Bradyrhizobium zaerense sp. nov., an efficient symbiotic nitrogen-fixing bacterium isolated from Lupinus luteus and Retama dasycarpa root nodules.

Three strains, LLZ isolated from root nodules of Lupinus luteus in agricultural soils in the vicinity of Rabat, and seven strains RDM, isolated from nodules of Retama dasycarpa in Maamora forest soil, were assigned to a new lineage within the genus Bradyrhizobium. The present study provides a detailed taxonomic analysis of the representative strain LLZ17T. Genome analysis revealed average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values far below the threshold (88.4% and 34%, respectively) with the closest type strains B. hipponense, B. rifense, and B. cytisi. Phylogenetic analyses using 81 up-to-date bacteria core genes and whole genome sequences grouped LLZ17T and RDM4 in a highly supported lineage, distinct from described Bradyrhizobium species. The complete genome of LLZ17T consists of a single 7.8 Mbp chromosome with a GC content of 63.19% and contains nitrogen fixation and nodulation genes required when forming root symbiosis. Furthermore, strains LLZ13, LLZ15, RDM4, RDM7, RDM9, RDM14, RDM15, RDM18, RDM30 and LLZ17T were described phenotypically and compared with their closest Bradyrhizobium-type strains. Genomic and phenotypic characterization confirmed the ten strains are novel species. Strain LLZ17T was designated as the type strain of this new species, for which the name Bradyrhizobium zaerense sp. nov. is proposed.