A non-canonical function of Arabidopsis Dicer-Like proteins in shaping the root microbiota assembly

Plants are naturally associated with a diverse community of soil microbes. Potential linkages between the assembly of root-associated microbiota and key cellular processes in plants remain to be explored. DNA methylation is an epigenetic mark important to many fundamental biological processes; however, it is unclear whether the establishment of DNA methylation in plants influences the associated microbiota. In this study we investigated the root-associated microbiota of Arabidopsis mutants defective in the canonical RNA-directed DNA methylation (RdDM) pathway. The microbiota was not altered in the examined RdDM mutants except for dcl234, which is defective in the Dicer-like proteins 2, 3, and 4 that are key to the biogenesis of small interfering RNAs. Subsequently metagenome sequencing identified higher abundance of drug resistance genes in microbes associated dcl234 than Col-0.