Two distinctive Rhizobium genospecies nodulating Vicia villosa Roth in alkaline soils of Northwest China

Aims To estimate the relative abundance, diversity and distribution of rhizobia associated with Vicia villosa Roth in soils of Northwest China. Method Rhizobia were trapped with V. villosa Roth plants from soils at seven sites and identified into genotypes by PCR-RFLP of IGS genes. They were further characterized by phylogenetic analyses of 16S rRNA, housekeeping genes ( atpD , recA, glnII ) and symbiotic genes ( nodC ). Soil physicochemical characteristics were recorded and Canonical Correlation Analysis was performed to correlate soil features and the distribution of IGS genotypes. Results 253 rhizobial strains were obtained from soils with pH 7.1–7.9. They were discriminated into 27 IGS types and further affiliated by phylogenetic analyses of 16S rRNA and multilocus sequence analysis (MLSA) into two clusters in Rhizobium. One corresponds to Rhizobium sophorae covering 228 strains in 25 IGS types and the other includes a novel genospecies containing two IGS types only detected in Shanxi Province, with higher soil pH and intermediate available phosphate and potassium contents. Representative strains of the novel genospecies show a specific phylogenetic nod C lineage, which may reflect differences in symbiosis properties. Furthermore, the Shanxi site was the less IGS diversified, based on Shannon diversity indices varying from 0.96 to 2.19 along the sampled area. Conclusions As the first study on diversity of rhizobia nodulating V. villosa Roth in China, R. sophorae and a novel Rhizobium genospecies with specific symbiotic genes were identified; and biogeographic patterns were found, mainly directed by soil pH, organic matter and soil salinity, including available phosphorus salts.