Plant associated bacteria are a rich reservoir for multidrug efflux pumps

Plants produce antibiotic substances and bacteria need to cope with those substances to colonize plants. We analyzed the inventory of genes encoding resistance-nodulation-cell division (RND) efflux pumps originating from 282 bacterial isolates from leaves or roots of the model plant Arabidopsis thaliana. We confirmed that, on average, plant associated bacteria hold a significantly increased repertoire of genes encoding RND antiporters homologs compared to strains isolated from other ecological niches, as reported in a previous study. While some RND antiporter clades were enriched in plant colonizers, other clades found in the genomes of isolates from other environments were underrepresented. An in-depth analysis of RND antiporters from plant colonizing bacteria revealed that conserved motifs can be found in each clade, possibly contributing to substrate specificity. Interestingly, we found horizontal gene transfer markers in 10% of the antiporter homologs, suggesting that horizontal gene transfer may significantly contribute to the adaptation of bacteria to the specific chemical environment created by different organs of plant hosts. In addition, homologs from leaf-isolated bacteria showed a lower diversification, and harbored markers of horizontal gene transfer in the heavy metal exporting clade. Sequence and structural analysis revealed a high diversity in RND-antiporters, with few residues under purifying selection, indicating that RND diversity is driven by random mutations. Our findings have major implications for the origin of multidrug resistances and for our understanding of the forces shaping the outcome of plant-microbe ecology in general.