Bradyrhizobium mercantei sp nov., a nitrogen-fixing symbiont isolated from nodules of Deguelia costata (syn. Lonchocarpus costatus)

Some bacteria collectively known as rhizobia can establish symbiotic relationships and the N-2-fixation process with several legumes used as green manure, in pastures and for wood production. Symbionts belonging to the genus Bradyrhizobium are predominant in the tropics, and an increasing number of studies report high genetic diversity within the genus. We performed a polyphasic study with two strains belonging to the genus Bradyrhizobium-SEMIA 6399(T) and SEMIA 6404-isolated from root nodules of Deguelia costata (syn. Lonchocarpus costatus), an important legume native to eastern Brazil. In general, sequences of the 16S rRNA gene were highly conserved in members of the genus Bradyrhizobium, and the two strains were positioned in the Bradyrhizobium elkanii superclade, sharing 100% nucleotide identity with Bradyrhizobium embrapense, Bradyrhizobium erythrophlei and Bradyrhizobium viridifuturi. However, multilocus sequence analysis with four housekeeping genes (dnaK, glnII, gyrB and recA) confirmed that the two strains belong to a distinct clade, sharing from 87.7 to 96.1% nucleotide identity with related species of the genus Bradyrhizobium, being most closely related to B. viridifuturi. Average nucleotide identity of genome sequences between SEMIA 6399(T) and related species was lower than 92 %, below the threshold of species circumscription. nifH phylogeny clustered the SEMIA strains in a clade separated from other species of the genus Bradyrhizobium, and the nodD phylogeny revealed that SEMIA 6399 T presents a more divergent sequence. Other phenotypic and genotypic traits were determined for the new group, and our data support the description of the SEMIA strains as representatives of Bradyrhizobium mercantei sp. nov.; SEMIA 6399(T) (= CNPSo 1165(T) = BR 6010(T) = U675(T) = LMG 30031(T)) was chosen as the type strain.