Hierarchical analysis of linkage disequilibrium in Rhizobium populations: evidence for sex?

Abstract

Many bacterial species exhibit strong linkage disequilibrium of their chromosomal genes, which apparently indicates restricted recombination between alleles at different loci. The extent to which restricted recombination reflects limited migration between geographically isolated populations versus infrequent mixis of genotypes within populations is more difficult to determine. We examined the genetic structure of Rhizobium kguminosarum biovar phaseoli populations associated with wild and cultivated beans (Phaseolus spp.) over several spatial scales, ranging from individual host plants to throughout the Western Hemisphere. We observed significant linkage disequilibrium at scales at least as small as a cultivated plot. However, the amount of disequilibrium was much greater among isolates collected throughout the Western Hemisphere than among isolates from one area of Mexico, even when disequilibrium was quantified using an index that scales for allelic diversity. This finding suggests that limited migration between populations contributes substantially to linkage disequilibrium in Rhizobium. We also compared the genetic structure for R. leguminosarum bv. phaseoli taken from a cultivated plot with that for Escherichia colt obtained from one human host in an earlier study. Even at this frne scale, linkage disequilibrium in E. coil was very near the theoretical maximum level, whereas it was much less extreme in the local population of Rhizobium. Thus, the genetic structure for R. leguminosarum bv. phaseoli does not exclude the possibility of frequent mixis within local populations.

Bacteria gone native vs. bacteria gone awry?: Plasmidic transfer and bacterial evolution

“…For example, in Rhizobium etli associated to beans in the state of Morelos, Central Mexico, it was found that the less disturbed populations had less chromosomal recombination (they are more clonal), whereas the more intensively managed populations, have substantially more chromosomal recombination (2,22); similar patterns were found in other populations in the state of Puebla, also in Central Mexico (23). If these ideas are right, and plasmids travel with the rest of the chromosome, in the less managed populations there should be both very specific plasmid͞chromosome association and high linkage disequilibirum among chromosomal loci (Fig.…”

A comparison of homologous recombination rates in bacteria and archaea

“…Similarly, ecotypes inhabiting identical micro-niches in different locations are less likely to exchange DNA than clones from the same location. Evidence for this process has been found in the soil bacterium Rhizobium leguminosarum, where clonality was less pronounced at a regional scale than it was at a global scale (Souza et al, 1992).…”

Biogeography: An Emerging Cornerstone for Understanding Prokaryotic Diversity, Ecology, and Evolution

“…phaseoli strains that live in soils and in nodules of wild and cultivated beans [70]. In those studies, target organisms were generally isolated in pure cultures and their genotypic diversity was determined based on sequence analysis of protein-coding genes [74], multilocus enzyme electrophoresis [63], or genome-wide polymerase chain reaction (PCR) amplification of repetitive elements [11]. Pairwise genetic distances between genotypes were then inferred from DNA sequences or fingerprinting patterns between isolates, and clades obtained by cluster analyses were compared with the geographic origins of the isolates.…”