1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 65, Issue Pt_12

sp. nov., encompassing nitrogen-fixing symbionts of legumes used for green manure and environmental services Free

Abstract

Symbiotic nitrogen-fixing bacteria, commonly called rhizobia, are agronomically important because they can provide significant amounts of nitrogen to plants and help in recovery of impoverished soils and improvement of degraded environments. In recent years, with advances in molecular techniques, several studies have shown that these bacteria have high levels of genetic diversity, resulting in taxonomic reclassifications and descriptions of new species. However, despite the advances achieved, highly conserved 16S ribosomal genes (16S rRNA) do not elucidate differences between species of several genera, including the genus . Other methodologies, such as multilocus sequence analysis (MLSA), have been used in such cases, with good results. In this study, three strains (SEMIAs 690, 6387 and 6428) of the genus , isolated from nitrogen-fixing nodules of and species, without clear taxonomic positions, were studied. These strains differed from genetically closely related species according to the results of MLSA of four housekeeping genes (, , and ) and nucleotide identities of the concatenated genes with those of related species ranged from 87.8 % to 95.7 %, being highest with DNA–DNA hybridization (less than 32 % DNA relatedness) and average nucleotide identity values of the whole genomes (less than 90.5 %) indicated that these strains represented a novel species, and phenotypic traits were determined. Our data supported the description of the SEMIA strains as sp. nov., and SEMIA 690 ( = CNPSo 991 = C 100a = BR 1804 = LMG 28866), isolated from , was chosen as type strain.

  • Published Online:
Funding
This study was supported by the:
  • CNPq (Award 02.13.08.001.00.00)
© 2015 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000591
2015-12-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/12/4441.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000591&mimeType=html&fmt=ahah

References

  1. Binde D. R., Menna P., Bangel E. V., Barcellos F. G., Hungria M. ( 2009;). rep-PCR fingerprinting and taxonomy based on the sequencing of the 16S rRNA gene of 54 elite commercial rhizobial strains. Appl Microbiol Biotechnol 83 897–908 [View Article] [PubMed].
     [Google Scholar]
  2. Chang Y. L., Wang J. Y., Wang E. T., Liu H. C., Sui X. H., Chen W. X. ( 2011;). Bradyrhizobium lablabi sp. nov., isolated from effective nodules of Lablab purpureus and Arachis hypogaea . Int J Syst Evol Microbiol 61 2496–2502 [View Article] [PubMed].
     [Google Scholar]
  3. Delamuta J. R. M., Ribeiro R. A., Menna P., Bangel E. V., Hungria M. ( 2012;). Multilocus sequence analysis (MLSA) of Bradyrhizobium strains: revealing high diversity of tropical diazotrophic symbiotic bacteria. Braz J Microbiol 43 698–710 [View Article] [PubMed].
     [Google Scholar]
  4. Delamuta J. R. M., Ribeiro R. A., Ormeño-Orrillo E., Melo I. S., Martínez-Romero E., Hungria M. ( 2013;). Polyphasic evidence supporting the reclassification of Bradyrhizobium japonicum group Ia strains as Bradyrhizobium diazoefficiens sp. nov. Int J Syst Evol Microbiol 63 3342–3351 [View Article] [PubMed].
     [Google Scholar]
  5. Durán D., Rey L., Mayo J., Zúñiga-Dávila D., Imperial J., Ruiz-Argüeso T., Martínez-Romero E., Ormeño-Orrillo E. ( 2014a;). Bradyrhizobium paxllaeri sp. nov. and Bradyrhizobium icense sp. nov., nitrogen-fixing rhizobial symbionts of Lima bean (Phaseolus lunatus L.) in Peru. Int J Syst Evol Microbiol 64 2072–2078. [CrossRef]
    [Google Scholar]
  6. Durán D., Rey L., Navarro A., Busquets A., Imperial J., Ruiz-Argüeso T. ( 2014b;). Bradyrhizobium valentinum sp. nov., isolated from effective nodules of Lupinus mariae-josephae, a lupine endemic of basic-lime soils in Eastern Spain. Syst Appl Microbiol 37 336–341. [CrossRef]
    [Google Scholar]
  7. Felsenstein J. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 368–376 [View Article] [PubMed].
     [Google Scholar]
  8. Felsenstein J. ( 1985;). Confidence-limits on phylogenies – an approach using the bootstrap. Evolution 39 783–791 [View Article].
     [Google Scholar]
  9. Germano M. G., Menna P., Mostasso F. L., Hungria M. ( 2006;). RFLP analysis of the rRNA operon of a Brazilian collection of bradyrhizobial strains from 33 legume species. Int J Syst Evol Microbiol 56 217–229 [View Article] [PubMed].
     [Google Scholar]
  10. Hall T. A. ( 1999;). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41 95–98.
     [Google Scholar]
  11. Hungria M., Chueire L. M. O., Coca R. G., Megías M. ( 2001;). Preliminary characterization of fast growing strains isolated from soyabean nodules in Brazil. Soil Biol Biochem 33 1349–1361 [View Article].
     [Google Scholar]
  12. Hungria M., Loureiro M. F., Mendes I. C., Campo R. J., Graham P. H. ( 2005;). Inoculant preparation, production and application. . In Nitrogen Fixation: Origins, Applications and Research Progress, pp. 223–254. Edited by Newton W. E. Dordrecht, Amsterdam: Springer;.
     [Google Scholar]
  13. Hungria M., Mendes I. C., Mercante F. M. ( 2013). A Fixação Biológica do Nitrogênio Como Tecnologia de Baixa Emissão de Carbono Para As Culturas do Feijoeiro e da Soja. Embrapa Soja. Documentos 337 Londrina: Embrapa Soja; (in Portuguese)
     [Google Scholar]
  14. Jaccard P. ( 1912;). The distribution of flora in the alpine zone. New Phytol 11 37–50 [View Article].
     [Google Scholar]
  15. Kaschuk G., Hungria M., Andrade D. S., Campo R. J. ( 2006;). Genetic diversity of rhizobia associated with common bean (Phaseolus vulgaris L.) grown under no-tillage and conventional systems in Southern Brazil. Appl Soil Ecol 32 210–220 [View Article].
     [Google Scholar]
  16. Kim M., Oh H.-S., Park S.-C., Chun J. ( 2014;). Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64 346–351 [View Article] [PubMed].
     [Google Scholar]
  17. Lloret L., Martínez-Romero E. ( 2005;). Evolution and phylogeny of rhizobia. Rev Latinoam Microbiol 47 43–60 (in Spanish) .
     [Google Scholar]
  18. MAPA (Ministério da Agricultura, Pecuária e Abastecimento). ( 2011;). Instrução Normativa N° 13, de 24/03/2011. Available http://www.normasbrasil.com.br/norma/instrucao-normativa-13-2011_78540.html . .
     [Google Scholar]
  19. 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 [View Article] [PubMed].
     [Google Scholar]
  20. Menna P., Hungria M. ( 2011;). Phylogeny of nodulation and nitrogen-fixation genes in Bradyrhizobium: supporting evidence for the theory of monophyletic origin, and spread and maintenance by both horizontal and vertical transfer. Int J Syst Evol Microbiol 61 3052–3067 [View Article] [PubMed].
     [Google Scholar]
  21. Menna P., Hungria M., Barcellos F. G., Bangel E. V., Hess P. N., Martínez-Romero E. ( 2006;). Molecular phylogeny based on the 16S rRNA gene of elite rhizobial strains used in Brazilian commercial inoculants. Syst Appl Microbiol 29 315–332 [View Article] [PubMed].
     [Google Scholar]
  22. Menna P., Barcellos F. G., Hungria M. ( 2009;). Phylogeny and taxonomy of a diverse collection of Bradyrhizobium strains based on multilocus sequence analysis of the 16S rRNA gene, ITS region and glnII, recA, atpD and dnaK genes. Int J Syst Evol Microbiol 59 2934–2950 [View Article] [PubMed].
     [Google Scholar]
  23. Norris D. O. ( 1965;). Acid production by Rhizobium a unifying concept. Plant Soil 22 143–166 [View Article].
     [Google Scholar]
  24. Ormeño-Orrillo E., Hungria M., Martínez-Romero E. ( 2013;). Dinitrogen-fixing prokaryotes. . In The Prokaryotes – Prokaryotic Physiology and Biochemistry, pp. 427–451. Edited by Rosenberg E., DeLong E. F., Stackebrandt E., Lory S., Thompson F. Berlin, Heidelberg: Springer-Verlag;.
     [Google Scholar]
  25. Parker M. A., Rousteau A. ( 2014;). Mosaic origins of Bradyrhizobium legume symbionts on the Caribbean island of Guadeloupe. Mol Phylogenet Evol 77 110–115 [View Article] [PubMed].
     [Google Scholar]
  26. Richter M., Rosselló-Móra R. ( 2009;). Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106 19126–19131 [View Article] [PubMed].
     [Google Scholar]
  27. Rivas R., Martens M., de Lajudie P., Willems A. ( 2009;). Multilocus sequence analysis of the genus Bradyrhizobium . Syst Appl Microbiol 32 101–110 [View Article] [PubMed].
     [Google Scholar]
  28. 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]
  29. Sneath P. H. A., Sokal R. R. ( 1973). Numerical Taxonomy: The Principles and Practice of Numerical Classification San Francisco, USA: W. H. Freeman and Company;.
     [Google Scholar]
  30. Tamura K., Nei M. ( 1993;). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10 512–526 [PubMed].
     [Google Scholar]
  31. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013;). mega6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30 2725–2729 [View Article] [PubMed].
     [Google Scholar]
  32. 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. [CrossRef]
    [Google Scholar]
  33. United Nations ( 2015;). World day to combat desertification. Available at: http://www.un.org/en/events/desertificationday/background.shtml. Access: 03/30/2015 .
     [Google Scholar]
  34. Vincent J. M. ( 1970). A Manual for the Practical Study of Root-Nodule Bacteria IBP handbook 15 Oxford: Blacwell Scientific;.
     [Google Scholar]
  35. 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]
  36. Zhang X. X., Guo H. J., Wang R., Sui X. H., Zhang Y. M., Wang E. T., Tian C. F., Chen W. X. ( 2014;). Genetic divergence of Bradyrhizobium strains nodulating soybeans as revealed by multilocus sequence analysis of genes inside and outside the symbiosis island. Appl Environ Microbiol 80 3181–3190. [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000591
Loading
Bradyrhizobium viridifuturi sp. nov., encompassing nitrogen-fixing symbionts of legumes used for green manure and environmental services
Int J Syst Evol Microbiol 65, 4441 (2015); https://doi.org/10.1099/ijsem.0.000591
/content/journal/ijsem/10.1099/ijsem.0.000591
/content/journal/ijsem/10.1099/ijsem.0.000591
Loading

Data & Media loading...

Supplements

Supplementary Data

PDF

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