1887

Abstract

Root-nodule bacteria were isolated from (Sw.) Willd. growing in the Cerrado Amazon region, State of Roraima, Brazil. The 16S rRNA gene sequences of six strains (BR 10250, BR 10248, BR 10249, BR 10251, BR 10252 and BR 10253) showed low similarities with currently described species of the genus . Phylogenetic analyses of sequences of five housekeeping genes (, , , and ) revealed EK05 to be the closest type strain (97.4 % sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [with the major components C and summed feature 8 (Cω6/Cω7)], the slow growth rate and carbon compound utilization patterns supported the assignment of our strains to the genus . Results from DNA–DNA hybridizations and physiological traits differentiated our strains from the closest related species of the genus with validly published names. Sequences of symbiosis-related genes for nodulation () and nitrogen fixation () grouped together with those of EK05 and sp. strains BR 6610 (used as a commercial inoculant for in Brazil) and TUXTLAS-10 (previously observed in Central America). Based on these data, the six strains represent a novel species, for which the name sp. nov. is proposed. The type strain is BR 10250 ( = HAMBI 3600).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.063727-0
2014-10-01
2019-11-16
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/10/3395.html?itemId=/content/journal/ijsem/10.1099/ijs.0.063727-0&mimeType=html&fmt=ahah

References

  1. Allen O. N., Allen E. K.. ( 1939;). Root nodule bacteria of some tropical leguminous plants. II. Cross-inoculation tests within the cowpea group. . Soil Sci 47:, 63–76. [CrossRef]
    [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. [CrossRef][PubMed]
    [Google Scholar]
  3. Araújo W. F., de Andrade Júnior A. S., de Medeiros R. D., Sampaio R. A.. ( 2001;). Precipitação pluviométrica mensal provável em Boa Vista, Estado de Roraima, Brasil. . Rev Bras Eng Agric Ambient 5:, 563–567 (in Portuguese). [CrossRef]
    [Google Scholar]
  4. Condé T. M., Tonini H.. ( 2013;). Fitossociologia de uma floresta ombrófila densa na Amazônia setentrional, Roraima, Brasil. . Acta Amazon 43:, 247–259 (in Portuguese). [CrossRef]
    [Google Scholar]
  5. 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. [CrossRef][PubMed]
    [Google Scholar]
  6. Ezaki T., Hashimoto Y., Yabuuchi E.. ( 1989;). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. . Int J Syst Bacteriol 39:, 224–229. [CrossRef]
    [Google Scholar]
  7. Farris J. S., Källersjö M., Kluge A. G., Bult C.. ( 1994;). Testing significance of incongruence. . Cladistics 10:, 315–319. [CrossRef]
    [Google Scholar]
  8. Felsenstein J.. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368–376. [CrossRef][PubMed]
    [Google Scholar]
  9. Filardi F. L. R., da Costa Rodrigues I. M., Garcia F. C. P., de Carvalho-Okano R. M.. ( 2008;). Padrões de distribuição geográfica de espécies arbóreas de Leguminosae ocorrentes no cerrado. . Rev Bras Biocienc 5:, 1116–1118 (in Portuguese).
    [Google Scholar]
  10. Franco A. A., de Faria S. M.. ( 1997;). The contribution of N2-fixing tree legumes to land reclamation and sustainability in the tropics. . Soil Biol Biochem 29:, 897–903. [CrossRef]
    [Google Scholar]
  11. Fred E. B., Waksman S. A.. ( 1928;). Yeast extract-mannitol agar. . In Laboratory Manual of General Microbiology. New York:: McGraw-Hill;.
    [Google Scholar]
  12. Goris J., Suzuki K., De Vos P., Nakase T., Kersters K.. ( 1998;). Evaluation of a microplate DNA-DNA hybridization method compared with the initial renaturation method. . Can J Microbiol 44:, 1148–1153. [CrossRef]
    [Google Scholar]
  13. Grossman J. M., Sheaffer C., Wyse D., Graham P. H.. ( 2005;). Characterization of slow-growing root nodule bacteria from Inga oerstediana in organic coffee agroecosystems in Chiapas, Mexico. . Appl Soil Ecol 29:, 236–251. [CrossRef]
    [Google Scholar]
  14. Howieson J. G., De Meyer S. E., Vivas-Marfisi A., Ratnayake S., Ardley J. K., Yates R. J.. ( 2013;). Novel Burkholderia bacteria isolated from Lebeckia ambigua – a perennial suffrutescent legume of the fynbos. . Soil Biol Biochem 60:, 55–64. [CrossRef]
    [Google Scholar]
  15. Islam M. S., Kawasaki H., Muramatsu Y., Nakagawa Y., Seki T.. ( 2008;). Bradyrhizobium iriomotense sp. nov., isolated from a tumor-like root of the legume Entada koshunensis from Iriomote Island in Japan. . Biosci Biotechnol Biochem 72:, 1416–1429. [CrossRef][PubMed]
    [Google Scholar]
  16. Kurppa M., Leblanc H., Nygren P.. ( 2010;). Detection of nitrogen transfer from N2-fixing shade trees to cacao saplings in 15N labelled soil: ecological and experimental considerations. . Agrofor Syst 80:, 223–239. [CrossRef]
    [Google Scholar]
  17. Laguerre G., Nour S. M., Macheret V., Sanjuan J., Drouin P., Amarger N.. ( 2001;). Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts. . Microbiology 147:, 981–993.[PubMed]
    [Google Scholar]
  18. Lindström, K. & Gyllenberg, H. ( 2007;). The species paradigm: proposal for a cross-disciplinary species concept. In Abstracts of the 11th International Congress on Culture Collections, Goslar, Germany. World Federation of Culture Collections.
  19. Martens M., Dawyndt P., Coopman R., Gillis M., De Vos P., Willems A.. ( 2008;). Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium). . Int J Syst Evol Microbiol 58:, 200–214. [CrossRef][PubMed]
    [Google Scholar]
  20. 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. [CrossRef][PubMed]
    [Google Scholar]
  21. 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. [CrossRef][PubMed]
    [Google Scholar]
  22. Mesbah M., Premachandran U., Whitman W. B.. ( 1989;). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. . Int J Syst Bacteriol 39:, 159–167. [CrossRef]
    [Google Scholar]
  23. Ormeño-Orrillo E., Rogel-Hernández M. A., Lloret L., López-López A., Martínez J., Barois I., Martínez-Romero E.. ( 2012;). Change in land use alters the diversity and composition of Bradyrhizobium communities and led to the introduction of Rhizobium etli into the tropical rain forest of Los Tuxtlas (Mexico). . Microb Ecol 63:, 822–834. [CrossRef][PubMed]
    [Google Scholar]
  24. Parker M. A.. ( 2003;). A widespread neotropical Bradyrhizobium lineage associated with Machaerium and Desmodium (Papilionoideae). . Plant Soil 254:, 263–268. [CrossRef]
    [Google Scholar]
  25. Pennington T. D.. ( 1997;). The Genus Inga: Botany. Kew, UK:: Royal Botanic Gardens;.
    [Google Scholar]
  26. Pitcher D. G., Saunders N. A., Owen R. J.. ( 1989;). Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. . Lett Appl Microbiol 8:, 151–156. [CrossRef]
    [Google Scholar]
  27. Possette R. F. S., Rodrigues W. A.. ( 2010;). O gênero Inga Mill. (Leguminosae - Mimosoideae) no estado do Paraná, Brasil. . Acta Bot Brasilica 24:, 354–368 (in Portuguese). [CrossRef]
    [Google Scholar]
  28. Radl V., Simões-Araújo J. L., Leite J., Passos S. R., Martins L. M. V., Xavier G. R., Rumjanek N. G., Baldani J. I., Zilli J. E.. ( 2014;). Microvirga vignae sp. nov., a root nodule symbiotic bacterium isolated from cowpea grown in semi-arid Brazil. . Int J Syst Evol Microbiol 64:, 725–730. [CrossRef][PubMed]
    [Google Scholar]
  29. Romero-Alvarado Y., Soto-Pinto L., García-Barrios L., Barrera-Gaytán J. F.. ( 2002;). Coffee yields and soil nutrients under the shades of Inga sp. vs. multiple species in Chiapas, Mexico. . Agrofor Syst 54:, 215–224. [CrossRef]
    [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. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S.. ( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28:, 2731–2739. [CrossRef][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][PubMed]
    [Google Scholar]
  33. Ueda T., Suga Y., Yahiro N., Matsuguchi T.. ( 1995;). Remarkable N2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. . J Bacteriol 177:, 1414–1417.[PubMed]
    [Google Scholar]
  34. Versalovic J., Schneider M., De Bruijn F., Lupski J. R.. ( 1994;). Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. . Methods Mol Cell Biol 5:, 25–40.
    [Google Scholar]
  35. Vinuesa P., Silva C., Werner D., Martínez-Romero E.. ( 2005;). Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation. . Mol Phylogenet Evol 34:, 29–54. [CrossRef][PubMed]
    [Google Scholar]
  36. Willems A., Coopman R., Gillis M.. ( 2001;). Phylogenetic and DNA–DNA hybridization analyses of Bradyrhizobium species. . Int J Syst Evol Microbiol 51:, 111–117.[PubMed]
    [Google Scholar]
  37. Zilli J. E., Valisheski R. R., Freire Filho F. R., Prata Neves M. C., Rumjanek N. G.. ( 2004;). Assessment of cowpea rhizobium diversity in cerrado areas of northeastern Brazil. . Braz J Microbiol 35:, 281–287. [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.063727-0
Loading
/content/journal/ijsem/10.1099/ijs.0.063727-0
Loading

Data & Media loading...

Supplements

Supplementary Data 

PDF

Most Cited This Month

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