Rhizobium etli and Rhizobium gallicum nodulate common bean (Phaseolus vulgaris) in a traditionally managed milpa plot in Mexico: population genetics and biogeographic implications

Abstract

The stability of the genetic structure of rhizobial populations nodulating Phaseolus vulgaris cultivated in a traditionally managed milpa plot in Mexico was studied over three consecutive years. The set of molecular markers analyzed (including partial rrs, glnII, nifH, and nodB sequences), along with host range experiments, placed the isolates examined in Rhizobium etli bv. phaseoli and Rhizobium gallicum bv. gallicum. Cluster analysis of multilocus enzyme electrophoresis and plasmid profile data separated the two species and identified numerically dominant clones within each of them. Population genetic analyses showed that there was high genetic differentiation between the two species and that there was low intrapopulation differentiation of the species over the 3 years. The results of linkage disequilibrium analyses are consistent with an epidemic genetic structure for both species, with frequent genetic exchange taking place within conspecific populations but not between the R. etli and R. gallicum populations. A subsample of isolates was selected and used for 16S ribosomal DNA PCR-restriction fragment length polymorphism analysis, nifH copy number determination, and host range experiments. Plasmid profiles and nifH hybridization patterns also revealed the occurrence of lateral plasmid transfer among distinct multilocus genotypes within species but not between species. Both species were recovered from nodules of the same plants, indicating that mechanisms other than host, spatial, or temporal isolation may account for the genetic barrier between the species. The biogeographic implications of finding an R. gallicum bv. gallicum population nodulating common bean in America are discussed.

FIG. 1.

Dendrograms showing the genetic relatedness among chromosomal and plasmidic genotypes of R. etli and R. gallicum and the chromosome-plasmid profile combinations. (A) Genetic relatedness of the multilocus genotypes based on 10 isoenzymatic loci. The ET designations are indicated. (B) Genetic relatedness of the plasmid profiles based on the presence or absence of the different plasmid size classes. The plasmid profile designations are indicated. The number of isolates for each multiple ET or plasmid profile is given in parentheses. The genetic distance between each pair of ETs or plasmid profiles was estimated by determining mean character differences, and data were clustered by the UPGMA. The four most abundant ETs and their plasmid profile combinations are indicated by boldface type and solid lines; the other combinations are indicated by dashed lines.