Multilocus sequence analysis of the Rhizobia from five woody legumes in southern China

A total of 11 rhizobial strains from five woody legumes (Acacia confusa, Dalbergia odorifera, Dalbergia fusca, Erythrophleum fordii and Pterocarpus macarocarpus) in Southern China were identified, using 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA) of three housekeeping genes (recA, glnII and dnaK). Among the 11 isolated rhizobia, seven were classified as Agrobacterium tumefaciens, Bradyrhizobium elkanii, Ensifer adhaerens and Rhizobium multihospitium and four were within the genus Rhizobium that might be novel species when considering their clustering independently in topology tree and relatively low recA gene sequence similarities(<94%) to the recognized species. In each gene phylogeny, the 16S rRNA gene was found to be incongruent with each house-keeping gene, indicated that this gene should not be used as a single marker in rhizobial taxonomy. In addition, more robust topology trees were produced through the analysis of a concatenation of three housekeeping genes than through each housekeeping gene and 16S rRNA gene trees, with high bootstrap support (>= 55%). Overall, our results support that the MLSA has higher discrimination potential in rhizobial taxonomy than the 16S rRNA gene and is suitable to estimate phylogenetic relationships among rhizobia species.