sp. nov. and sp. nov., nitrogen-fixing rhizobial symbionts of the medicinal legume Free

Abstract

Five bacterial strains representing 45 isolates originated from root nodules of the medicinal legume were defined as two novel groups in the genus based on their phylogenetic relationships estimated from 16S rRNA genes and the housekeeping genes , and . These groups were distantly related to USDA 2370 (95.6 % similarity for group I) and ATCC 14482 (93.4 % similarity for group II) in multilocus sequence analysis. In DNA–DNA hybridization experiments, the reference strains CCBAU 03386 (group I) and CCBAU 03470 (group II) showed levels of relatedness of 17.9–57.8 and 11.0–42.9 %, respectively, with the type strains of related species. Both strains CCBAU 03386 and CCBAU 03470 contained ubiquinone 10 (Q-10) as the major respiratory quinone and possessed 16 : 0, 18 : 0, 19 : 0 cyclo ω8, summed feature 8 and summed feature 2 as major fatty acids, but did not contain 20 : 3 ω6,8,12. Phenotypic features distinguishing both groups from all closely related species of the genus were found. Therefore, two novel species, sp. nov. for group I (type strain CCBAU 03386 = E5 = LMG 27901 = HAMBI 3615) and sp. nov. for group II (type strain CCBAU 03470 = C-5-1 = LMG 27898 = HAMBI 3510), are proposed. Both groups were able to nodulate and their hosts of origin () effectively and their nodulation gene was phylogenetically located in the symbiovar .

Funding
This study was supported by the:
  • Chinese Universities Scientific Fund (Award 2014QT003)
  • National Natural Science Foundation of China (Award 31270052)
  • Instituto Politecnico Nacional, Mexico (Award 20140124 and SIP 20130828)
  • Northern China Standardized Plant Base Optimization and Upgrading and Series Products Comprehensive Development of Sophora flavescens (Award 2011BA107B03)
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2015-02-01
2024-03-28
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References

  1. Chen W. X., Wang E. T., Wang S. Y., Li Y. B., Chen X. Q., Li Y. ( 1995 ). Characteristics of Rhizobium tianshanense sp. nov., a moderately and slowly growing root nodule bacterium isolated from an arid saline environment in Xinjiang, People’s Republic of China. . Int J Syst Bacteriol 45, 153159. [View Article] [PubMed]
    [Google Scholar]
  2. Cole J. R., Wang Q., Cardenas E., Fish J., Chai B., Farris R. J., Kulam-Syed-Mohideen A. S., McGarrell D. M., Marsh T. & other authors ( 2009 ). The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. . Nucleic Acids Res 37 (Database issue), D141D145. [View Article] [PubMed]
    [Google Scholar]
  3. Euzéby J. P. ( 1997 ). List of bacterial names with standing in nomenclature: a folder available on the internet. . Int J Syst Bacteriol 47, 590592. [View Article] [PubMed]
    [Google Scholar]
  4. 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 Bacteriol 44, 151158. [View Article]
    [Google Scholar]
  5. Graham P., Sadowsky M., Keyser H., Barnet Y., Bradley R., Cooper J., De Ley D., Jarvis B., Roslycky E. & 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]
  6. Hanage W. P., Fraser C., Spratt B. G. ( 2006 ). Sequences, sequence clusters and bacterial species. . Philos Trans R Soc Lond B Biol Sci 361, 19171927. [View Article] [PubMed]
    [Google Scholar]
  7. Hurek T., Wagner B., Reinhold-Hurek B. ( 1997 ). Identification of N2-fixing plant- and fungus-associated Azoarcus species by PCR-based genomic fingerprints. . Appl Environ Microbiol 63, 43314339.[PubMed]
    [Google Scholar]
  8. 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]
  9. Komagata K., Suzuki K. ( 1987 ). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19, 161207. [View Article]
    [Google Scholar]
  10. 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]
  11. 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]
  12. Parte A. C. ( 2014 ). LPSN–list of prokaryotic names with standing in nomenclature. . Nucleic Acids Res 42 (Database issue), D613D616. [View Article] [PubMed]
    [Google Scholar]
  13. R Core Team ( 2012 ). R: A Language and Environment for Statistical Computing. Vienna:: R Foundation for Statistical Computing;.
    [Google Scholar]
  14. Ramírez-Bahena M. H., García-Fraile P., Peix A., Valverde A., Rivas R., Igual J. M., Mateos P. F., Martínez-Molina E., Velázquez E. ( 2008 ). Revision of the taxonomic status of the species Rhizobium leguminosarum (Frank 1879) Frank 1889AL, Rhizobium phaseoli Dangeard 1926AL and Rhizobium trifolii Dangeard 1926AL. R. trifolii is a later synonym of R. leguminosarum. Reclassification of the strain R. leguminosarum DSM 30132 ( = NCIMB 11478) as Rhizobium pisi sp. nov.. Int J Syst Evol Microbiol 58, 24842490. [View Article] [PubMed]
    [Google Scholar]
  15. Rincón-Rosales R., Villalobos-Escobedo J. M., Rogel M. A., Martinez J., Ormeño-Orrillo E., Martínez-Romero E. ( 2013 ). Rhizobium calliandrae sp. nov., Rhizobium mayense sp. nov. and Rhizobium jaguaris sp. nov., rhizobial species nodulating the medicinal legume Calliandra grandiflora . . Int J Syst Evol Microbiol 63, 34233429. [View Article] [PubMed]
    [Google Scholar]
  16. Sarita S., Sharma P. K., Priefer U. B., Prell J. ( 2005 ). Direct amplification of rhizobial nodC sequences from soil total DNA and comparison to nodC diversity of root nodule isolates. . FEMS Microbiol Ecol 54, 111. [View Article] [PubMed]
    [Google Scholar]
  17. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc;.
    [Google Scholar]
  18. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, vol. 5, pp. 611654. Edited by Gerhardt P., Murray R. G., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  19. Somasegaran P., Hoben H. J. ( 1994 ). Handbook for Rhizobia, Methods in Legume-Rhizobium Technology. New York:: Springer;. [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. 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]
  22. Tian C. F., Wang E. T., Wu L. J., Han T. X., Chen W. F., Gu C. T., Gu J. G., Chen W. X. ( 2008 ). Rhizobium fabae sp. nov., a bacterium that nodulates Vicia faba . . Int J Syst Evol Microbiol 58, 28712875. [View Article] [PubMed]
    [Google Scholar]
  23. Tighe S. W., de Lajudie P., Dipietro K., Lindström K., Nick G., Jarvis B. D. ( 2000 ). Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium species using the Sherlock Microbial Identification System. . Int J Syst Evol Microbiol 50, 787801. [View Article] [PubMed]
    [Google Scholar]
  24. 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]
  25. Versalovic J., Schneider M., de Bruijn F., Lupski J. ( 1994 ). Genomic fingerprinting of bacteria using repetitive sequence based PCR (rep-PCR). . Methods Mol Cell Biol 5, 2540.
    [Google Scholar]
  26. Vinuesa P., Silva C., Werner D., Martínez-Romero E. ( 2005a ). Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation. . Mol Phylogenet Evol 34, 2954. [View Article] [PubMed]
    [Google Scholar]
  27. Vinuesa P., Silva C., Lorite M. J., Izaguirre-Mayoral M. L., Bedmar E. J., Martínez-Romero E. ( 2005b ). Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands. . Syst Appl Microbiol 28, 702716. [View Article] [PubMed]
    [Google Scholar]
  28. Wilson K. ( 1987 ). Preparation of genomic DNA from bacteria. . In Current Protocols in Molecular Biology, pp. 2.4.12.4.5. Edited by Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. . New York:: Green Publishing & Wiley-Interscience;.
    [Google Scholar]
  29. Zhang Y. M., Tian C. F., Sui X. H., Chen W. F., Chen W. X. ( 2012 ). Robust markers reflecting phylogeny and taxonomy of rhizobia. . PLoS ONE 7, e44936. [View Article] [PubMed]
    [Google Scholar]
  30. Zhao L. F., Deng Z. S., Yang W. Q., Cao Y., Wang E. T., Wei G. H. ( 2010 ). Diverse rhizobia associated with Sophora alopecuroides grown in different regions of Loess Plateau in China. . Syst Appl Microbiol 33, 468477. [View Article] [PubMed]
    [Google Scholar]
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