). . Int J Syst Evol Microbiol 58, 200214. [View Article] [PubMed]
    [Google Scholar]
  21. 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]
  22. Ramana ChV., 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]
  23. Ren W., Chen W. F., Sui X. H., Wang E. T., Chen W. X. ( 2011 ). Rhizobium vignae sp. nov., a symbiotic bacterium isolated from multiple legume species. . Int J Syst Evol Microbiol 61, 580586. [View Article] [PubMed]
    [Google Scholar]
  24. Tamura K., Dudley J., Nei M., Kumar S. ( 2007 ). mega4: molecular evolutionary genetics analysis (mega) software version 4.0. . Mol Biol Evol 24, 15961599. [View Article] [PubMed]
    [Google Scholar]
  25. Tan Z., Hurek T., Vinuesa P., Müller P., Ladha J. K., Reinhold-Hurek B. ( 2001 ). Specific detection of Bradyrhizobium and Rhizobium strains colonizing rice (Oryza sativa) roots by 16S-23S ribosomal DNA intergenic spacer-targeted PCR. . Appl Environ Microbiol 67, 36553664. [View Article] [PubMed]
    [Google Scholar]
  26. Terefework Z., Kaijalainen S., Lindström K. ( 2001 ). AFLP fingerprinting as a tool to study the genetic diversity of Rhizobium galegae isolated from Galega orientalis and Galega officinalis . . J Biotechnol 91, 169180. [View Article] [PubMed]
    [Google Scholar]
  27. Thompson J. D., Higgins D. G., Gibson T. J. ( 1994 ). clustal_w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. . Nucleic Acids Res 22, 46734680. [View Article] [PubMed]
    [Google Scholar]
  28. Turner S. L., Young J. P. W. ( 2000 ). The glutamine synthetases of rhizobia: phylogenetics and evolutionary implications. . Mol Biol Evol 17, 309319. [View Article] [PubMed]
    [Google Scholar]
  29. Ueda T., Suga Y., Yahiro N., Matsuguchi T. ( 1995 ). Remarkable N2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. . J Bacteriol 177, 14141417.[PubMed]
    [Google Scholar]
  30. Vincent J. M. ( 1970 ). A Manual for the Practical Study of Root-Nodule Bacteria. Oxford, UK:: Blackwell Scientific Publications;.
    [Google Scholar]
  31. Wang E. T., van Berkum P., Beyene D., Sui X. H., Dorado O., Chen W. X., Martínez-Romero E. ( 1998 ). Rhizobium huautlense sp. nov., a symbiont of Sesbania herbacea that has a close phylogenetic relationship with Rhizobium galegae . . Int J Syst Bacteriol 48, 687699. [View Article] [PubMed]
    [Google Scholar]
  32. 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]
  33. Yan Q. X., Wang Y. X., Li S. P., Li W. J., Hong Q. ( 2010 ). Sphingobium qiguonii sp. nov., a carbaryl-degrading bacterium isolated from a wastewater treatment system. . Int J Syst Evol Microbiol 60, 27242728. [View Article] [PubMed]
    [Google Scholar]
  34. Yanni Y. G., Rizk R. Y., Corich V., Squartini A., Ninke K., Philip-Hollingsworth S., Orgambide G., De Bruijn F., Stoltzfus J. & other authors ( 1997 ). Natural endophytic association between Rhizobium leguminosarum bv. trifolii and rice roots and assessment of its potential to promote rice growth. . Plant Soil 194, 99114. [View Article]
    [Google Scholar]
  35. Zhang X. Y., Zhang Y. J., Chen X. L., Qin Q. L., Zhao D. L., Li T. G., Dang H. Y., Zhang Y. Z. ( 2008 ). Myroides profundi sp. nov., isolated from deep-sea sediment of the southern Okinawa Trough. . FEMS Microbiol Lett 287, 108112. [View Article] [PubMed]
    [Google Scholar]
  36. Zhang X. X., Sun L., Ma X. T., Sui X. H., Jiang R. B. ( 2011 ). Rhizobium pseudoryzae sp. nov., isolated from the rhizosphere of rice. . Int J Syst Evol Microbiol 61, 24252429. [View Article] [PubMed]
    [Google Scholar]
  37. Zhang X. X., Li B. M., Wang H. S., Sui X. H., Ma X. T., Hong Q., Jiang R. B. ( 2012 ). Rhizobium petrolearium sp. nov., isolated from oil-contaminated soil. . Int J Syst Evol Microbiol 62, 18711876. [View Article] [PubMed]
    [Google Scholar]
  38. Zhao F., Qiu G., Huang Z., He L. Y., Sheng X. F. ( 2013 ). Characterization of Rhizobium sp. Q32 isolated from weathered rocks and its role in silicate mineral weathering. . Geomicrobiol J 30, 616622. [View Article]
    [Google Scholar]
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