ABSTRACT
Three strains of nitrogen-fixing bacteria isolated from nodules of Inga sp. (INPA54BT) and Swartzia sp. (INPA86A and INPA01-91A) in soils under native forest in the Brazilian Amazon were previously identified as belonging to the Bradyrhizobium genus. In this study, these strains were characterized using a polyphasic approach to establish their taxonomic position. The three strains shared more than 99.5% sequence similarity of the 16S rRNA gene with the type strains of five Bradyrhizobium species (B. japonicum USDA 6T, B. liaoningense LMG 18230T, B. ottawaense OO99T, B. subterraneum 58 2-1T and B. yuanmingense LMG 21827T). However, multilocus sequence analysis of two (recA and glnII) or three (atpD, gyrB, and recA) housekeeping genes indicated that these three strains represent a new Bradyrhizobium species, which is closely related to B. subterraneum 58 2-1T and B. yuanmingense LMG 21827T. DNA-DNA hybridization values between INPA54BT and B. subterraneum 58 2-1T and B. yuanmingense LMG 21827T were only 41.5 and 30.9%, respectively. Phenotypic characterization also allowed the differentiation of the novel species from B. subterraneum 58 2-1T and B. yuanmingense LMG 21827T. In the phylogenetic analysis of the nodC and nifH genes, the three strains showed similar sequences that were divergent from those of type strains of all Bradyrhizobium species. We concluded that these strains represent a novel species, for which the name Bradyrhizobium forestalis is proposed, with INPA54BT (= LMG 10044T) as type strain. The G+C content in the DNA of INPA54BT is 63.7 mol%.
Subject(s)
Bradyrhizobium/genetics , Fabaceae/microbiology , Root Nodules, Plant/microbiology , Base Composition , Bradyrhizobium/classification , Bradyrhizobium/isolation & purification , Brazil , DNA, Bacterial/genetics , Forests , Genes, Bacterial , Genes, Essential , Multilocus Sequence Typing , Nitrogen Fixation , Nucleic Acid Hybridization , Phylogeny , RNA, Ribosomal, 16S/geneticsABSTRACT
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 %.
