1887

Abstract

The taxonomic position of isolates of a new genomic species (designated genomic species 2) obtained from several annual Medicago species and originating from different geographical locations was established through the results of phenotypic tests (including the of auxanographic and biochemical tests and symbiotic properties) and 16S rRNA phylogenetic inferences. A comparison of the complete 16S rRNA sequence of a representative of genomic species 2 (strain A 321 [T = type strain]) with the 16S rRNA sequences of other members of the and closely related taxa showed that genomic species 2 was phylogenetically related to , and . The levels of sequence similarity and observed numbers of nucleotide substitutions in strains indicated that A 321 and exhibited the highest level of sequence similarity (99.7%), with four nucleotide substitutions and one deletion. The results of a numerical analysis based on data from 63 auxanographic and biochemical tests clearly separated genomic species 2 isolates from . Genomic species 2 isolates nodulated and fixed nitrogen with , whereas isolates were ineffective and formed rudimentary nodules on this host plant. On the basis of phenotypic and 16S sequence analysis data, genomic species 2 isolates cannot be assigned to a previously described species. We propose that these isolates belong to a new species, .

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/00207713-46-4-972
1996-10-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/46/4/ijs-46-4-972.html?itemId=/content/journal/ijsem/10.1099/00207713-46-4-972&mimeType=html&fmt=ahah

References

  1. Brenner D. J., McWhorter A. C., Leete Knutson J. K., Steigerwalt A. G. 1982; Escherichia vulneris: a new species of Enterobacteriaceae associated with human wounds. J. Clin. Microbiol 15:1133–1140
    [Google Scholar]
  2. Brockwell J., Hely F. W. 1966; Symbiotic characteristics of Rhizobium meliloti: an appraisal of systematic treatment of nodulation and nitrogen fixation interaction between hosts and rhizobia of diverse origins. Aust. J. Agric. Res 17:885–899
    [Google Scholar]
  3. Brunel B., Rome S., Ziani R., Cleyet-Marel J. C. 1996; Comparison of nucleotide diversity and symbiotic properties of Rhizobium meliloti populations from annual species of Medicago. FEMS Microbiol. Ecol 19:71–82
    [Google Scholar]
  4. Chen W. X., Yan G. H., Li J. L. 1988; Numerical taxonomic study of fast-growing soybean rhizobia and a proposal that Rhizobium fredii be assigned to Sinorhizobium gen. nov. Int. J. Syst. Bacteriol 38:392–397
    [Google Scholar]
  5. De Lajudie P., Willems A., Pot B., Dewettinck D., Maestrojuan G., Neyra M., Collins M. D., Dreyfus B., Kersters K., Gillis M. 1994; Polyphasic 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]
  6. Dobert R. C., Breil B. T., Triplett E. W. 1994; DNA sequence of the common nodulation genes of Bradyrhizobium elkanii and their phylogenetic relationships to those of other nodulating bacteria. Mol. Plant-Microbe Interact 5:564–572
    [Google Scholar]
  7. Eardly B. D., Materon L. A., Smith N. H., Johnson D. A., Rumbaugh M. D., Selander R. K. 1990; Genetic structure of natural populations of the nitrogen-fixing bacterium Rhizobium meliloti. Appl. Environ. Microbiol 56:187–194
    [Google Scholar]
  8. Eardly B. D., Young J. P. W., Selander R. K. 1992; Phylogenetic position of Rhizobium sp. strain Orl91, a symbiont of both Medicago sativa and Phaseolus vulgaris, based on partial sequences of the 16S rRNA and nifH genes. Appl. Environ. Microbiol 58:1809–1815
    [Google Scholar]
  9. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
    [Google Scholar]
  10. Fred E. B., Baldwin I. L., McCoy E. 1932 Root nodule bacteria and leguminous plants University of Wisconsin press; Madison:
    [Google Scholar]
  11. Gibson A. H. 1980 Methods for legumes in glasshouse and controlled environment cabinets. 139–184 Bergersen F. J.ed Methods for evaluating biological nitrogen fixation John Wiley and Sons; New York:
    [Google Scholar]
  12. Graham P. H., Sadowsky M. J., Keyser H. H., Barnet Y. M., Bradley R. S., Cooper J. E., De Ley D. J., Jarvis B. D. W., Roslycky E. B., Strijdom B. W., Young J. P. W. 1991; Proposed minimal standards for the description of new genera and species of rootand stem-nodulating bacteria. Int. J. Syst. Bacteriol 41:582–587
    [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. Hillis D. M., Dixon M. T. 1991; Ribosomal DNA: molecular evolution and phylogenetic inference. Q. Rev. Biol 4:411–453
    [Google Scholar]
  15. Jarvis B. D. W., Downer H. L., Young J. P. W. 1992; Phylogeny of fast-growing soybean-nodulating rhizobia supports synonymy of Sinorhizobium and Rhizobium and assignment to Rhizobium fredii. Int. J. Syst. Bacteriol 42:93–96
    [Google Scholar]
  16. Jordan D. C. 1984 Rhizobiaceae Conn 1938, 321AL. 234–256 Krieg N. R., Holt J. G.ed Bergey’s manual of systematic bacteriology 1 The Williams & Wilkins Co.; Baltimore:
    [Google Scholar]
  17. 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]
  18. Laguerre G., Allard M. R., Revoy F., Amarger N. 1994; Rapid identification of rhizobia by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl. Environ. Microbiol 60:56–63
    [Google Scholar]
  19. Lesins K., Lesins I. 1979 Genus Medicago (Leguminosae). A taxogenic study Junk, The Hague; The Netherlands:
    [Google Scholar]
  20. Mullis K. B., Faloona F. A. 1987; Specific synthesis of DNA in vitro via a polymerase catalysed chain reaction. Methods Enzymol 153:335–350
    [Google Scholar]
  21. Provorov N. A. 1994; The interdependence between taxonomy of legumes and specificity of their interaction with rhizobia in relation to evolution of the symbiosis. Symbiosis 24:183–200
    [Google Scholar]
  22. Rome S., Brunel B., Fernandez M. P., Normand P., Cleyet-Marel J. C. 1996; Evidence of two genomic species of Rhizobium associated with Medicago truncatula revealed by PCR/RFLP and DNA/DNA hybridizations. Arch. Microbiol 165:285–288
    [Google Scholar]
  23. Saitou N., Nei M. 1987; A neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol 44:406–425
    [Google Scholar]
  24. Sanger F., Nicklen S., Coulson A. R. 1977; DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463–5467
    [Google Scholar]
  25. Scholia M. H., Moorefield J. A., Elkan G. H. 1990; DNA homology between species of rhizobia. Syst. Appl. Microbiol 13:288–294
    [Google Scholar]
  26. Sneath P. H. A., Sokal R. R. 1973 The principles and practice of numerical classification. 223–234 W. H. Freeman and Sons; San Francisco:
    [Google Scholar]
  27. Vincent J. M. 1970; A manual for the practical study of root nodule bacteria. IBP (Int. Biol. Programme) Handb 15:3–4
    [Google Scholar]
  28. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. 1991; 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol 173:697–703
    [Google Scholar]
  29. Willems A., Collins M. D. 1993; Phylogenetic analysis of rhizobia and agrobacteria based on 16S rRNA gene sequences. Int. J. Syst. Bacteriol 43:305–313
    [Google Scholar]
  30. Yanagi M., Yamasato K. 1993; Phylogenetic analysis of the family Rhizobiaceae and related bacteria by sequencing of 16S rRNA gene using PCR and DNA sequencer. FEMS Microbiol. Lett 107:115–120
    [Google Scholar]
  31. Young J. P. W., Johnston A. W. B. 1989; The evolution of specificity in the \egume-Rhizobium symbiosis. Trends Evol. Ecol 4:341–348
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/00207713-46-4-972
Loading
/content/journal/ijsem/10.1099/00207713-46-4-972
Loading

Data & Media loading...

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