Bradyrhizobium agreste sp. nov., Bradyrhizobium glycinis sp. nov. and Bradyrhizobium diversitatis sp. nov., isolated from a biodiversity hotspot of the genus Glycine in Western Australia

Abstract

Strains of the genus Bradyrhizobium associated with agronomically important crops such as soybean (Glycine max) are increasingly studied; however, information about symbionts of wild Glycine species is scarce. Australia is a genetic centre of wild Glycine species and we performed a polyphasic analysis of three Bradyrhizobium strains—CNPSo 4010T, CNPSo 4016T, and CNPSo 4019T—trapped from Western Australian soils with Glycine clandestina, Glycine tabacina and Glycine max, respectively. The phylogenetic tree of the 16S rRNA gene clustered all strains into the Bradyrhizobium japonicum superclade; strains CNPSo 4010T and CNPSo 4016T had Bradyrhizobium yuanmingense CCBAU 10071T as the closest species, whereas strain CNPSo 4019T was closer to Bradyrhizobium liaoningense LMG 18230T. The multilocus sequence analysis (MLSA) with five housekeeping genes—dnaK, glnII, gyrB, recA and rpoB—confirmed the same clusters as the 16S rRNA phylogeny, but indicated low similarity to described species, with nucleotide identities ranging from 93.6 to 97.6% of similarity. Considering the genomes of the three strains, the average nucleotide identity and digital DNA–DNA hybridization values were lower than 94.97 and 59.80 %, respectively, with the closest species. In the nodC phylogeny, strains CNPSo 4010T and CNPSo 4019T grouped with Bradyrhizobium zhanjiangense and Bradyrhizobium ganzhouense , respectively, while strain CNPSo 4016T was positioned separately from the all symbiotic Bradyrhizobium species. Other genomic (BOX-PCR), phenotypic and symbiotic properties were evaluated and corroborated with the description of three new lineages of Bradyrhizobium . We propose the names of Bradyrhizobium agreste sp. nov. for CNPSo 4010T (=WSM 4802T=LMG 31645T) isolated from Glycine clandestina, Bradyrhizobium glycinis sp. nov. for CNPSo 4016T (=WSM 4801T=LMG 31649T) isolated from Glycine tabacina and Bradyrhizobium diversitatis sp. nov. for CNPSo 4019T (=WSM 4799T=LMG 31650T) isolated from G. max.

Bradyrhizobium cenepequi sp. nov., Bradyrhizobium semiaridum sp. nov., Bradyrhizobium hereditatis sp. nov. and Bradyrhizobium australafricanum sp. nov., symbionts of different leguminous plants of Western Australia and South Africa and definition of three novel symbiovars

“…The evolutionary pattern was maintained for the strains of this study; however, strains WSM 1738 T and CNPSo 4026 T , presented a basal position with high [23]. Since the MLSA using the complete sequences is a larger dataset, the NI values and bootstrap support were slightly higher for the analyses on this dataset versus those based on the alignment with the partial sequences (Table 2), as also observed in other studies [38,39].…”

“…Strains CNPSo 4026 T described in this study and B. glycinis CNPSo 4016 T recently described as a novel species by our research group [39] did not cluster with any Bradyrhizobium strain in the nodC phylogeny and presented NI values equal or lower than 91.6 and 92.5 %, respectively; therefore, we propose two novel symbiovars named cenepequi and glycinis, respectively, named as the first and only species described so far in these symbiovars. The evolutionary history, as well as the host range of these symbiovars should be further investigated as more isolates belonging to these symbiovars become available.…”

“…Interestingly, all strains from sv. cajani tested for nodulation ability with soybean were unable to nodulate this legume [39,50,[54][55][56][57][58].…”

New Insights into the Taxonomy of Bacteria in the Genomic Era and a Case Study with Rhizobia

“…Therefore, the methodology aggregates sufficient phylogenetic signals, offering a buffer effect to the noncongruent signals that influence smaller datasets, being more reliable [ 77 , 94 , 96 ]. However, it is worth mentioning that the single housekeeping genes analysis does not reflect the entire evolutionary pattern of the strain; it is recommended to proceed to the comparison between the 16S rRNA and each housekeeping gene phylogeny to detect and avoid potential HGT and recombination events, since each housekeeping gene may have a different history of evolution [ 75 , 92 ].…”

Genomic Diversity of Bradyrhizobium from the Tree Legumes Inga and Lysiloma (Caesalpinioideae-Mimosoid Clade)

“…A novel metric to define species arose with genomics, i.e., ANI with a limit of 95/96% between species. Here we discovered upon inspection of ANI results that Bradyrhizobium liaoningense [115] and Bradyrhizobium diversitatis [116] share a large ANI (98.65%), suggesting that they are synonymous species. The ANI of B51278 was 97% in comparison to Bradyrhizobium brasilense, and that of B51279 was 99.99% compared to B. cajani; thus, they were assigned to their corresponding species.…”