Strains of Bradyrhizobium cosmicum sp. nov., isolated from contrasting habitats in Japan and Canada possess photosynthesis gene clusters with the hallmark of genomic islands

Abstract

The taxonomic status of two previously characterized Bradyrhizobium strains (58S1T and S23321) isolated from contrasting habitats in Canada and Japan was verified by genomic and phenotypic analyses. Phylogenetic analyses of five and 27 concatenated protein-encoding core gene sequences placed both strains in a highly supported lineage distinct from named species in the genus Bradyrhizobium with Bradyrhizobium betae as the closest relative. Average nucleotide identity values of genome sequences between the test and reference strains were between 84.5 and 94.2 %, which is below the threshold value for bacterial species circumscription. The complete genomes of strains 58S1T and S23321 consist of single chromosomes of 7.30 and 7.23 Mbp, respectively, and do not have symbiosis islands. The genomes of both strains have a G+C content of 64.3 mol%. Present in the genome of these strains is a photosynthesis gene cluster (PGC) containing key photosynthesis genes. A tRNA gene and its partial tandem duplication were found at the boundaries of the PGC region in both strains, which is likely the hallmark of genomic island insertion. Key nitrogen-fixation genes were detected in the genomes of both strains, but nodulation and type III secretion system genes were not found. Sequence analysis of the nitrogen fixation gene, nifH, placed 58S1T and S23321 in a novel lineage distinct from described Bradyrhizobium species. Data for phenotypic tests, including growth characteristics and carbon source utilization, supported the sequence-based analyses. Based on the data presented here, a novel species with the name Bradyrhizobium cosmicum sp. nov. is proposed with 58S1T (=LMG 31545T=HAMBI 3725T) as the type strain.

Strains of Bradyrhizobium barranii sp. nov. associated with legumes native to Canada are symbionts of soybeans and belong to different subspecies (subsp. barranii subsp. nov. and subsp. apii subsp. nov.) and symbiovars (sv. glycinearum and sv. septentrionale)

“…jicamae and B. elkanii ), a result that is in accord with the topology of robust gene trees generated from recent phylogenomic studies of the genus Bradyrhizobium [4, 7, 21]. The tree in further shows that novel strains 323S2 and 144S4 T (sv.…”

“…The genus Bradyrhizobium is a diverse group of species that includes economically important bacteria capable of forming nitrogenfixing symbioses with agricultural legumes such as soybeans [e.g., [2][3][4][5][6][7][8].…”

Bradyrhizobium septentrionale sp. nov. (sv. septentrionale) and Bradyrhizobium quebecense sp. nov. (sv. septentrionale) associated with legumes native to Canada possess rearranged symbiosis genes and numerous insertion sequences

“…The grouping of Bradyrhizobium reference strains into these four superclades is consistent with the results of other phylogenetic studies of the genus Bradyrhizobium [ e.g . 1, 17, 18]. further shows that the novel strains are placed in two highly supported lineages corresponding to the proposed species ( B. septentrionale sp.…”

“…amphicarpaeae 39S1MB T [27], and, B. cosmicum 58S1 T and S23321 [18] lacking both symbiosis islands and plasmids contained the fewest ISs (range 5–15) whereas between 41 and 134 ISs were detected in Bradyrhizobium sp. DOA9 [28], Bradyrhizobium sp.…”

Symbiosis Contribution of Non-nodulating <i>Bradyrhizobium cosmicum</i> S23321 after Transferal of the Symbiotic Plasmid pDOA9

“…The internal nodes of B. cosmicum S23321 and 58S1 were located on the same branch as B. lupini USDA-3051 and B. canariense SEMIA-928, which are symbionts of Lupinus agustifolius and Lupinus sp., and, thus, shared the most recent common ancestor. However, an assessment of branch lengths showed that the Lupinus symbiont was older than S23321 ( Wasai-Hara et al , 2020 ). The close phylogenetic background of the S23321 chromosome with other bradyrhizobia strains implies that this strain has the potential for mutualism after receiving the symbiosis toolkit from neighboring strains.…”