High-throughput characterization of antibiotic resistome in soil amended with commercial organic fertilizers

Abstract

The use and abuse of antibiotics in the livestock industry are believed to have contributed to the enhancement of antibiotic resistance in agricultural settings through the application of animal manure. The use of manure-based commercial organic fertilizers (COFs) shows promise for the abatement of potential dissemination of antibiotic resistance. This study aims to assess the effects of repeated COF applications on the soil antibiotic resistome and bacterial communities and to reveal potential correlations. High-throughput quantitative PCR was used to characterize the shift of the antibiotic resistance gene (ARG) contents after repeated COF applications. Illumina sequencing was employed to investigate changes in the bacterial community composition. Applications of COFs increased the diversity and abundance of a wide spectrum of ARGs and mobile genetic elements (MGEs) in the soil. The first and second COF applications enhanced the proliferation of genes encoding resistance to beta lactam and vancomycin. Procrustes analysis and mantel test revealed that ARG profiles were significantly correlated with bacterial community composition, indicating that the microbial community composition might be a determinant of the soil resistome. Network analysis further demonstrated significant associations between ARGs and MGEs, highlighting the likelihood of the horizontal gene transfer of ARGs in the COF-amended soils. COFs are vast ARG reservoirs that should be categorized as ARG contamination sources in agriculturally related environments. The application of COFs increased the diversity, abundance, and potential horizontal transfer of ARGs in soil.