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. 2019 Jun;71(3):004742.
doi: 10.1099/ijsem.0.004742. Epub 2021 Mar 12.

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

Milena Serenato Klepa  1   2   3 , Luisa Caroline Ferraz Helene  1   2 , Graham O'Hara  4 , Mariangela Hungria  1   2   3
Affiliations

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

Milena Serenato Klepa et al. Int J Syst Evol Microbiol. 2019 Jun.

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.

Keywords: ANI; Bradyrhizobium; Glycine; MLSA; dDDH; nodulation; wild soybean.

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Conflict of interest statement

The authors declare that there are no conflicts of interest.

Figures

Fig. 1.
Fig. 1.
Maximum-likelihood phylogeny based on 16S rRNA alignment (1312 bp), using the T92 (Tamura three-parameter+G+I) model by mega version 7. Accession numbers are indicated in parentheses and in Table S1. The novel species are shown in bold. Bootstrap values >70 % are indicated at the nodes. Xanthobacter autotrophicus Py2 was used as an outgroup. Bar indicates two substitutions per 100 nucleotide positions.
Fig. 2.
Fig. 2.
Maximum-likelihood phylogeny based on alignment of dnaK+glnII+gyrB+recA+rpoB concatenated genes (2009 bp), using the GTR (general time reversible)+G+I model by mega version 7. Accession numbers are indicated in Table S1. The novel species are shown in bold. Bootstrap values >70 % are indicated at the nodes. Xanthobacter autotrophicus Py2 was used as an outgroup. Bar indicates five substitution per 100 nucleotide positions.
Fig. 3.
Fig. 3.
Maximum-likelihood phylogeny based on nodC alignment (426 bp), using the T92 (Tamura three-parameter+G+I) model by mega version 7. Accession numbers are indicated in parentheses. The novel species are shown in bold. Bootstrap values >70 % are indicated at the nodes. Bar indicates five substitutions per 100 nucleotide positions.
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