1887

Abstract

Highly diverse strains nodulate genistoid legumes (brooms) in the Canary Islands, Morocco, Spain and the Americas. Phylogenetic analyses of ITS, , and sequences revealed that these isolates represent at least four distinct evolutionary lineages within the genus, namely and three unnamed genospecies. DNA–DNA hybridization experiments confirmed that one of the latter represents a new taxonomic species for which the name is proposed. populations experience homologous recombination at housekeeping loci, but are sexually isolated from sympatric bv. strains in soils of the Canary Islands. strains are highly acid-tolerant, nodulate diverse legumes in the tribes Genisteae and Loteae, but not species, whereas acid-sensitive soybean isolates such as USDA 6 and USDA 110 do not nodulate genistoid legumes. Based on host-range experiments and phylogenetic analyses of symbiotic and sequences, the biovarieties and for the genistoid legume and soybean isolates, respectively, were proposed. bv. strains display an overlapped host range with bv. isolates, both sharing monophyletic and alleles, possibly due to the lateral transfer of a conjugative chromosomal symbiotic island across species. is the sister species of , as inferred from a maximum-likelihood species phylogeny estimated from congruent + sequence partitions, which resolves eight species clades. In addition to the currently described species, this phylogeny uncovered the novel genospecies alpha and beta and the photosynthetic strains as independent evolutionary lineages. The type strain for is BTA-1 (=ATCC BAA-1002=LMG 22265=CFNE 1008).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.63292-0
2005-03-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/55/2/ijs550569.html?itemId=/content/journal/ijsem/10.1099/ijs.0.63292-0&mimeType=html&fmt=ahah

References

  1. Cohan F. M. 2002; What are bacterial species?. Annu Rev Microbiol 56:457–487 [CrossRef]
    [Google Scholar]
  2. Dupuy N., Willems A., Pot B. 7 other authors 1994; Phenotypic and genotypic characterization of bradyrhizobia nodulating the leguminous tree Acacia albida . Int J Syst Bacteriol 44:461–473 [CrossRef]
    [Google Scholar]
  3. Eckhardt T. 1978; A rapid method for the identification of plasmid desoxyribonucleic acid in bacteria. Plasmid 1:584–588 [CrossRef]
    [Google Scholar]
  4. Felsenstein J. 2004 Inferring Phylogenies Sunderland, MA: Sinauer Associates;
    [Google Scholar]
  5. Göttfert M., Rothlisberger S., Kundig C., Beck C., Marty R., Hennecke H. 2001; Potential symbiosis-specific genes uncovered by sequencing a 410-kilobase DNA region of the Bradyrhizobium japonicum chromosome. J Bacteriol 183:1405–1412 [CrossRef]
    [Google Scholar]
  6. Graham P. H., Sadowsky M. J., Keyser H. H. 8 other authors 1991; Proposed minimal standards for the description of new genera and species of root- and stem-nodulating bacteria. Int J Syst Bacteriol 41:582–587 [CrossRef]
    [Google Scholar]
  7. Jarabo-Lorenzo A., Velazquez E., Perez-Galdona R., Vega-Hernandez M. C., Martinez-Molina E., Mateos P. E., Vinuesa P., Martinez-Romero E., Leon-Barrios M. 2000; Restriction fragment length polymorphism analysis of 16S rDNA and low molecular weight RNA profiling of rhizobial isolates from shrubby legumes endemic to the Canary Islands. Syst Appl Microbiol 23:418–425 [CrossRef]
    [Google Scholar]
  8. Jarabo-Lorenzo A., Pérez-Galdona R., Donate-Correa J. 7 other authors 2003; Genetic diversity of bradyrhizobial populations from diverse geographic origins that nodulate Lupinus spp. and Ornithopus spp. Syst Appl Microbiol 26:611–623 [CrossRef]
    [Google Scholar]
  9. Jarvis B. D. W., Gillis M., De Ley J. 1986; Intra- and intergeneric similarities between the ribosomal ribonucleic acid cistrons of Rhizobium and Bradyrhizobium species and some related bacteria. Int J Syst Bacteriol 36:129–138 [CrossRef]
    [Google Scholar]
  10. Jordan D. C. 1982; Transfer of Rhizobium japonicum Buchanan 1980 to Bradyrhizobium gen. nov., a genus of slow-growing root nodule bacteria from leguminous plants. Int J Syst Bacteriol 32:136–139 [CrossRef]
    [Google Scholar]
  11. Jordan D. C. 1984; Family III. Rhizobiaceae Conn 1938. In Bergey's Manual of Systematic Bacteriology pp  234–244 Edited by Krieg N. R., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
  12. Kaneko T., Nakamura Y., Sato S. 14 other authors 2002; Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res 9:189–197 [CrossRef]
    [Google Scholar]
  13. Kuykendall L. D., Saxena B., Devine T. E., Udell S. E. 1992; Genetic diversity in Bradyrhizobium japonicum Jordan 1982 and a proposal for Bradyrhizobium elkanii sp. nov. Can J Microbiol 38:501–505 [CrossRef]
    [Google Scholar]
  14. Ladha J. K., So R. B. 1994; Numerical taxonomy of photosynthetic rhizobia nodulating Aeschynomene species. Int J Syst Bacteriol 44:62–73 [CrossRef]
    [Google Scholar]
  15. Lan R. T., Reeves P. R. 2000; Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol 8:396–401 [CrossRef]
    [Google Scholar]
  16. Lan R., Reeves P. R. 2001; When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol 9:419–424 [CrossRef]
    [Google Scholar]
  17. León-Barrios M., Gutiérrez-Navarro A. M., Pérez-Galdona R., Corzo J. 1991; Characterization of Canary Island isolates of Bradyrhizobium sp. ( Chamaecytisus proliferus . Soil Biol Biochem 23:487–489 [CrossRef]
    [Google Scholar]
  18. Mayr E. 1970 Populations, Species, and Evolution Harvard University, MA: Belknap Press;
    [Google Scholar]
  19. Nichols R. 2001; Gene trees and species trees are not the same. Trends Ecol Evol 16:358–364 [CrossRef]
    [Google Scholar]
  20. 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]
  21. Santamaría M., Corzo J., León-Barrios M., Gutiérrez-Navarro A. M. 1997; Characterization and differentiation of indigenous rhizobia isolated from Canarian shrub legumes of agricultural and ecological interest. Plant Soil 190:143–152 [CrossRef]
    [Google Scholar]
  22. So R. B., Ladha J. K., Young J. P. 1994; Photosynthetic symbionts of Aeschynomene spp. form a cluster with bradyrhizobia on the basis of fatty acid and rRNA analyses. Int J Syst Bacteriol 44:392–403 [CrossRef]
    [Google Scholar]
  23. Stackebrandt E., Frederiksen W., Garrity G. M. 10 other authors 2002; Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047 [CrossRef]
    [Google Scholar]
  24. Sullivan J. T., Ronson C. W. 1998; Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. Proc Natl Acad Sci U S A 95:5145–5149 [CrossRef]
    [Google Scholar]
  25. Templeton A. R. 1989; The meaning of species and speciation: a genetic perspective. In Speciation and its Consequences pp  3–27 Edited by Otte D., Endler J. A. Sunderland, MA: Sinauer Associates;
    [Google Scholar]
  26. van Berkum P., Eardly B. D. 1998; Molecular evolutionary systematics of the Rhizobiaceae . In The Rhizobiaceae: Molecular Biology of Plant-associated Bacteria pp  1–24 Edited by Spaink H. P., Kondorosi A., Hooykaas P. J. J. Dordrecht: Kluwer Academic;
    [Google Scholar]
  27. Vandamme P., Pot B., Gillis M., de Vos P., Kersters K., Swings J. 1996; Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438
    [Google Scholar]
  28. van Rossum D., Schuurmans F. P., Gillis M., Muyotcha A., Van Verseveld H. W., Stouthamer A. H., Boogerd F. C. 1995; Genetic and phenetic analyses of Bradyrhizobium strains nodulating peanut ( Arachis hypogaea L.) roots. Appl Environ Microbiol 61:1599–1609
    [Google Scholar]
  29. Vinuesa P., Silva C. 2004; Species delineation and biogeography of symbiotic bacteria associated with cultivated and wild legumes. In Biological Resources and Migration pp  143–155 Edited by Werner D. Berlin: Springer;
    [Google Scholar]
  30. Vinuesa P., Rademaker J. L. W., de Bruijn F. J., Werner D. 1998; Genotypic characterization of Bradyrhizobium strains nodulating endemic woody legumes of the Canary Islands by PCR-restriction fragment length polymorphism analysis of genes encoding 16S rRNA (16S rDNA) and 16S-23S rDNA intergenic spacers, repetitive extragenic palindromic PCR genomic fingerprinting and partial 16S rDNA sequencing. Appl Environ Microbiol 64:2096–2104
    [Google Scholar]
  31. Vinuesa P., Rademaker J. L. W., de Bruijn F. J., Werner D. 1999; Characterization of Bradyrhizobium spp. strains by RFLP analysis of amplified 16S rDNA and rDNA intergenic spacer regions. In Highlights on Nitrogen Fixation pp  275–279 Edited by Martínez E., Hernández G. New York: Plenum;
    [Google Scholar]
  32. Vinuesa P., Neumann-Silkow F., Pacios-Bras C., Spaink H. P., Martinez-Romero E., Werner D. 2003; Genetic analysis of a pH-regulated operon from Rhizobium tropici CIAT899 involved in acid tolerance and nodulation competitiveness. Mol Plant Microbe Interact 16:159–168 [CrossRef]
    [Google Scholar]
  33. Vinuesa P., Silva C., Werner D., Martínez-Romero E. 2005; 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]
  34. Ward D. M. 1998; A natural species concept for prokaryotes. Curr Opin Microbiol 1:271–277 [CrossRef]
    [Google Scholar]
  35. Wernegreen J., Riley M. A. 1999; Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: a case for the genetic coherence of rhizobial lineages. Mol Biol Evol 16:98–113 [CrossRef]
    [Google Scholar]
  36. Wiley E. 1978; The evolutionary species concept reconsidered. Syst Zool 27:17–26 [CrossRef]
    [Google Scholar]
  37. Willems A., Coopman R., Gillis M. 2001a; Comparison of sequence analysis of 16S-23S rDNA spacer regions, AFLP analysis and DNA-DNA hybridizations in Bradyrhizobium . Int J Syst Evol Microbiol 51:623–632
    [Google Scholar]
  38. Willems A., Coopman R., Gillis M. 2001b; Phylogenetic and DNA-DNA hybridization analyses of Bradyrhizobium species. Int J Syst Evol Microbiol 51:111–117
    [Google Scholar]
  39. Willems A., Munive A., de Lajudie P., Gillis M. 2003; In most Bradyrhizobium groups sequence comparison of 16S-23S rDNA internal transcribed spacer regions corroborates DNA-DNA hybridizations. Syst Appl Microbiol 26:203–210 [CrossRef]
    [Google Scholar]
  40. 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 [CrossRef]
    [Google Scholar]
  41. 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 [CrossRef]
    [Google Scholar]
  42. Zhang X., Nick G., Kaijalainen S., Terefework Z., Paulin L., Tighe S. W., Graham P. H., Lindström K. 1999; Phylogeny and diversity of Bradyrhizobium strains isolated from the root nodules of peanut ( Arachis hypogaea ) in Sichuan, China. Syst Appl Microbiol 22:378–386 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.63292-0
Loading
/content/journal/ijsem/10.1099/ijs.0.63292-0
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