Purpose: Metagenomics of microbial communities of vegetables can provide overviews of dominant ARGs present on vegetables. The objective of this study was sequence metagenomes of the microbial communities from greenhouse radish bulb surfaces that were grown in soils amended with manure or compost originating from dairy or beef cattle of different histories of antibiotic administration.
Methods: Beef cattle were administered chlortetracycline, sulfamethazine, and tylosin while dairy cattle were administered cephapirin and pirlimycin. Manure was collected from antibiotic-treated cattle and nontreated control cattle. The four manure types were composted using a static method. The four manure types and four compost types were amended to two soil types (sandy loam and silty clay loam), in addition to fertilizer controls. Radish seeds were directly sown, and DNA was collected from microbes dislodged off the surfaces of mature taproots. After Illumina HiSeq, metagenomic sequences were mined for ARGs using the Comprehensive Antibiotic Resistance Database.
Results: Over 500 ARGs were identified among radish taproot surfaces. Some genes identified in all samples were dfrE, (trimethoprim resistance), rosB (polymyxin B resistance), and rosA (polymyxin B resistance). Genes that were not present on radishes grown in fertilizer control soils were ramA (multidrug resistance) and marA (induces transcription of efflux pump gene acrAB). However, those genes were present on radishes grown in soils amended with beef- and dairy-based manure and compost.
Significance: Further analysis will continue to identify ARGs. While ARGs will inevitably appear on vegetables regardless of biological soil amendment application, other ARGs can still be introduced into production by their use.