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Archives of Microbiology

, Volume 199, Issue 8, pp 1211–1221 | Cite as

Bradyrhizobium brasilense sp. nov., a symbiotic nitrogen-fixing bacterium isolated from Brazilian tropical soils

  • Elaine Martins da Costa
  • Amanda Azarias Guimarães
  • Rayssa Pereira Vicentin
  • Paula Rose de Almeida Ribeiro
  • Aniele Carolina Ribas Leão
  • Eduardo Balsanelli
  • Liesbeth Lebbe
  • Maarten Aerts
  • Anne Willems
  • Fatima Maria de Souza MoreiraEmail author
Original Paper

Abstract

Four strains of rhizobia isolated from nodules of Vigna unguiculata (UFLA03-321T, UFLA03-320 and UFLA03-290) and Macroptilium atropurpureum (UFLA04-0212) in Brazilian soils were previously reported as a new group within the genus Bradyrhizobium. To determine their taxonomic position, these strains were characterized in this study using a polyphasic approach. The analysis of the 16S rRNA gene grouped the four strains with Bradyrhizobium pachyrhizi PAC48T. However, the concatenated sequence analysis of the two (recA and glnII) or three (atpD, gyrB and recA) housekeeping genes indicated that these strains represent a novel species of Bradyrhizobium, which is very closely related to B. pachyrhizi PAC48T and B. elkanii USDA 76T. Genomic relatedness analyses between the UFLA03-321T strain and B. elkanii USDA 76T and B. pachyrhizi PAC48T revealed an average nucleotide identity below 96% and values of estimated DNA–DNA hybridization below 70%, confirming that they represent genomically distinct species. Analysis of MALDI-TOF MS (Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry) profiles and phenotypic characteristics also allowed differentiation of the novel species from its two neighboring species. In phylogenetic analysis of nodC and nifH genes, UFLA03-321T exhibited maximum similarity with B. tropiciagri CNPSo 1112T. The data suggest that these four UFLA strains represent a novel species, for which the name Bradyrhizobium brasilense sp. nov. is proposed, with UFLA03-321T (=LMG 29353 =CBAS645) as type strain. G + C content in the DNA of UFLA03-321T is 63.9 mol %.

Keywords

Bradyrhizobium Vigna unguiculata L. Polyphasic taxonomy Genomics MALDI-TOF MS 

Notes

Acknowledgements

We thank the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) (Process: 99999.002753/2015-04), the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (Process: 304574/2010-4), and the Fundação de Amparo e Pesquisa de Minas Gerais (Fapemig) (PACCSS/PPGCS-2009–2012) for financial support and for granting scholarships.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Human and animal rights

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

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Supplementary material 1 (TIFF 1402 kb)
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Supplementary material 2 (TIFF 317 kb)
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Supplementary material 3 (TIFF 1633 kb)

References

  1. Auch AF, Von Jan M, Klenk HP, Göker M (2010) Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134CrossRefPubMedPubMedCentralGoogle Scholar
  2. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477CrossRefPubMedPubMedCentralGoogle Scholar
  3. Chahboune R, Carro L, Peix A, Barrijal S, Velázquez E, Bedmar EJ (2011) Bradyrhizobium cytisi sp. nov., isolated from effective nodules of Cytisus villosus. Int Int J Syst Evol Microbiol 61:2922–2927CrossRefPubMedGoogle Scholar
  4. Costa EM, Nóbrega RSA, Carvalho F, Trochmann A, Ferreira LVM, Moreira FMS (2013) Plant growth promotion and genetic diversity of bacteria isolated from cowpea nodules. Pesq Agropec Bras 48:1275–1284CrossRefGoogle Scholar
  5. Costa EM, Nóbrega RSA, Ferreira LVM, Amaral FHC, Nóbrega JCA, Silva AFT, Moreira FMS (2014) Growth and yield of the cowpea cultivar BRS Guariba inoculated with rhizobia strains in Southwest Piauí. Semin Cienc Agrar 35:3073–3084CrossRefGoogle Scholar
  6. Costa EM, Ribeiro PRA, Lima W, Farias TP, Moreira FMS (2017) Lima bean nodulates efficiently with Bradyrhizobium strains isolated from diverse legume species. Symbiosis 71:1–9CrossRefGoogle Scholar
  7. De Meyer SE, Van Hoorde K, Vekeman B, Braeckman T, Willems A (2011) Genetic diversity of rhizobia associated with indigenous legumes in different regions of Flanders (Belgium). Soil Biol Biochem 43:2384–2396CrossRefGoogle Scholar
  8. Durán D, Rey L, Navarro A, Busquets A, Imperial J, Ruiz-Argüeso T (2014) 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 37:336–341CrossRefPubMedGoogle Scholar
  9. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefPubMedGoogle Scholar
  10. Florentino LA, Guimarães AP, Rufini M, Silva K, Moreira FMS (2009) Sesbania virgata stimulates the occurrence of its microsymbiont in soils but does not inhibit microsymbionts of other species. Sci Agric 66:667–676CrossRefGoogle Scholar
  11. Florentino LA, Sousa PM, Silva JS, Silva KB, Moreira FMS (2010) Diversity and efficiency of Bradyrhizobium strains isolated from soil samples collected from around Sesbania virgata roots using cowpea as trap species. Rev Bras Cienc Solo 34:1113–1123CrossRefGoogle Scholar
  12. Fred EB, Waksman SA (1928) Laboratory manual of general microbiology with special reference to the microorganisms of the soil. McGraw-Hill Book, New YorkGoogle Scholar
  13. Gaby JC, Buckley DH (2012) A Comprehensive evaluation of PCR primers to amplify the nifH gene of nitrogenase. PLoS One 7:e42149CrossRefPubMedPubMedCentralGoogle Scholar
  14. González-Castillo A, Enciso-Ibarrra J, Bolán-Mejia MC, Balboa S, Lasa A, Romalde JL, Cabanillas-Beltrán H, Gomez-Gil B (2015) Vibrio mexicanus sp. nov., isolated from a cultured oyster Crassostrea corteziensis. Antonie Van Leeuwenhoek 108:355–364CrossRefPubMedGoogle Scholar
  15. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91CrossRefPubMedGoogle Scholar
  16. Grönemeyer JL, Chimwamurombe P, Reinhold-Hurek B (2015a) Bradyrhizobium subterraneum sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of groundnuts. Int J Syst Evol Microbiol 65:3241–3247CrossRefPubMedGoogle Scholar
  17. Grönemeyer JL, Hurek T, Reinhold-Hurek B (2015b) Bradyrhizobium kavangense sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of traditional Namibian pulses. Int Int J Syst Evol Microbiol 65:4886–4894CrossRefGoogle Scholar
  18. Grönemeyer JL, Hurek T, Bünger W, Reinhold-Hurek B (2016) Bradyrhizobium vignae sp. nov., a nitrogen-fixing symbiont isolated from effective nodules of Vigna and Arachis. Int Int J Syst Evol Microbiol 66:62–69CrossRefPubMedGoogle Scholar
  19. Guimarães AA, Jaramillo PMD, Nóbrega RSA, Florentino LA, Silva KB, Moreira FMS (2012) Genetic and symbiotic diversity of nitrogen-fixing bacteria isolated from agricultural soils in the western Amazon by using cowpea as the trap plant. Appl Environ Microb 78:6726–6733CrossRefGoogle Scholar
  20. Guimarães AA, Florentino LA, Almeida KA, Lebbe L, Silva KB, Willems A, Moreira FMS (2015) High diversity of Bradyrhizobium strains isolated from several legume species and land uses in Brazilian tropical ecosystems. Syst Appl Microbiol 38:433–441CrossRefGoogle Scholar
  21. Guizelini D, Raittz RT, Cruz LM, Souza EM, Steffens MBR, Pedrosa FO (2016) GFinisher: a new strategy to refine and finish bacterial genome assemblies. Sci Rep 6:1–8CrossRefGoogle Scholar
  22. Jaramillo PMD, Guimarães AA, Florentino LA, Silva KB, Nóbrega RSA, Moreira FMS (2013) Symbiotic nitrogen-fixing bacterial populations trapped from soils under agroforestry systems. Sci Agric 70:397–404CrossRefGoogle Scholar
  23. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefPubMedGoogle Scholar
  24. Lima AS, Nòbrega RSA, Barberi A, Silva K, Ferreira DF, Moreira FMS (2009) Nitrogen-fixing bacteria communities occurring in soils under different uses in the Western Amazon region as indicated by nodulation of siratro (Macroptilium atropurpureum). Plant Soil 320:1–19CrossRefGoogle Scholar
  25. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60CrossRefGoogle Scholar
  26. Niemann S, Puehler A, Tichy HV, Simon R, Selbitshka W (1997) Evaluation of the resolving power of three different DNA fingerprinting methods to discriminate among isolates of a natural Rhizobium meliloti population. J Appl Microbiol 82:477–484CrossRefPubMedGoogle Scholar
  27. Orata FD, Xu Y, Gladney LM, Rishishwar L, Case RJ, Boucher Y, Jordan IK, Tarr CL (2016) Characterization of clinical and environmental isolates of Vibrio cidicii sp. nov., a close relative of Vibrio navarrensis. Int J Syst Evol Microbiol 66:4148–4415CrossRefPubMedGoogle Scholar
  28. Ramírez-Bahena MH, Peix A, Rivas R, Camacho M, Rodríguez-Navarro DN, Mateos PF, Martínez-Molina E, Willems A, Velázquez E (2009) Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus. Int J Syst Evol Microbiol 59:1929–1934CrossRefPubMedGoogle Scholar
  29. Ramírez-Bahena MH, Chahboune R, Peix A, Velázquez E (2012) Reclassification of Agromonas oligotrophica into genus Bradyrhizobium as Bradyrhizobium oligotrophicum comb. nov. Int J Syst Evol Microbiol 63:1013–1016CrossRefPubMedGoogle Scholar
  30. Ribeiro PRA, Santos JV, Costa EM, Lebbe L, Louzada MO, Guimarães AA, Assis ES, Willems A, Moreira FMS (2015) Symbiotic efficiency and genetic diversity of soybean bradyrhizobia in Brazilian soils. Agr Ecosyst Environ 212:85–93CrossRefGoogle Scholar
  31. Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131CrossRefPubMedPubMedCentralGoogle Scholar
  32. Rufini M, Silva MAP, Ferreira PAA, Cassetari AS, Soares BL, Andrade MJB, Moreira FMS (2014) Symbiotic efficiency and identification of rhizobia that nodulate cowpea in a Rhodic Eutrudox. Biol Fert Soils 50:115–122CrossRefGoogle Scholar
  33. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  34. Sánchez-Juanes F, Ferreira L, La Veja PA, Valverde A, Barrios ML, Rivas R, Mateos PF, Martínez-Molina E, González-Buitrago JM, Trujillo ME, Velázquez E (2013) MALDI-TOF mass spectrometry as a tool for differentiation of Bradyrhizobium species: application to the identification of Lupinus nodulating strains. Syst Appl Microbiol 36:565–571CrossRefPubMedGoogle Scholar
  35. Santana-Filho AP, Noleto GR, Gorin PAJ, De Souza LM, Iacomini M, Sassak GL (2012) GC–MS detection and quantification of lipopolysaccharides in polysaccharides through 3-O-acetyl fatty acid methyl esters. Carbohydr Polym 87:2730–2734CrossRefGoogle Scholar
  36. Sarita S, Sharma PK, Priefer UB, Prell J (2005) Direct amplification of rhizobial nodC sequences from soil total DNA and comparison to nodC diversity of root nodule isolates. FEMS Microbiol Ecol 54:1–11CrossRefPubMedGoogle Scholar
  37. Sassaki GL, Souza LM, Serrato RV, Cipriani TR, Gorin PA, Iacomini M (2008) Application of acetate derivatives for gas chromatography-mass spectrometry: novel approaches on carbohydrates, lipids and amino acids analysis. J Chromatogr A 1208:215–222CrossRefPubMedGoogle Scholar
  38. Silva FV, Simões-Araújo JL, Silva Júnior JP, Xavier GR, Rumjanek NG (2012) Genetic diversity of rhizobia isolates from Amazon soils using cowpea (Vigna unguiculata) as trap plant. Braz J Microbiol 43:682–691CrossRefPubMedPubMedCentralGoogle Scholar
  39. Silva FV, De Meyer SE, Simões-Araújo JL, Barbé TC, Xavier GR, O’Hara G, Ardley JK, Rumjanek NG, Willems A, Zilli JE (2014) Bradyrhizobium manausense sp. nov., isolated from effective nodules of Vigna unguiculata grown in Brazilian Amazon rainforest soils. Int J Syst Evol Microbiol 64:2358–2363CrossRefPubMedGoogle Scholar
  40. Soares ALL, Pereira JPAR, Ferreira PAA, Vale HMM, Lima AS, Andrade MJB, Moreira FMS (2006) Agronomic efficiency of selected rhizobia strains and diversity of native nodulating populations in Perdões (MG—Brazil). II—beans. Rev Bras Cienc Solo 30:795–802CrossRefGoogle Scholar
  41. Soares BL, Ferreira PAA, Oliveira-Longatti SM, Marra LM, Rufini M, Andrade MJB, Moreira FMS (2014) Cowpea symbiotic efficiency, pH and aluminum tolerance in nitrogen-fixing bacteria. Sci Agric 71:171–180CrossRefGoogle Scholar
  42. 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 28:2731–2739CrossRefPubMedPubMedCentralGoogle Scholar
  43. Tighe SW, De Lajudie P, Dipietro K, Lindstrom K, Nick G, Jarvis BDW (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 50:787–801CrossRefPubMedGoogle Scholar
  44. Vincent JM (1970) A manual for the practical study of root nodule bacteria. Blackwell Scientific, Oxford, p 164pGoogle Scholar
  45. Vinuesa P, León-Barrios M, Silva C, Willems A, Jarabo-Lorenzo A, Pérez-Galdona R, Werner D, Martínez-Romero E (2005) Bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (Papilionoideae: Genisteae) from the Canary Islands, along with Bradyrhizobium japonicum bv. genistearum, Bradyrhizobium genospecies alpha and Bradyrhizobium genospecies beta. Int J Syst Evol Microbiol 55:569–575CrossRefPubMedGoogle Scholar
  46. Wang JY, Wang R, Zhang YM, Liu HC, Chen WF, Wang ET, Sui XH, Chen WX (2012) Bradyrhizobium daqingense sp. nov., isolated from soybean nodules. Int J Syst Evol Microbiol 63:616–624CrossRefPubMedGoogle Scholar
  47. Wang R, Chang YL, Zheng WT, Zhang D, Zhang XX, Sui XH, Wang ET, Hu JQ, Zhang LY, Chen WX (2013) Bradyrhizobium arachidis sp. nov., isolated from effective nodules of Arachis hypogaea grown in China. Syst Appl Microbiol 36:101–105CrossRefPubMedGoogle Scholar
  48. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematic. Int J Syst Bacteriol 37:463–464CrossRefGoogle Scholar
  49. Wieme AD, Spitaels F, Aerts M, Bruyne K, Landschoot AV, Vandamme P (2014) Identification of beer-spoilage bacteria using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Int J Food Microbiol 185:41–50CrossRefPubMedGoogle Scholar
  50. Willems A, Coopman R, Gillis M (2001) Phylogenetic and DNA-DNA hybridization analyses of Bradyrhizobium species. Int J Syst Evol Microbiol 51:111–117CrossRefPubMedGoogle Scholar
  51. Yao Y, Sui XH, Zhang XX, Wang ET, Chen WX (2015) Bradyrhizobium erythrophlei sp. nov. and Bradyrhizobium ferriligni sp. nov., isolated from effective nodules of Erythrophleum fordii. Int J Syst Evol Microbiol 65:1831–1837CrossRefPubMedGoogle Scholar
  52. Zilli JE, Baraúna AC, Silva K, Meyer SE, Farias ENC, Kaminski PE, Costa IB, Ardley JK, Willems A, Camacho NN, Dourado FS, O’Hara G (2014) Bradyrhizobium neotropicale sp. nov., isolated from effective nodules of Centrolobium paraense. Int J Syst Evol Microbiol 64:3950–3957CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Elaine Martins da Costa
    • 1
    • 2
  • Amanda Azarias Guimarães
    • 1
  • Rayssa Pereira Vicentin
    • 1
  • Paula Rose de Almeida Ribeiro
    • 1
  • Aniele Carolina Ribas Leão
    • 3
  • Eduardo Balsanelli
    • 3
  • Liesbeth Lebbe
    • 4
  • Maarten Aerts
    • 4
  • Anne Willems
    • 4
  • Fatima Maria de Souza Moreira
    • 1
    Email author
  1. 1.Setor de Biologia, Microbiologia e Processos Biológicos do Solo, Departamento de Ciência do SoloUniversidade Federal de LavrasLavrasBrazil
  2. 2.Universidade Federal de Mato Grosso Do Sul-Campus de Chapadão do SulChapadão do SulBrazil
  3. 3.Departamento de Bioquímica e Biologia MolecularUniversidade Federal do ParanáCuritibaBrazil
  4. 4.Department of Biochemistry and MicrobiologyGhent UniversityGhentBelgium

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