The soil is an environment inhabited by a large/diverse population of bacteria, many of which can produce antibiotics that can be harmful to plants. Plants have evolved genes that confer antibiotic resistance. In Arabidopsis WBC19 confers resistance to the aminoglycoside kanamycin. We assessed the prevalence and diversity of bacterial antibiotic resistance genes in metagenomics samples derived from Arabidopsis roots. Thirty metagenomics samples collected from old or young plants representing 3 different Arabidopsis ecotypes were analyzed. Reads were mapped on the 26,253 antibiotic resistance genes from the FARME Database. Our results show that the profile of antibiotic resistance genes remained constant across genotypes and plant age with no antibiotic resistance gene showing significant changes. There was an under-representation of folate synthesis inhibitor genes in the microbiome relative to the FARME DB while there was an increase of aminoglycoside resistance genes. Several were bacterial ABC transporters which are typically found in aminoglycoside-producing bacteria but can also be found among non-producers. In conclusion, our results indicate that the Arabidopsis microbiome is stable with regards to the antibiotic resistance genes it harbors and is dominated by B-lactam resistance genes. In our next steps, we are co-assembling and annotating scaffolds to capture additional aminoglycoside resistance genes.
