Revision of the taxonomic status of the species Rhizobium lupini and reclassification as Bradyrhizobium lupini comb. nov.

Abstract

The species Rhizobium lupini was isolated from Lupinus nodules and included in the Approved Lists of Bacterial Names in 1980. Nevertheless, on the basis of the analysis of the type strain of this species available in DSMZ, DSM 30140 T , whose 16S rRNA gene was identical to that of the type strain of Bradyrhizobium japonicum, R. lupini was considered a later synonym of this species. In this study we confirmed that the strain DSM 30140 T belongs to the species B. japonicum, but also that it cannot be the original strain of R. lupini because this species effectively nodulated Lupinus whereas strain DSM 30140 T was able to nodulate soybean but not Lupinus. Since the original type strain of R. lupini was deposited into the USDA collection by L. W. Erdman under the accession number USDA 3051 T we analysed the taxonomic status of this strain showing that although it belongs to the genus Bradyrhizobium instead of genus Rhizobium, it is phylogenetically distant from B. japonicum and closely related to Bradyrhizobium canariense. The type strains R. lupini USDA 3051 T and B. canariense BTA-1 T share 16S rRNA, recA and glnII gene sequences with similarities of 99.8 %, 96.5 % and 97.1 %, respectively. They presented a DNA-DNA hybridization value of 36 % and also differed in phenotypic characteristics and slightly in the proportions of some fatty acids. Therefore we propose the reclassification of the species Rhizobium lupini as Bradyrhizobium lupini comb. nov. The type strain is USDA 3051 T (5CECT 8630 T 5LMG 28514 T ).

Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes – a genome comparison

“…Similarly, BF49 clusters with the top hits from the NCBI and RDP databases (SEMIA928 and LG-6) in addition to B. lupini USDA 3051 which was the second hit from the NCBI database [Accession number: NR_134836]. This strain was originally isolated from Lupinus and was reclassified from Rhizobium lupini to B. lupini in 2015 17 . Both G22 and BF49 are in the same clade as the free-living strain, S23321, and the soybean-nodulating strains, E109, USDA 6 and USDA 110.…”

Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov., isolated from effective nodules of peanut

“…Although our results suggest that the 16S rRNA gene phylogeny is not consistent with that of the combined housekeeping genes (Zilli et al , 2014), neither phylogeny is well resolved in this subclade of Bradyrhizobium , and none of the discrepancies is supported by significant bootstrap values (>70 %). The recently described species Bradyrhizobium lupini (Peix et al , 2015) was not closely related to the two groups based on analysis of the combined glnII and recA gene sequences (Figs S3 and S4). All these results, and especially the clearly distinct multilocus sequences (), support the proposal that Groups A and B represent two novel species in the genus Bradyrhizobium.…”

Bradyrhizobium centrosemae (symbiovar centrosemae) sp. nov., Bradyrhizobium americanum (symbiovar phaseolarum) sp. nov. and a new symbiovar (tropici) of Bradyrhizobium viridifuturi establish symbiosis with Centrosema species native to America

“…The phenotypic characterization was performed as was previously described for Bradyrhizobium [14]. API 20NE galleries and Biolog GN2 MicroPlates were inoculated according to the manufacturer's instructions.…”