1887

Abstract

During a study of the diversity and phylogeny of rhizobia in the root nodules of grown in north-western China, four strains were classified in the genus on the basis of their 16S rRNA gene sequences. The 16S rRNA gene sequences of three of these strains were identical and that of the other strain, which was the only one isolated in Yangling, differed from the others by just 1 bp. The16S rRNA gene sequences of the four strains showed a mean similarity of 99.3 % with the most closely related, recognized species, . The corresponding and gene sequences showed similarities with established species of of less than 86.5 % and less than 89.6 %, respectively. These low similarities indicated that the four strains represented a novel species of the genus . The strains were also found to be distinguishable from the closest related, established species () by rep-PCR DNA fingerprinting, analysis of cellular fatty acid profiles and from the results of a series of phenotypic tests. The level of DNA–DNA relatedness between the representative strain CCNWSX 0483 and IAM 14140 was only 40.13 %. Therefore, a novel species, sp. nov., is proposed, with strain CCNWSX 0483 ( = ACCC 14971 = HAMBI 3214) as the type strain. In nodulation and pathogenicity tests, none of the four strains of sp. nov. was able to induce any nodule or tumour formation on plants. As no amplicons were detected when DNA from the strains was run in PCR with primers for the detection of , and gene sequences, the strains probably do not carry or genes.

Funding
This study was supported by the:
  • 973 Project of China (Award 2010CB126502)
  • National Science Foundation of China (Award 30630054, 30900215 and 30970003)
  • International Science and Technology Cooperation Program of China (Award 2010DFA91930)
  • Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production and Construction Group (Award BRZD1002)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.029108-0
2012-02-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/62/2/335.html?itemId=/content/journal/ijsem/10.1099/ijs.0.029108-0&mimeType=html&fmt=ahah

References

  1. Allen O. N., Allen E. K. 1981 The Leguminosae: A Source Book of Characteristics, Uses and Nodulation Madison, WI: The University of Wisconsin Press;
    [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[PubMed] [CrossRef]
    [Google Scholar]
  3. Conn H. J. 1942; Validity of the genus Alcaligenes . J Bacteriol 44:353–360[PubMed]
    [Google Scholar]
  4. Cui G. L., Xie R. M., Yue J. J., Liang J. Q., Duan X. D., Fan L. M., Wei G. H. 2010; Diversity and phylogeny of rhizobia isolated from Kummerowia in northwest of China. J Agric Biotechnol 18:867–875 (in Chinese)
    [Google Scholar]
  5. De Ley J., Cattoir H., Reynaerts A. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142 [View Article][PubMed]
    [Google Scholar]
  6. Farrand S. K., Van Berkum P. B., Oger P. 2003; Agrobacterium is a definable genus of the family Rhizobiaceae . Int J Syst Evol Microbiol 53:1681–1687 [View Article][PubMed]
    [Google Scholar]
  7. Gao J. L., Sun J. G., Li Y., Wang E. T., Chen W. X. 1994; Numerical taxonomy and DNA relatedness of tropical rhizobia isolated from Hainan province, China. Int J Syst Bacteriol 44:151–158 [View Article]
    [Google Scholar]
  8. Gao J. L., Terefework Z., Chen W. X., Lindström K. 2001; Genetic diversity of rhizobia isolated from Astragalus adsurgens growing in different geographical regions of China. J Biotechnol 91:155–168 [View Article][PubMed]
    [Google Scholar]
  9. 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 [View Article][PubMed]
    [Google Scholar]
  10. 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. 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 [View Article]
    [Google Scholar]
  11. Haukka K., Lindström K., Young J. P. W. 1998; Three phylogenetic groups of nodA and nifH genes in Sinorhizobium and Mesorhizobium isolates from leguminous trees growing in Africa and Latin America. Appl Environ Microbiol 64:419–426[PubMed]
    [Google Scholar]
  12. Jarvis B. D. W., Sivakumaran S., Tighe S. W., Gillis M. 1996; Identification of Agrobacterium and Rhizobium species based on cellular fatty acid composition. Plant Soil 184:143–158 [View Article]
    [Google Scholar]
  13. Jordan D. C. 1984; Genus I. Rhizobium Frank 1889, 338AL . In Bergey’s Manual of Systematic Bacteriology vol. 1 pp. 235–242 Edited by Krieg N. R., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
  14. Jukes T. H., Cantor C. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism pp. 21–132 Edited by Munro H. N. London: Academic Press;
    [Google Scholar]
  15. Kawaguchi A., Sawada H., Ichinose Y. 2008; Phylogenetic and serological analyses reveal genetic diversity of Agrobacterium vitis strains in Japan. Plant Pathol 57:747–753 [View Article]
    [Google Scholar]
  16. Kersters K., De Ley J., Sneath P. H. A., Sackin M. 1973; Numerical taxonomic analysis of Agrobacterium . J Gen Microbiol 78:227–239 [CrossRef]
    [Google Scholar]
  17. Kimura M. 1983 The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; [CrossRef]
    [Google Scholar]
  18. Kumar S., Nei M., Dudley J., Tamura K. 2008; mega: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9:299–306 [View Article][PubMed]
    [Google Scholar]
  19. Laguerre G., Louvrier P., Allard M. R., Amarger N. 2003; Compatibility of rhizobial genotypes within natural populations of Rhizobium leguminosarum biovar viciae for nodulation of host legumes. Appl Environ Microbiol 69:2276–2283 [View Article][PubMed]
    [Google Scholar]
  20. Marmur J. 1961; A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3:208–218 [View Article]
    [Google Scholar]
  21. Marmur J., Doty P. 1962; Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5:109–118 [View Article][PubMed]
    [Google Scholar]
  22. Menna P., Pereira A. A., Bangel E. V., Hungria M. 2009; rep-PCR of tropical rhizobia for strain fingerprinting, biodiversity appraisal and as a taxonomic and phylogenetic tool. Symbiosis 48:120–130 [View Article]
    [Google Scholar]
  23. MIDI 1999 Sherlock Microbial Identification System Operating Manual, version 3. Newark, DE: MIDI Inc;
    [Google Scholar]
  24. Moffett M. L., Colwell R. R. 1968; Adansonian analysis of the Rhizobiaceae. J Gen Microbiol 51:245–266[PubMed] [CrossRef]
    [Google Scholar]
  25. Moore L. W., Kado C. I., Bouzar H. 1988; Agrobacterium . In Laboratory Guide for Identification of Plant Pathogenic Bacteria, 2nd edn. pp. 16–36 Edited by Schaad N. W. St Paul, MN: American Phytopathology Society;
    [Google Scholar]
  26. Moore L. W., Bouzar H., Burr T. 2001; Agrobacterium . In Laboratory Guide for Identification of Plant Pathogenic Bacteria, 3rd edn. pp. 17–35 Edited by Schaad N. W., Jones J. B., Chun W. St Paul, MN: American Phytopathology Society;
    [Google Scholar]
  27. Moulin L., Béna G., Boivin-Masson C., Stępkowski T. 2004; Phylogenetic analyses of symbiotic nodulation genes support vertical and lateral gene co-transfer within the Bradyrhizobium genus. Mol Phylogenet Evol 30:720–732 [View Article][PubMed]
    [Google Scholar]
  28. New Medicine College of Jiangsu 1977 Dictionary of Chinese Traditional Medicine, Part 1 Shanghai: Shanghai People Publishing Company;
    [Google Scholar]
  29. Rzhetsky A., Nei M. 1993; Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 10:1073–1095[PubMed]
    [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[PubMed]
    [Google Scholar]
  31. Sawada H., Ieki H., Matsuda I. 1995; PCR detection of Ti and Ri plasmids from phytopathogenic Agrobacterium strains. Appl Environ Microbiol 61:828–831[PubMed]
    [Google Scholar]
  32. Smibert R. M., Krieg N. R. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology pp. 607–654 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  33. Sneath P. H. A., Sokal R. B. 1973 Numerical Taxonomy. The Principles and Practice of Numerical Classification San Francisco: W. H. Freeman and Co;
    [Google Scholar]
  34. Swofford D. L. 1993; paup: Phylogenetic analysis using parsimony, version 3.1.1. Champaign, IL: Illinois Natural History Survey;
  35. Tajima F., Nei M. 1984; Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol 1:269–285[PubMed]
    [Google Scholar]
  36. Tamura K., Nei M., Kumar S. 2004; Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101:11030–11035 [CrossRef]
    [Google Scholar]
  37. Tan Z. Y., Xu X. D., Wang E. T., Gao J. L., Martinez-Romero E., Chen W. X. 1997; Phylogenetic and genetic relationships of Mesorhizobium tianshanense and related rhizobia. Int J Syst Bacteriol 47:874–879 [View Article][PubMed]
    [Google Scholar]
  38. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [View Article][PubMed]
    [Google Scholar]
  39. Tighe S. W., de Lajudie P., Dipietro K., Lindström K., Nick G., Jarvis B. D. W. 2000; Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium species using the Sherlock Microbial Identification System. Int J Syst Evol Microbiol 50:787–801 [View Article][PubMed]
    [Google Scholar]
  40. Turner S. L., Young J. P. W. 2000; The glutamine synthetases of rhizobia: phylogenetics and evolutionary implications. Mol Biol Evol 17:309–319[PubMed] [CrossRef]
    [Google Scholar]
  41. Versalovic J., Koeuth T., Lupski J. R. 1991; Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19:6823–6831 [View Article][PubMed]
    [Google Scholar]
  42. Versalovic J., Schneider M., de Bruijn F. J., Lupski J. R. 1994; Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol Cell Biol 5:25–40
    [Google Scholar]
  43. Vincent J. M. 1970 A Manual for the Practical Study of Root Nodule Bacteria Oxford: Blackwell Scientific;
    [Google Scholar]
  44. Vinuesa P., Silva C., Lorite M. J., Izaguirre-Mayoral M. L., Bedmar E. J., Martínez-Romero E. 2005; 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 [View Article][PubMed]
    [Google Scholar]
  45. Wang E. T., van Berkum P., Beyene D., Sui X. H., Dorado O., Chen W. X., Martínez-Romero E. 1998; Rhizobium huautlense sp. nov., a symbiont of Sesbania herbacea that has a close phylogenetic relationship with Rhizobium galegae . Int J Syst Bacteriol 48:687–699 [View Article][PubMed]
    [Google Scholar]
  46. Woese C. R., Stackebrandt E., Weisburg W. G., Paster B. J., Madigan M. T., Fowler V. J., Hahn C. M., Blanz P., Gupta R. other authors 1984; The phylogeny of purple bacteria: the alpha subdivision. Syst Appl Microbiol 5:315–326[PubMed] [CrossRef]
    [Google Scholar]
  47. Yoo H. H., Kim T., Ahn S., Kim Y. J., Kim H. Y., Piao X. L., Park J. H. 2005; Evaluation of the estrogenic activity of Leguminosae plants. Biol Pharm Bull 28:538–540 [View Article][PubMed]
    [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[PubMed] [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.029108-0
Loading
/content/journal/ijsem/10.1099/ijs.0.029108-0
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