Zinc-Driven Antibiotic Resistance Gene Dynamics During Vermicomposting: Insights into Co-Contamination Mitigation for Sustainable Manure Management

Background: The coexistence of antibiotic resistance genes (ARGs) and heavy metals in livestock manure poses critical challenges to vermicomposting technology. Objectives: This study aimed to clarify the zinc (Zn)-driven ARG dynamics over 60-day vermicomposting for livestock manure and provide a reference for taking appropriate measures to reduce the spread of ARGs in the environment. Methods: In a vermicomposting system using Eisenia fetida and treated with varying concentrations of Zn, high-throughput sequencing was employed to analyze microbial succession, while quantitative real-time PCR (qPCR) was performed to track the fluctuation patterns of ARG (tet-, erm-, qnr-, str-, chl-, bla-, mcr-ARGs) and mobile genetic element (MGE, intI1 and intI2) abundances over the 60-day treatment period. Results: Generally, sul- (10−3–10−1 copies/16S rRNA), tet- (10−3–10−2 copies/16S rRNA), and str-ARGs (10−3–10−2 copies/16S rRNA) are dominant in dairy manure. Vermicomposting significantly reduced total ARGs (88.62% removal), but Zn stress triggered concentration-dependent shifts. Low Zn (100–250 mg/kg) elevated tet-, erm-, and chl-ARGs via co-selective pressure and disrupted bacterial succession, while high Zn (500–1000 mg/kg) suppressed qnr- and mcr-ARGs but intensified horizontal transfer via cross-resistance. Conclusions: Vermicomposting maintained a greater ARG removal capacity across the Zn gradient (100–1000 mg/kg) than natural composting, proving an effective approach for reducing the threat of antibiotic resistance in bacteria even under high Zn stress. The link between Zn residues and the increased ARG dissemination risks underscores the challenge of co-contaminants, providing essential insights for developing vermicomposting strategies to mitigate ARG risks and ensure sustainable manure management.