Reticulated and epidemic population genetic structure of Rhizobium etli biovar phaseoli in a traditionally managed locality in Mexico

We conducted a multilocus enzyme electrophoresis (MLEE) study to assess the genetic structure of the nitrogen-fixing bacteria Rhizobium etli bv. phase oli. We analysed the genetic variation at 10 enzyme-encoding chromosomal lo ci of 482 isolates from root nodules of Phaseolus vulgaris and P. coccineus bean plants. The isolates were obtained from six traditionally managed agr icultural plots in two localities in the State of Puebla, in Central Mexico . The total mean genetic diversity (H-E) for the six plots was 0.531. Among the 482 isolates collected, 126 distinctive multilocus genotypes (electrop horetic types [Ets]) were obtained, and approximately half of the isolates are represented by five widespread ETs. A significant degree of genetic dif ferentiation among the six plots (G(ST) = 0.072) and between the two locali ties (G(ST) = 0.022) was detected. The main part of the observed variabilit y (70%) was found among the isolates within the plants. The cluster analysi s revealed two deeply diverging lineages, separated at a genetic distance o f 0.7. When a multilocus linkage disequilibrium analysis was performed at d ifferent hierarchical levels, we found significant linkage disequilibrium, but when the analysis was performed for the genotypes within the two diverg ing lineages, we found evidence of recombination. We propose for R. etli bv . phaseoli a reticulated and epidemic genetic structure, in which few genot ypes increase in frequency to produce numerically dominant clones, and gene tic exchange occurs mainly among genotypes within each lineage.