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 N2-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 6399T 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 Bradyrhizobiumelkanii superclade, sharing 100 % nucleotide identity with Bradyrhizobiumembrapense, Bradyrhizobiumerythrophlei and Bradyrhizobiumviridifuturi. 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 6399T 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 6399T 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 6399T (=CNPSo 1165T=BR 6010T=U675T=LMG 30031T) was chosen as the type strain.