1887

Abstract

Several strains isolated from nodules have been characterized based on their diverse genetic, phenotypic and symbiotic characteristics. According to 16S rRNA gene sequence analysis, the isolates formed a group that was closely related to BTA-1 with 99.4 % similarity. Analysis of three housekeeping genes, and , suggested that the strains represent a novel species most closely related to BTA-1 with similarities of 94.2, 96.7 and 94.5 %, respectively. All these differences were congruent with DNA–DNA hybridization analysis, which revealed 31 % relatedness between a representative strain (CTAW11) isolated from nodules and BTA-1. Phenotypic differences among the strains isolated from and were based on assimilation of carbon and nitrogen sources. The and genes of strain CTAW11 were phylogenetically related to those of strains belonging to bv. genistearum and divergent from those of bv. glycinearum and, accordingly, they do not nodulate soybean. Based on the genotypic and phenotypic data obtained in this study, our strains should be classified as representatives of a novel species for which the name sp. nov. is proposed; the type strain is CTAW11 ( = LMG 25866 = CECT 7749).

Funding
This study was supported by the:
  • JCYL
  • MICINN
  • ERDF (Award RNM-4746)
  • Consejería de Economía, Innovación y Ciencia
  • CSIC
  • CNRST (Award 2009MA0013)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.027649-0
2011-12-01
2024-12-07
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/61/12/2922.html?itemId=/content/journal/ijsem/10.1099/ijs.0.027649-0&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. 1990; Basic local alignment search tool. J Mol Biol 215:403–410[PubMed] [CrossRef]
    [Google Scholar]
  2. Chun J., Goodfellow M. 1995; A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45:240–245 [View Article][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 57:2259–2261 [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 39:224–229 [View Article]
    [Google Scholar]
  5. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [View Article][PubMed]
    [Google Scholar]
  6. Felsenstein J. 1983; Parsimony in systematics: biological and statistical issues. Annu Rev Ecol Syst 14:313–333 [View Article]
    [Google Scholar]
  7. Herrera-Cervera J. A., Caballero-Mellado J., Laguerre G., Tichy H. V., Requena N., Amarger N., Martínez-Romero E., Olivares J., Sanjuán J. 1999; At least five rhizobial species nodulate Phaseolus vulgaris in a Spanish soil. FEMS Microbiol Lett 30:87–97 [View Article]
    [Google Scholar]
  8. Islam M. S., Kawasaki H., Muramatsu Y., Nakagawa Y., Seki T. 2008; Bradyrhizobium iriomotense sp. nov., isolated from a tumor-like root of the legume Entada koshunensis from Iriomote Island in Japan. Biosci Biotechnol Biochem 72:1416–1429 [View Article][PubMed]
    [Google Scholar]
  9. Islam M. S., Kawasaki H., Muramatsu Y., Nakagawa Y., Seki T. 2010; Bradyrhizobium iriomotense sp. nov. In List of new names and new combinations previously effectively, but not validly, published, List no. 132. Int J Syst Evol Microbiol 60:469–472 [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 16:111–120 [View Article][PubMed]
    [Google Scholar]
  11. 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 147:981–993[PubMed]
    [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 12B:195–206 [View Article]
    [Google Scholar]
  13. Menna P., Barcellos F. G., Hungria M. 2009; Phylogeny and taxonomy of a diverse collection of Bradyrhizobium strains based on multilocus sequence analysis of the 16S rRNA gene, ITS region and glnII, recA, atpD and dnaK genes. Int J Syst Evol Microbiol 59:2934–2950 [View Article][PubMed]
    [Google Scholar]
  14. Ramírez-Bahena M. H., Peix A., Rivas R., Camacho M., Rodríguez-Navarro D. N., Mateos P. F., Martínez-Molina E., Willems A., Velázquez E. 2009; Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus . Int J Syst Evol Microbiol 59:1929–1934 [View Article][PubMed]
    [Google Scholar]
  15. Rivas R., Willems A., Palomo J. L., García-Benavides P., Mateos P. F., Martínez-Molina E., Gillis M., Velázquez E. 2004; Bradyrhizobium betae sp. nov., isolated from roots of Beta vulgaris affected by tumour-like deformations. Int J Syst Evol Microbiol 54:1271–1275 [View Article][PubMed]
    [Google Scholar]
  16. Rivas R., Peix A., Mateos P. F., Trujillo M. E., Martínez-Molina E., Velázquez E. 2006; Biodiversity of populations of phosphate solubilizing rhizobia that nodulate chickpea in different Spanish soils. Plant Soil 287:23–33 [View Article]
    [Google Scholar]
  17. Rivas R., Martens M., de Lajudie P., Willems A. 2009; Multilocus sequence analysis of the genus Bradyrhizobium . Syst Appl Microbiol 32:101–110 [View Article][PubMed]
    [Google Scholar]
  18. Rodríguez-Echeverría S., Pérez-Fernández M. A. 2005; Potential use of Iberian shrubby legumes and rhizobial inoculations in revegetation projects under acidic soil conditions. Appl Soil Ecol 29:203–208 [View Article]
    [Google Scholar]
  19. Saitou N., Nei M. 1987; The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  20. Swofford D. L. 2002; paup*: Phylogenetic analysis using parsimony (and other methods), version 4. Sunderland, MA: Sinauer Associates.;
  21. Tamura K., Dudley J., Nei M., Kumar S. 2007; mega4: Molecular Evolutionary Genetics Analysis (mega) software version 4.0. Mol Biol Evol 24:1596–1599 [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 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  23. Tindall B. J., Rosselló-Móra R., Busse H. J., Ludwig W., Kämpfer P. 2010; Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266 [View Article][PubMed]
    [Google Scholar]
  24. Velázquez E., Valverde A., Rivas R., Gomis V., Peix A., Gantois I., Igual J. M., León-Barrios M., Willems A. et al. other authors 2010; Strains nodulating Lupinus albus on different continents belong to several new chromosomal and symbiotic lineages within Bradyrhizobium . Antonie van Leeuwenhoek 97:363–376 [View Article][PubMed]
    [Google Scholar]
  25. Vincent J. M. 1970; The cultivation, isolation and maintenance of rhizobia. In A Manual for the Practical Study of Root-Nodule Bacteria pp. 1–13 Edited by Vincent J. M. Oxford: Blackwell Scientific Publications;
    [Google Scholar]
  26. Vinuesa P., León-Barrios M., Silva C., Willems A., Jarabo-Lorenzo A., Pérez-Galdona R., Werner D., Martínez-Romero E. 2005a; Bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (Papilionoideae: Genisteae) from the Canary Islands, along with Bradyrhizobium japonicum bv. genistearum, Bradyrhizobium genospecies alpha and Bradyrhizobium genospecies beta. Int J Syst Evol Microbiol 55:569–575 [View Article][PubMed]
    [Google Scholar]
  27. Vinuesa P., Silva C., Werner D., Martínez-Romero E. 2005b; Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation. Mol Phylogenet Evol 34:29–54 [View Article][PubMed]
    [Google Scholar]
  28. 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. et al. other authors 1987; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [View Article]
    [Google Scholar]
  29. Weir B. S., Turner S. J., Silvester W. B., Park D. C., Young J. M. 2004; Unexpectedly diverse Mesorhizobium strains and Rhizobium leguminosarum nodulate native legume genera of New Zealand, while introduced legume weeds are nodulated by Bradyrhizobium species. Appl Environ Microbiol 70:5980–5987 [View Article][PubMed]
    [Google Scholar]
  30. Willems A., Doignon-Bourcier F., Goris J., Coopman R., de Lajudie P., De Vos P., Gillis M. 2001; DNA-DNA hybridization study of Bradyrhizobium strains. Int J Syst Evol Microbiol 51:1315–1322[PubMed]
    [Google Scholar]
  31. Xu L. M., Ge C., Cui Z., Li J., Fan H. 1995; Bradyrhizobium liaoningense sp. nov., isolated from the root nodules of soybeans. Int J Syst Bacteriol 45:706–711 [View Article][PubMed]
    [Google Scholar]
  32. Yao Z. Y., Kan F. L., Wang E. T., Wei G. H., Chen W. X. 2002; Characterization of rhizobia that nodulate legume species of the genus Lespedeza and description of Bradyrhizobium yuanmingense sp. nov.. Int J Syst Evol Microbiol 52:2219–2230 [View Article][PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijs.0.027649-0
Loading
/content/journal/ijsem/10.1099/ijs.0.027649-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error