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

Abstract

Four strains of rhizobia isolated from nodules of Vigna unguiculata (UFLA03-321, 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 PAC48. 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 PAC48 and B. elkanii USDA 76. Genomic relatedness analyses between the UFLA03-321 strain and B. elkanii USDA 76 and B. pachyrhizi PAC48 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, UFLA03-321 exhibited maximum similarity with B. tropiciagri CNPSo 1112. The data suggest that these four UFLA strains represent a novel species, for which the name Bradyrhizobium brasilense sp. nov. is proposed, with UFLA03-321 (=LMG 29353 =CBAS645) as type strain. G + C content in the DNA of UFLA03-321 is 63.9 mol %.

Phylogenomic Analysis of the Gammaproteobacterial Methanotrophs (Order Methylococcales) Calls for the Reclassification of Members at the Genus and Species Levels

“…Several comparisons within this group, however, showed 95–96% ANI. In cases where ANI is near the threshold for species delineation (i.e., 94–96%), dDDH is proven to be more discriminatory, as demonstrated with Vibrio cidicii (Orata et al, 2016) and “ Bradyrhizobium brasilense ” (Martins da Costa et al, 2017), where dDDH values were below the threshold when the species were compared against their closest relatives and ANI was inconclusive. Therefore, the Methylobacter genomes were reclassified into several unidentified species (clusters 1–4 and 6) within a known genus (i.e., Methylobacter ) (Figure 2).…”

Widespread Distribution of Highly Adapted Bradyrhizobium Species Nodulating Diverse Legumes in Africa

“…Later, two Bradyrhizobium species [i.e., Bradyrhizobium kavangense (Grönemeyer et al, 2015b) and B. vignae (Grönemeyer et al, 2016)] were isolated from cowpea root nodules in Southern Africa (Namibia and Angola, respectively). More recently, B. brasilense (da Costa et al, 2017) was also identified in Brazilian soils (Table 1).…”

Plant growth‐promoting rhizobacterial communities from an area under the influence of iron mining and from the adjacent phytophysiognomies which have high genetic diversity

“…The experimental design used was completely randomized, with seven treatments and three replications: inoculations with the soil suspensions from each of the four phytophysiognomies; a positive control inoculated with a strain effective in siratro, called UFLA 04-212 (Bradyrhizobium brasilense) (Costa et al, 2018); and two non-inoculated negative controls, one with high N concentration (52.5 mg/L) and another with low N concentration (5.25 mg/L), to check for possible contaminations of the experiment and to compare with the plants inoculated with the soil solutions. The treatments inoculated with the soil suspensions and with the UFLA 04-212 strain were grown in a solution with low concentration of N (5.25 mg/L of N).…”