Genotypic diversity of Sinorhizobium (formerly Rhizobium) meliloti strains isolated directly from a soil and from nodules of alfalfa (Medicago sativa) grown in the same soil

Abstract

The genetic structure of a population of Sinorhizobium meliloti (formerly Rhizobium meliloti) isolated from nodules of alfalfa (Medicago sativa cv. Europe) or isolated directly from the soil using an elective medium and colony hybridization was assessed by three molecular methods. Sixty-seven S. meliloti isolates were obtained from alfalfa nodules and 61 directly from soil. Plasmid profiles of S. meliloti isolates were analyzed as well as insertion sequence (IS) fingerprints using probes corresponding to the two indigenous IS elements: ISRm1 and ISRm5. The presence of a gene involved in nodule forming efficiency (nfeA gene) was also determined by PCR using specific primers, among S. meliloti isolates. Plasmid profile analysis revealed the presence of 23 distinct plasmid types among the 128 isolates tested and the distribution of plasmid types was significantly different between isolates obtained from nodules and isolates obtained from soil. The distributions of plasmid types among S. meliloti nodule isolates were similar to those in a collection of nodule isolates obtained from the same field 8 years previously. We have thus demonstrated that the distribution of plasmid types in alfalfa nodules has not varied over long periods in the absence of the host plant. IS fingerprinting was more discriminative than plasmid profiling as a total of 65 distinct IS genotypes were found among the same isolates. The distribution of IS genotypes was different between isolates obtained from nodules and those isolated from soil. These results suggest that sampling S. meliloti populations using the host plant may not be representative of existing soil populations. Genes like nfeA were detected in neither the nodule nor soil isolates. The dominant plasmid type in nodule isolates (30% of the population), carrying a large plasmid of 230 kb, is poorly represented among soil isolates (8%). This result suggests that this plasmid might be involved in the competitiveness of S. meliloti strains.