1887

Abstract

The species is a promiscuous legume nodulated by several species of the family . During a study of rhizobia nodulating this legume in Portugal, we isolated several strains that nodulate effectively and also and , but they form ineffective nodules in . According to phylogenetic analysis of the 16S rRNA gene sequence, the strains from this study belong to the genus , with and as the closest related species, with 99.9 and 99.2 % similarity, respectively, between the type strains of these species and strain P1-7. The and genes carried by strain P1-7 are phylogenetically related to those of other species nodulating . This strain does not carry virulence genes present in the type strain of , ATCC 11325. Analysis of the and genes confirms this phylogenetic arrangement, showing low similarity with respect to those of ATCC 11325 (91.9 and 94.1 % similarity, respectively) and IIB CIAT 899 (90.6 % and 91.8 % similarity, respectively). The intergenic spacer (ITS) of the strains from this study is phylogenetically divergent from those of ATCC 11235 and CIAT 899, with 85.9 and 82.8 % similarity, respectively, with respect to strain P1-7. The tRNA profile and two-primer random amplified polymorphic DNA pattern of strain P1-7 are also different from those of ATCC 11235 and CIAT 899. The strains isolated in this study can be also differentiated from and by several phenotypic characteristics. The results of DNA–DNA hybridization showed means of 28 and 25 % similarity between strain P1-7 and ATCC 11235 and CIAT 899, respectively. All these data showed that the strains isolated in this study belong to a novel species of the genus , for which we propose the name sp. nov.; the type strain is P1-7 (=LMG 22705=CECT 7016).

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2006-11-01
2019-08-19
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References

  1. Acosta-Durán, C. & Martínez-Romero, E. ( 2002; ). Diversity of rhizobia from nodules of the leguminous tree Gliricidia sepium, a natural host of Rhizobium tropici. Arch Microbiol 178, 161–164.[CrossRef]
    [Google Scholar]
  2. 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.[CrossRef]
    [Google Scholar]
  3. Amarger, N., Macheret, V. & Laguerre, G. ( 1997; ). Rhizobium gallicum sp. nov. and Rhizobium giardinii sp. nov., from Phaseolus vulgaris nodules. Int J Syst Bacteriol 47, 996–1006.[CrossRef]
    [Google Scholar]
  4. Bergersen, F. J. ( 1961; ). The growth of Rhizobium in synthetic media. Aust J Biol 14, 349–360.
    [Google Scholar]
  5. Chun, J. & Goodfellow, M. ( 1995; ). A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45, 240–245.[CrossRef]
    [Google Scholar]
  6. Corich, V., Giacomini, A., Carlot, M., Simon, R., Tichy, H. V., Squartini, A. & Nuti, M. P. ( 2001; ). Comparative strain typing of Rhizobium leguminosarum bv. viciae natural populations. Can J Microbiol 47, 580–584.[CrossRef]
    [Google Scholar]
  7. de Oliveira, V. M., Coutinho, H. L., Sobral, B. W., Guimaraes, C. T., van Elsas, J. D. & Manfio, G. P. ( 1999; ). Discrimination of Rhizobium tropici and R. leguminosarum strains by PCR-specific amplification of 16S-23S rDNA spacer region fragments and denaturing gradient gel electrophoresis (DGGE). Lett Appl Microbiol 28, 137–141.[CrossRef]
    [Google Scholar]
  8. 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.[CrossRef]
    [Google Scholar]
  9. Felsenstein, J. ( 1983; ). Parsimony in systematics: biological and statistical issues. Annu Rev Ecol Syst 14, 313–333.[CrossRef]
    [Google Scholar]
  10. 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, 2037–2048.[CrossRef]
    [Google Scholar]
  11. Höfle, M. G. ( 1990; ). Transfer RNAs as genotypic fingerprints of eubacteria. Arch Microbiol 153, 299–304.[CrossRef]
    [Google Scholar]
  12. Igual, J. M., Valverde, A., Rivas, R., Mateos, P. F., Rodríguez-Barrueco, C., Martínez-Molina, E., Cervantes, E. & Velázquez, E. ( 2003; ). Genomic fingerprinting of Frankia strains by PCR-based techniques. Assessment of a primer based on the sequence of 16S rRNA gene of Escherichia coli. Plant Soil 254, 115–123.[CrossRef]
    [Google Scholar]
  13. Jordan, D. C. ( 1984; ). Family III. Rhizobiaceae. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 234–242. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
  14. Jukes, T. H. & Cantor, C. R. ( 1969; ). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21–132. Edited by H. N. Munro. London: Academic Press.
  15. Kersters, K. & De Ley, J. ( 1984; ). Genus III. Agrobacterium. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 244–254. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
  16. 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.[CrossRef]
    [Google Scholar]
  17. Kumar, S., Tamura, K., Jakobsen, I.-B. & Nei, M. ( 2001; ). Molecular Evolutionary Genetics Analysis Software. Tempe, AZ: Arizona State University.
  18. Kwon, S. W., Park, J. Y., Kim, J. S., Kang, J. W., Cho, Y. H., Lim, C. K., Parker, M. A. & Lee, G. B. ( 2005; ). Phylogenetic analysis of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium on the basis of 16S rRNA gene and internally transcribed spacer region sequences. Int J Syst Evol Microbiol 55, 263–270.[CrossRef]
    [Google Scholar]
  19. 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.
    [Google Scholar]
  20. Martínez-Romero, E. ( 2003; ). Diversity of Rhizobium–Phaseolus vulgaris symbiosis: overview and perspectives. Plant Soil 252, 11–23.[CrossRef]
    [Google Scholar]
  21. Martínez-Romero, E., Segovia, L., Mercante, F. M., Franco, A. A., Graham, P. & Pardo, M. A. ( 1991; ). Rhizobium tropici, a novel species nodulating Phaseolus vulgaris L. beans and Leucaena sp. trees. Int J Syst Bacteriol 41, 417–426.[CrossRef]
    [Google Scholar]
  22. Moore, L. W., Warren, G. & Strobel, G. ( 1979; ). Involvement of a plasmid in the hairy root disease of plants caused by Agrobacterium rhizogenes. Plasmid 2, 617–626.[CrossRef]
    [Google Scholar]
  23. Moschetti, G., Peluso, A., Protopapa, A., Anastasio, M., Pepe, O. & Defez, R. ( 2005; ). Use of nodulation pattern, stress tolerance, nodC gene amplification, RAPD-PCR and RFLP-16S rDNA analysis to discriminate genotypes of Rhizobium leguminosarum biovar viciae. Syst Appl Microbiol 28, 619–631.[CrossRef]
    [Google Scholar]
  24. Plazinski, J., Chen, Y. H. & Rolfe, B. G. ( 1985; ). General method for the identification of plasmid species in fast-growing soil microorganisms. Appl Environ Microbiol 48, 1001–1003.
    [Google Scholar]
  25. Rivas, R., Velázquez, E., Valverde, A., Mateos, P. F. & Martínez-Molina, E. ( 2001; ). A two primers random amplified polymorphic DNA procedure to obtain polymerase chain reaction fingerprints of bacterial species. Electrophoresis 22, 1086–1089.[CrossRef]
    [Google Scholar]
  26. Rivas, R., Velázquez, E., Palomo, J.-L., Mateos, P. F., García-Benavides, P. & Martínez-Molina, E. ( 2002a; ). Rapid identification of Clavibacter michiganensis subspecies sepedonicus using two primers random amplified polymorphic DNA (TP-RAPD) fingerprints. Eur J Plant Pathol 108, 179–184.[CrossRef]
    [Google Scholar]
  27. Rivas, R., Velázquez, E., Willems, A., Vizcaíno, N., Subba-Rao, N. S., Mateos, P. F., Gillis, M., Dazzo, F. B. & Martínez-Molina, E. ( 2002b; ). 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, 5217–5222.[CrossRef]
    [Google Scholar]
  28. 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.[CrossRef]
    [Google Scholar]
  29. Rzhetsky, A. & Nei, M. ( 1993; ). Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 10, 1073–1095.
    [Google Scholar]
  30. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  31. Segovia, L., Young, J. P. W. & Martínez-Romero, E. ( 1993; ). Reclassification of American Rhizobium leguminosarum biovar phaseoli type I strains as Rhizobium etli sp. nov. Int J Syst Bacteriol 43, 374–377.[CrossRef]
    [Google Scholar]
  32. Tajima, F. & Nei, M. ( 1984; ). Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol 1, 269–285.
    [Google Scholar]
  33. Tamura, K. & Nei, M. ( 1993; ). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. J Mol Evol 10, 512–526.
    [Google Scholar]
  34. 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.[CrossRef]
    [Google Scholar]
  35. Toro, N. & Olivares, J. ( 1986; ). Characterization of a large plasmid of Rhizobium meliloti involved in enhancing nodulation. Mol Gen Genet 202, 331–335.[CrossRef]
    [Google Scholar]
  36. van Berkum, P., Terefework, Z., Paulin, L., Suomalaien, S., Lindström, K. & Eardly, B. D. ( 2003; ). Discordant phylogenies within the rrn loci of rhizobia. J Bacteriol 185, 2988–2998.[CrossRef]
    [Google Scholar]
  37. Velázquez, E., Igual, J. M., Willems, A. & 9 other authors ( 2001a; ). Description of Mesorhizobium chacoense sp. nov. that nodulates Prosopis alba in the Chaco Arido region (Argentina). Int J Syst Evol Microbiol 51, 1011–1021.[CrossRef]
    [Google Scholar]
  38. Velázquez, E., Martínez-Romero, E., Rodríguez-Navarro, D. N., Trujillo, M. E., Daza, A., Mateos, P. F., Martinez-Molina, E. & Van Berkum, P. ( 2001b; ). Characterization of rhizobial isolates of Phaseolus vulgaris by staircase electrophoresis of low molecular weight RNA. Appl Environ Microbiol 67, 1008–1010.[CrossRef]
    [Google Scholar]
  39. Velázquez, E., Palomo, J. L., Lastra, B., Mateos, P., García-Benavides, P. & Martínez-Molina, E. ( 2001c; ). Rapid identification of Agrobacterium species by staircase electrophoresis of low molecular weight RNA profiles. Eur J Plant Pathol 107, 931–938.[CrossRef]
    [Google Scholar]
  40. Velázquez, E., Trujillo, M. E., Peix, A., Palomo, J. L., García-Benavides, P., Mateos, P. F., Ventosa, A. & Martínez-Molina, E. ( 2001d; ). Stable low molecular weight RNA analyzed by staircase electrophoresis, a molecular signature for both prokaryotic and eukaryotic microorganisms. Syst Appl Microbiol 24, 490–499.[CrossRef]
    [Google Scholar]
  41. Velázquez, E., Peix, A., Zurdo-Piñeiro, J. L. & 7 other authors ( 2005; ). The coexistence of symbiosis and pathogenicity-determining genes in Rhizobium rhizogenes strains enables them to induce nodules and tumors or hairy roots in plants. Mol Plant Microbe Interact 18, 1325–1332.[CrossRef]
    [Google Scholar]
  42. Velázquez, E., Rivas, R., Villar, M., Valverde, A., Peix, A., Mateos, P. F., Velázquez, E. & Martínez-Molina, E. ( 2006; ). A new approach for separating LMW RNA molecules by staircase electrophoresis in non-sequencing gels. Electrophoresis 27, 1732–1738.[CrossRef]
    [Google Scholar]
  43. 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 J. M. Vincent. Oxford: Blackwell Scientific.
  44. Vinuesa, P., Silva, C., Lorite, M. J., Izaguirre-Mayoral, M. L., Bedmar, E. J. & Martínez-Romero, E. ( 2005a; ). 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, 702–716.[CrossRef]
    [Google Scholar]
  45. 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.[CrossRef]
    [Google Scholar]
  46. Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors ( 1987; ). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.[CrossRef]
    [Google Scholar]
  47. Willems, A., Doignon-Bourcier, F., Goris, J., Coopman, R., De Lajudie, P. & Gillis, M. ( 2001; ). DNA–DNA hybridization study of Bradyrhizobium strains. Int J Syst Evol Microbiol 51, 1315–1322.
    [Google Scholar]
  48. 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, 89–103.
    [Google Scholar]
  49. Zurdo-Piñeiro, J. L., Velázquez, E., Lorite, M. J., Brelles-Mariño, G., Schröder, E. C., Bedmar, E. J., Mateos, P. F. & Martínez-Molina, E. ( 2004; ). Identification of fast-growing rhizobia nodulating tropical legumes from Puerto Rico as Rhizobium gallicum and Rhizobium tropici. Syst Appl Microbiol 27, 469–477.[CrossRef]
    [Google Scholar]
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vol. , part 11, pp. 2631 - 2637

Plasmid profiles of the isolates from this study.

Comparative analysis of (Fig. S2) and (Fig. S3) gene sequences from sp. nov. P1-7 and representative related strains from GenBank.

RAPD (Fig. S4) and TP-RAPD (Fig. S5) patterns of isolates from this study.

Neighbour-joining tree based on nearly complete 16S rRNA gene sequences of strain P1-7 ( sp. nov.) and other related organisms of the family .

Neighbour-joining trees based on partial (Fig. S7) and (Fig. S8) gene sequences of strains of sp. nov. and other related organisms.

ITS fragments of various strains.

Neighbour-joining tree based on 16S–23S rRNA intergenic sequences of sp. nov. strains and phylogenetically related species of the genus .

Low-molecular-weight RNA profiles of sp. nov. P1-7 and related strains.

Results of DNA-DNA hybridization experiments.

[PDF file of Supplementary Figs S1-S11 and Supplementary Table S1](1145 KB)



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