Bradyrhizobium dasycarpae sp. nov. a novel rhizobial species lacking canonical nod genes, isolated from the Moroccan endemic legume Retama dasycarpa.

A novel bacterial symbiont, strain Bradyrhizobium sp. RDT46T, was previously isolated from root nodules of Retama dasycarpa, a Moroccan endemic legume shrub. Phylogenetic analysis of the 16S rRNA gene placed the strain within the Bradyrhizobium japonicum supergroup, and Multi-Locus Sequence Analysis (MLSA) of four concatenated housekeeping genes (atpD, glnII, gyrB and recA) revealed that strain RDT46T is 93.91% closely related to B. frederickii CNPSo 3426T. Phylogenomic analysis of 81 single copy-core gene sequences further confirmed that the type strain B. frederickii is its closest relative. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were below the species delineation thresholds when compared to the closest type strain, with values of 93.8 and 52.2%, respectively. Genomic analysis revealed the absence of the canonical nod genes, the presence of nitrogen-fixation genes and few type III secretion system related genes. These findings combined with morphophysiological and fatty acid content analyses, as well as the ability of strain RDT46T to renodulate R. dasycarpa, support the designation of strain RDT46T as a novel species within the genus Bradyrhizobium, for which we propose the name Bradyrhizobium dasycarpae sp. nov. RDT46T (=CCMM B1347T=DSM 120572T) as type strain.