Tracing antibiotic fate and antimicrobial resistance dynamics across the manure–soil–plant continuum

Antimicrobial resistance (AMR) represents a critical One Health challenge, linking human, animal, and environmental health. Agriculture, particularly the use of livestock manure as fertilizer, contributes significantly to the dissemination of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) through soils and crops, posing risks to food security and public health. This study integrates multiple experiments to elucidate the fate of antibiotics and the dynamics of ARGs across the manure–soil–plant continuum. Pot experiments with pig manure-amended soil revealed enriched ARGs in the carrot rhizosphere and phyllosphere. Manure application increased ARG bioaccumulation in carrot tubers (up to 124-fold for specific genes) and facilitated transfer from skin to tuber. Estimated daily human ARG intake from manured carrots reached ~3 × 107 copies, but peeling reduced this by 28–91%. Field-scale isotope tracing (13C-labeled sulfamethoxazole) in lettuce demonstrated rapid antibiotic dissipation in non-planted soils (>98% in 180 days), yet rhizosphere accumulation and root-to-leaf translocation. Co-application with swine manure amplified soil ARG abundance (up to 5.35-fold) and root enrichment (2.38-fold), driven primarily by MGEs. High-risk ARGs persisted in leaves despite low residues. In paddy fields, swine compost elevated ARG abundance in soil and rice roots over growth stages, with increased detection frequencies indicating transfer from compost and irrigation water. No significant ARG differences appeared in grains across treatments. Metagenomic analysis via 13C-DNA stable isotope probing distinguished antibiotic-degrading bacteria (ADB) from non-degrading ones in contrasting soils. ADB harbored diverse chromosomal ARGs co-localized with MGEs and degradation genes, suggesting high horizontal gene transfer potential and soil-specific resistome networks. Hydroponic lettuce studies showed that manure sterilization reduced endophytic ARG/MGE subtypes by 50–86%, diminished pathogenic bacteria, and lowered high-risk ARG intake, highlighting its efficacy for risk mitigation. These findings provide comprehensive evidence that manure application propagates AMR through synergistic antibiotic–fertilizer effects, MGE-mediated transfer, and plant uptake. Integrated management, including manure sterilization, peeling of root vegetables, and soil-specific strategies, is essential to mitigate risks at the human–animal–environment interface.