1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 45, Issue 4

Genomic Heterogeneity of Strains Nodulating Chickpeas ( L.) and Description of sp. nov. Free

Abstract

The genetic diversity of chickpea strains was studied by using 30 isolates obtained from nodules on chickpeas growing in uninoculated fields over a wide geographic range. The following taxonomic approaches were used: DNA-DNA relatedness analysis, restriction fragment length polymorphism analysis of the amplified 16S ribosomal DNA (rDNA) intergenic spacer (IGS), and total 16S rRNA sequence analysis. The division of chickpea-infective strains into two major phylogenetic groups (groups A and B) that has been described previously was confirmed by the polymorphism of the 16S IGS rDNA. We identified a total of five genomic species, including the previously described species . All of the group B strains except one were homogeneous and belonged to a single genomic species corresponding to . Group A was heterogeneous, containing three genomic species and five strains that remained unclassified, and its members had very different PCR restriction fragment length polymorphism profiles. The complete 16S rRNA sequences of strains representing the two major groups. UPM-Ca7 (T = type strain) and genomic species 2 strain UPM-Ca36, exhibited 19 mismatches. Both of these strains belonged to the branch; UPM-Ca7 was closely related to , and strain UPM-Ca36 was clearly separated from and closely related to . Thus, genomic species 2 could be distinguished from by its 16S rRNA sequence, by DNA relatedness data, by the polymorphism of the 16S IGS rDNAs, and by previously described multilocus enzyme electrophoresis results and phenotypic characteristics. Therefore, we propose that strains belonging to genomic species 2 should be classified in a new species, , and that strain UPM-Ca36 should be the type strain.

  • Published Online:
Copyright © 1995 International Union of Microbiological Societies
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/00207713-45-4-640
1995-10-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/45/4/ijs-45-4-640.html?itemId=/content/journal/ijsem/10.1099/00207713-45-4-640&mimeType=html&fmt=ahah

References

  1. Bosco M., Jamann S., Chapelon C., Simonet P., Normand P. 1994; Frankia microsymbiont in Dryas drummondii nodules is closely related to the microsymbiont of Coriaria and genetically distinct from other characterized Frankia strains. 173–183 Hegazi N. A., Fayez M., Monib M. Nitrogen fixation with non-legumes The American University in Cairo Press; Cairo:
     [Google Scholar]
  2. Brenner D. J., McWorter A. C., Knuston J. K. L., Steigerwalt A. G. 1982; Escherichia vulneris: a new species of Enterobacteriaceae associated with human wounds. J. Clin. Microbiol 15:1133–1140
     [Google Scholar]
  3. Cadahia E., Leyvar A., Ruiz-Argueso T. 1986; Indigenous plasmids and cultural characteristics of rhizobia nodulating chickpeas (Cicer arietinum L.). Arch. Microbiol 146:239–244
     [Google Scholar]
  4. Chen W. X., Li G. S., Qi Y. L., Wang E. T., Yuan H. L., Li J. L. 1991; Rhizobium huakuii sp. nov. isolated from the root nodules of Astragalus sinicus . Int. J. Syst. Bacteriol 41:275–280
     [Google Scholar]
  5. Crosa J. M., Brenner D. J., Falkow S. 1973; Use of a single-strand-specific nuclease for analysis of bacterial and plasmid deoxyribonucleic acid homo- and heteroduplexes. J. Bacteriol 115:904–911
     [Google Scholar]
  6. Dadarwal K. R. 1980; Host bacterium factors involved in legume symbiosis. Indian J. Microbiol 20:245–252
     [Google Scholar]
  7. De Lajudie P., Willems A., Pot B., Dewettinck D., Maestrojuan G., Neyra M., Collins M. D., Dreyfus B., Kersters K., Gillis M. 1994; Poly-phasic taxonomy of rhizobia: emendation of the genus Sinorhizobium and description of Sinorhizobium meliloti comb, nov., Sinorhizobium saheli sp. nov., and Sinorhizobium teranga sp. nov. Int. J. Syst. Bacteriol 44:715–733
     [Google Scholar]
  8. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
     [Google Scholar]
  9. Fernandez M. P., Meugnier H., Grimont P. A. D., Bardin R. 1989; Deoxyribonucleic acid relatedness among members of the genus Frankia . Int. J. Syst. Bacteriol 39:424–429
     [Google Scholar]
  10. Gaur Y. D., Sen A. N. 1979; Cross inoculation group specificity in Cicer rhizobium symbiosis. New Phytol 83:745–754
     [Google Scholar]
  11. Grimont P. A. D. 1988; Use of DNA reassociation in bacterial classification. Can. J. Bacteriol 34:541–546
     [Google Scholar]
  12. Grimont P. A. D., Popoff M. Y., Grimont F., Coynault C., Lemelin M. 1980; Reproducibility and correlation study of three deoxyribonucleic acid hybridization procedures. Curr. Microbiol 4:325–330
     [Google Scholar]
  13. Higgins D. G., Sharp P. M. 1988; Clustal: a package for performing multiple alignment on a microcomputer. Gene 73:237–244
     [Google Scholar]
  14. Jarvis B. D. W., Pankhurst C. E., Patel J. J. 1982; Rhizobium loti, a new species of legume-root nodule bacteria. Int. J. Syst. Bacteriol 32:378–380
     [Google Scholar]
  15. Jordan D. C. 1984; Family III. Rhizobiaceae . 234–242 Krieg N. R., Holt J. G. Bergey’s manual of systematic bacteriology 1 The Williams & Wilkins Co; Baltimore:
     [Google Scholar]
  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
     [Google Scholar]
  17. Kingsley M. T., Bohlool B. B. 1983; Characterization of Rhizobium sp. (Cicer arietinum L.) by immunofluorescence, immunodiffusion and intrinsic antibiotic resistance. Can. J. Microbiol 29:518–526
     [Google Scholar]
  18. Lindstrom K. 1989; Rhizobium galegae, a new species of legume root nodule bacteria. Int. J. Syst. Bacteriol 39:365–367
     [Google Scholar]
  19. Maniatis T., Fritsch E. F., Sambrook J. 1982 Molecular cloning: a laboratory manual Cold Spring Harbor Laboratory; Cold Spring Harbor, N.Y:
     [Google Scholar]
  20. Martinez-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
     [Google Scholar]
  21. Mullis K. B., Faloona F. A. 1987; Specific synthesis of DNA in vitro via a polymerase catalysed chain reaction. Methods Enzymol 155:335–350
     [Google Scholar]
  22. Nei M., Li W. H. 1979; Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. SciUSA 76:5269–5273
     [Google Scholar]
  23. Normand P., Cournoyer B., Simonet P., Nazaret S. 1992; Analysis of a ribosomal RNA operon in the actinomycete Frankia . Gene 111:119–124
     [Google Scholar]
  24. Nour S. M., Cleyet-Marel J. C., Beck D., Effosse A., Fernandez M. P. 1994; Genotypic and phenotypic diversity of Rhizobium isolated from chickpea (Cicer arietinum L.). Can. J. Microbiol 40:345–354
     [Google Scholar]
  25. Nour S. M., Fernandez M. P., Normand P., Cleyet-Marel J. C. 1994; Rhizobium ciceri sp. nov., consisting of strains that nodulate chickpeas (Cicer arietinum L.). Int. J. Syst. Bacteriol 44:511–522
     [Google Scholar]
  26. Rigby P. W. J., Dieckmann M., Rhodes C., Berg P. 1977; Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. Int. J. Syst. Bacteriol 27:237–251
     [Google Scholar]
  27. Saitou N., Nei M. 1987; A neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol 44:406–425
     [Google Scholar]
  28. Sanger F., Nicklen S., Coulson A. R. 1977 DNA sequencing with chain-terminating inhibitorsProc. Natl. Acad. SciUSA 74:5463–5467
     [Google Scholar]
  29. Scholia M. H., Elkan G. H. 1984; Rhizobium fredii sp. nov., a fast- growing species that effectively nodulates soybeans. Int. J. Syst. Bacteriol 34:484–486
     [Google Scholar]
  30. Segovia L., Young J. P. W., Martinez-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
     [Google Scholar]
  31. Sneath P. H. A., Sokal R. R. 1973 Numerical taxonomy W. H. Freeman and Sons; San Francisco:
     [Google Scholar]
  32. Vincent J. M. 1970 A manual for the practical study of root-nodule bacteria I. B. P. Handbook no. 15 3–4 Blackwell Scientific Publications; Oxford:
     [Google Scholar]
  33. 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., Stackebrandt E., Starr M. P., Truper H. G. 1987; Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int. J. Syst. Bacteriol 37:463–464
     [Google Scholar]
  34. Willems A., Collins M. D. 1993; Phylogenetic analysis of rhizobia and agro-bacteria based on 16S rRNA gene sequences. Int. J. Syst. Bacteriol 43:305–313
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/00207713-45-4-640
Loading
Genomic Heterogeneity of Strains Nodulating Chickpeas (Cicer arietinum L.) and Description of Rhizobium mediterraneum sp. nov.
Int J Syst Evol Microbiol 45, 640 (1995); https://doi.org/10.1099/00207713-45-4-640
/content/journal/ijsem/10.1099/00207713-45-4-640
/content/journal/ijsem/10.1099/00207713-45-4-640
Loading

Data & Media loading...

Most cited Most Cited RSS feed

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