Purpose: This study was conducted to determine the effects of antibiotic administration and soil amendment practices on antibiotic resistance and microbial diversity of the edible surfaces of lettuce and radishes grown using recommended application rates.
Methods: Lettuce and radishes were planted in field plots amended with raw manure from antibiotic-treated dairy cows, compost from cows with different histories of antibiotic administration, or no amendment at recommended application rates (12 plots, n=3). Lettuce and radishes were harvested at maturity and the bacterial communities of the edible surfaces compared for each treatment using culture and non-culture based methods. Bacterial log CFU/ml were determined on R2A plates containing seven different antibiotics. DNA was extracted from the surface of mature radish taproots and lettuce leaves. Illumina sequencing of 16S rDNA amplicons, 515F–926R, was performed via Earth Microbiome Project protocol.
Results: Overall the type of soil amendment was not associated with significant differences in total culturable bacteria recovered from the radish taproots or lettuce phyllosphere plated on R2A or on R2A supplemented with the majority of antibiotics. However, bacteria resistant to clindamycin were more numerous on lettuce leaves grown in the soil amendments compared to the fertilizer control (P<0.01). Bacterial diversity (richness, evenness) was influenced by vegetable type, but not soil amendment or antibiotic history.
Significance: Analysis of shot-gun metagenomics sequencing data is underway and used to determine relationships between phylogeny and the resistome. This study will help inform management practices for limiting the dissemination of antimicrobial resistance from farm-to-fork.