Characterization of Bradyrhizobium strains indigenous to Western Australia and South Africa indicates remarkable genetic diversity and reveals putative new species

Helene, Luisa Caroline Ferraz; O’Hara, G.W.; Hungría, Mariangela

doi:10.1016/j.syapm.2020.126053

Cited by 16 publications

(16 citation statements)

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“…The NI values among the strains from our study and related type strains ranged from 99.4 to 99.9 % (). The results agree with several reports that the 16S rRNA sequences are highly conserved in the genus Bradyrhizobium , with many species sharing more than 99 % NI, not allowing proper evolutionary information [7, 12, 13, 34].…”

Section: Phylogenysupporting

confidence: 90%

“…Nowadays, the suggested threshold for species delineation for the genus Bradyrhizobium using five concatenated genes is 97 % NI [22]. Several phylogenetic studies have suggested a minimum of four [6, 12], or even three [8] concatenated housekeeping genes in the MLSA, and a considerable number of Bradyrhizobium species have been described using four genes and an NI value of 97 % as the threshold for species delineation [2, 13, 33, 35, 36]. In our study, both sets of genes on the MLSA presented NI for the new groups compared with the most related species far below 97 %; the only exception was of group GII.III, which shared from 97 to 97.3 % NI with B.…”

Section: Phylogenymentioning

confidence: 60%

“… Bradyrhizobium is considered as the probable ancestor lineage of all rhizobia and, in the last decade, several studies reported remarkable genetic diversity within the genus, as well as symbiotic associations with an increasing number of legumes [e.g. [1, 2, 6–13]. The environmental and economic applications of Bradyrhizobium and its high diversity reassure the importance of characterization and seeking for strains with biotechnological potential.…”

Section: Full-textmentioning

confidence: 99%

“…The eight Bradyrhizobium strains used in this study are listed in . All strains were isolated in the north-west of WA from root nodules of indigenous legumes collected and isolated in a previous study [24] and preliminary characterized [12].…”

Section: Isolation and Ecologymentioning

confidence: 99%

“…[26]. The other gene sequences (housekeeping and symbiotic genes) were obtained from our previous study [12]. The PCR products were purified using PureLinkTMQuick PCR Purification Kit (Invitrogen), according to the manufacturer’s procedure.…”

Section: Phylogenymentioning

confidence: 99%

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Bradyrhizobium archetypum sp. nov., Bradyrhizobium australiense sp. nov. and Bradyrhizobium murdochi sp. nov., isolated from nodules of legumes indigenous to Western Australia

Helene

Klepa

O’Hara

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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The genus Bradyrhizobium is considered as the probable ancestor lineage of all rhizobia, broadly spread in a variety of ecosystems and with remarkable diversity. A polyphasic study was performed to characterize and clarify the taxonomic position of eight bradyrhizobial strains isolated from indigenous legumes to Western Australia. As expected for the genus, the 16S rRNA gene sequences were highly conserved, but the results of multilocus sequence analysis with four housekeeping genes (dnaK, glnII, gyrB and recA) confirmed three new distinct clades including the following strains: (1) WSM 1744T, WSM 1736 and WSM 1737; (2) WSM 1791T and WSM 1742; and (3) WSM 1741T, WSM 1735 and WSM 1790. The highest ANI values of the three groups in relation to the closest type strains were 92.4, 92.3 and 93.3 %, respectively, below the threshold of species circumscription. The digital DNA–DNA hybridization analysis also confirmed new species descriptions, with less than 52 % relatedness with the closest type strains. The phylogeny of the symbiotic gene nodC clustered the eight strains into the symbiovar retamae, together with seven Bradyrhizobium type strains, sharing from 94.2–98.1 % nucleotide identity (NI), and less than 88.7 % NI with other related strains and symbiovars. Morpho-physiological, phylogenetics, genomic and symbiotic traits were determined for the new groups and our data support the description of three new species, Bradyrhizobium archetypum sp. nov., Bradyrhizobium australiense sp. nov. and Bradyrhizobium murdochi sp. nov., with WSM 1744T (=CNPSo 4013T=LMG 31646T), WSM 1791T (=CNPSo 4014T=LMG 31647T) and WSM 1741T (=CNPSo 4020T=LMG 31651T) designated as type strains, respectively.

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Section: Phylogenysupporting

confidence: 90%