Comparison of nucleotide diversity and symbiotic properties of Rhizobium meliloti populations from annual Medicago species

Forty-three isolates of Rhizobium meliloti were trapped from soil with five annual species of Medicago (M. polymorpha, M. runcatula, M. rigidula, M. orbicularis and M. minima) and one perennial species of Medicago (M. sativa). The annual species were growing naturally near the soil sampling site, and the commonly studied perennial species was used for comparison. Each R. meliloti was characterized by PCR-RFLP methods applied to two DNA regions nested between 16S rRNA and 23S rRNA genes and between nifD and nifK genes. They fell into two highly divergent groups (groups I and II), separated at a genetic distance of 0.024 by rDNA-amplified pattern analysis (profiles R1 and R2) and at 0.029 by nif-amplified pattern analysis (profiles N1-N2 and N3). These two groups were consistent with some cross-nodulation and fixation results: rhizobia with the R1 genetic background elicited rudimentary nodules and could not fix nitrogen on M. polymorpha, while they were able to nodulate the five other species of Medicago. In contrast, rhizobia with an R2 profile were highly effective on M. polymorpha and poorly nodulated M. rigidula species, but were able to nodulate efficiently the other species. The striking phenotypic traits on M. polymorpha were also shared by reference strains: strains genetically closed to R2 type triggered typical and efficient nodules on M. polymorpha while those close to R1 type elicited rudimentary and non-efficient ones. Our results suggest that the presence of R. meliloti with R2 genetic backgrounds could be favoured by the distribution of M. polymorpha species.