1887

Abstract

Two novel related species, sp. nov. and sp. nov., were identified by a polyphasic approach using DNA–DNA hybridization, whole-genome sequencing and phylogenetic and phenotypic characterization including nodulation of and (bean). As similar bacteria were found in the Los Tuxtlas rainforest in Mexico and in Central America, we suggest the existence of a Mesoamerican microbiological corridor. The type strain of sp. nov. is CCGE 502 ( = ATCC BAA-2124  = CFN 242  = Dal4  = HAMBI 3152) and that of sp. nov. is CCGE 501 ( = ATCC BAA-2123  = HAMBI 3151  = CIP 110148  = 1847).

Funding
This study was supported by the:
  • GEF-PNUMA
  • CIAT
  • PAPIIT (Award IN205412 and IN200907)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.033555-0
2012-09-01
2024-12-03
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/62/9/2264.html?itemId=/content/journal/ijsem/10.1099/ijs.0.033555-0&mimeType=html&fmt=ahah

References

  1. Barrett C. F., Parker M. A. 2006; Coexistence of Burkholderia, Cupriavidus, and Rhizobium sp. nodule bacteria on two Mimosa spp. in Costa Rica. Appl Environ Microbiol 72:1198–1206 [View Article][PubMed]
    [Google Scholar]
  2. Chen W.-X., Tan Z.-Y., Gao J.-L., Li Y., Wang E.-T. 1997; Rhizobium hainanense sp. nov., isolated from tropical legumes. Int J Syst Bacteriol 47:870–873 [View Article][PubMed]
    [Google Scholar]
  3. Delgado-Salinas A., Bibler R., Lavin M. 2006; Phylogeny of the genus Phaseolus (Leguminosae): a recent diversification in an ancient landscape. Syst Bot 31:779–791 [View Article]
    [Google Scholar]
  4. del Papa, M. F.,, Balague L. J., Sowinski S. C., Wegener C., Segundo E., Abarca F. M., Toro N., Niehaus K., Aguilar O. M., Martínez-Drets G., Lagares A. 1999; Isolation and characterization of alfalfa-nodulating rhizobia present in acidic soils of central Argentina and Uruguay. Appl Environ Microbiol 65:1420–1427[PubMed]
    [Google Scholar]
  5. del Papa M. F., Pistorio M., Draghi W. O., Lozano M. J., Giusti M. A., Medina C., van Dillewijn P., Martínez-Abarca F., Moron Flores B. other authors 2007; Identification and characterization of a nodH ortholog from the alfalfa-nodulating Or191-like rhizobia. Mol Plant Microbe Interact 20:138–145 [View Article][PubMed]
    [Google Scholar]
  6. Eardly B. D., Young J. P. W., Selander R. K. 1992; Phylogenetic position of Rhizobium sp. strain Or 191, 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[PubMed]
    [Google Scholar]
  7. Guindon S., Dufayard J.-F., Lefort V., Anisimova M., Hordijk W., Gascuel O. 2010; New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321 [View Article][PubMed]
    [Google Scholar]
  8. 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]
  9. Han T. X., Wang E. T., Wu L. J., Chen W. F., Gu J. G., Gu C. T., Tian C. F., Chen W. X. 2008; Rhizobium multihospitium sp. nov., isolated from multiple legume species native of Xinjiang, China. Int J Syst Evol Microbiol 58:1693–1699 [View Article][PubMed]
    [Google Scholar]
  10. Hernández-Lucas I., Segovia L., Martínez-Romero E., Pueppke S. G. 1995; Phylogenetic relationships and host range of Rhizobium spp. that nodulate Phaseolus vulgaris L.. Appl Environ Microbiol 61:2775–2779[PubMed]
    [Google Scholar]
  11. Hernández-Lucas I., Rogel-Hernández M. A., Segovia L., Rojas-Jiménez K., Martínez-Romero E. 2004; Phylogenetic relationships of rhizobia based on citrate synthase gene sequences. Syst Appl Microbiol 27:703–706 [View Article][PubMed]
    [Google Scholar]
  12. Hou B. C., Wang E. T., Li Y. Jr, Jia R. Z., Chen W. F., Gao Y., Dong R. J., Chen W. X. 2009; Rhizobium tibeticum sp. nov., a symbiotic bacterium isolated from Trigonella archiducis-nicolai (Sirj.) Vassilcz.. Int J Syst Evol Microbiol 59:3051–3057 [View Article][PubMed]
    [Google Scholar]
  13. Hungria M., Andrade D. S., Chueire L. M. O., Probanza A., Guttierrez-Mañero F. J., Megías M. 2000; Isolation and characterization of new efficient and competitive bean (Phaseolus vulgaris L.) rhizobia from Brazil. Soil Biol Biochem 32:1515–1528 [View Article]
    [Google Scholar]
  14. Lloret L., Ormeño-Orrillo E., Rincón R., Martínez-Romero J., Rogel-Hernández M. A., Martínez-Romero E. 2007; Ensifer mexicanus sp. nov. a new species nodulating Acacia angustissima (Mill.) Kuntze in Mexico. Syst Appl Microbiol 30:280–290 [View Article][PubMed]
    [Google Scholar]
  15. López-López A., Rogel M. A., Ormeño-Orrillo E., Martínez-Romero J., Martínez-Romero E. 2010a; Phaseolus vulgaris seed-borne endophytic community with novel bacterial species such as Rhizobium endophyticum sp. nov.. Syst Appl Microbiol 33:322–327 [View Article][PubMed]
    [Google Scholar]
  16. López-López A., Rosenblueth M., Martínez J., Martínez-Romero E. 2010b; Rhizobial symbioses in tropical legumes and non-legumes. In Soil Biology and Agriculture in the Tropics (Soil Biology, vol. 21) pp. 163–184 Edited by Dion P. Berlin & Heidelberg: Springer; [View Article]
    [Google Scholar]
  17. Martínez E., Pardo M. A., Palacios R., Cevallos M. A. 1985; Reiteration of nitrogen fixation gene sequences and specificity of Rhizobium in nodulation and nitrogen fixation in Phaseolus vulgaris . J Gen Microbiol 131:1779–1786
    [Google Scholar]
  18. Martínez-Romero E. 2003; Diversity of RhizobiumPhaseolus vulgaris symbiosis: overview and perspectives. Plant Soil 252:11–23 [View Article]
    [Google Scholar]
  19. Martínez-Romero E., Rosenblueth M. 1990; Increased bean (Phaseolus vulgaris L.) nodulation competitiveness of genetically modified Rhizobium strains. Appl Environ Microbiol 56:2384–2388[PubMed]
    [Google Scholar]
  20. 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]
  21. Ormeño-Orrillo E., Rogel M. A., Lloret L., López A., Martínez J., Vinuesa P., Martínez-Romero E. 2009; Rhizobial diversity in different land use systems in the rain forest of Los Tuxtlas, Mexico. In Below-Ground Biodiversity in Sierra de Santa Marta, Los Tuxtlas, Veracruz, Mexico pp. 65–84 Edited by Barois I., Huising E. J., Okoth P., Trejo D., De los Santos M. Xalapa, Mexico: Instituto de Ecología;
    [Google Scholar]
  22. Posada D., Buckley T. R. 2004; Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol 53:793–808 [View Article][PubMed]
    [Google Scholar]
  23. Ramírez-Bahena M. H., García-Fraile P., Peix A., Valverde A., Rivas R., Igual J. M., Mateos P. F., Martínez-Molina E., Velázquez E. 2008; Revision of the taxonomic status of the species Rhizobium leguminosarum (Frank 1879) Frank 1889AL, Rhizobium phaseoli Dangeard 1926AL and Rhizobium trifolii Dangeard 1926AL. R. trifolii is a later synonym of R. leguminosarum. Reclassification of the strain R. leguminosarum DSM 30132 ( = NCIMB 11478) as Rhizobium pisi sp. nov. Int J Syst Evol Microbiol 58:2484–2490 [View Article][PubMed]
    [Google Scholar]
  24. Reinhardt J. A., Baltrus D. A., Nishimura M. T., Jeck W. R., Jones C. D., Dangl J. L. 2009; De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res 19:294–305 [View Article][PubMed]
    [Google Scholar]
  25. Ribeiro R. A., Rogel M. A., López-López A., Ormeño-Orrillo E., Barcellos F. G., Martínez J., Thompson F. L., Martínez-Romero E., Hungria M. 2012; Reclassification of Rhizobium tropici type A strains as Rhizobium leucaenae sp. nov.. Int J Syst Evol Microbiol 62:1179–1184 [View Article][PubMed]
    [Google Scholar]
  26. Rincón-Rosales R., Lloret L., Ponce E., Martínez-Romero E. 2009; Rhizobia with different symbiotic efficiencies nodulate Acaciella angustissima in Mexico, including Sinorhizobium chiapanecum sp. nov. which has common symbiotic genes with Sinorhizobium mexicanum . FEMS Microbiol Ecol 67:103–117 [View Article][PubMed]
    [Google Scholar]
  27. Rogel M. A., Ormeño-Orrillo E., Martinez Romero E. 2011; Symbiovars in rhizobia reflect bacterial adaptation to legumes. Syst Appl Microbiol 34:96–104 [View Article][PubMed]
    [Google Scholar]
  28. Segovia L., Young J. P. W., Martínez-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 [View Article][PubMed]
    [Google Scholar]
  29. Silva C., Vinuesa P., Eguiarte L. E., Souza V., Martínez-Romero E. 2005; Evolutionary genetics and biogeographic structure of Rhizobium gallicum sensu lato, a widely distributed bacterial symbiont of diverse legumes. Mol Ecol 14:4033–4050 [View Article][PubMed]
    [Google Scholar]
  30. 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]
  31. Tighe S. W., de Lajudie P., Dipietro K., Lindström K., Nick G., Jarvis B. D. 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]
  32. Toledo I., Lloret L., Martínez-Romero E. 2003; Sinorhizobium americanus sp. nov., a new Sinorhizobium species nodulating native Acacia spp. in Mexico. Syst Appl Microbiol 26:54–64 [View Article][PubMed]
    [Google Scholar]
  33. Valverde A., Igual J. M., Peix A., Cervantes E., Velázquez E. 2006; Rhizobium lusitanum sp. nov. a bacterium that nodulates Phaseolus vulgaris . Int J Syst Evol Microbiol 56:2631–2637 [View Article][PubMed]
    [Google Scholar]
  34. Velázquez E., Peix A., Zurdo-Piñiro J. L., Palomo J. L., Mateos P. F., Rivas R., Muñoz-Adelantado E., Toro N., García-Benavides P., Martínez-Molina E. 2005; The coexistence of symbiosis and pathogenicity-determining genes in Rhizobium rhizogenes strains enables them to induce nodules and tumors or hairy roots in plants. Mol Plant Microbe Interact 18:1325–1332 [View Article][PubMed]
    [Google Scholar]
  35. Vincent J. M. 1970 A Manual for the Practical Study of the Root-Nodule Bacteria (IBP Handbook no. 15) Oxford: Blackwell Scientific;
    [Google Scholar]
  36. 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]
  37. Wang F., Wang E. T., Wu L. J., Sui X. H., Li Y. Jr, Chen W. X. 2011; Rhizobium vallis sp. nov., isolated from nodules of three leguminous species. Int J Syst Evol Microbiol 61:2582–2588 [View Article][PubMed]
    [Google Scholar]
  38. Zerbino D. R., Birney E. 2008; Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829 [View Article][PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijs.0.033555-0
Loading
/content/journal/ijsem/10.1099/ijs.0.033555-0
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