Effect of Soil Type, Composting, and Antibiotic Use on Fate of Antibiotic Resistance Genes and Microbial Community Composition in Dairy and Beef Manure Applied Soils
Pankow, Christine Ann
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Manure is a commonly used soil fertilizer, but there are concerns that this practice could affect the spread of antibiotic resistance genes (ARGs) from farm to fork. A microcosm-scale study evaluated the effect of prior antibiotic use (manure-based soil amendments generated from dairy and beef cattle with or without antibiotic administration), composting, and soil type on the quantity of ARGs and the microbial community composition of dairy and beef manure applied soil. ARGs were analyzed through novel metagenomic techniques and quantitative polymerase chain reaction of sul1, tet(W), and 16S rRNA gene, while the microbial community composition was determined via 16S rRNA amplicon sequencing. The results indicated that while prior antibiotic administration elevated the relative abundance of ARGs and changed the microbial community of raw manure applied soils, composting reduced this effect. However, compost applied soils still had a higher relative abundance of ARGs than the unamended soils and occasionally soil applied with raw manure of untreated cattle. Soil type may be a mediating factor as there were differences observed between the three soil types (sandy loam, silty clay loam, and silty loam) with sandy loam amended soils often having the least attenuation of ARGs. As the relative abundance of ARGs was still elevated and the microbial community composition still significantly different from the unamended soils after 120 days, these results suggest that 120 days is not a long enough waiting period between biological soil amendments and crop harvest for ARG dissipation.
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