Virus-Mediated Fate of Antimicrobial Resistance Genes in Livestock Manure Composting

Composting mitigates the global burden of antimicrobial resistance (AMR) in livestock manure, yet the viral biosphere's role in resistome dynamics remains a black box. Leveraging a massive global dataset of 420 metagenomes and 42 viromes, we decipher the phage-host evolutionary arms race during ecological succession. While composting reduces total antimicrobial resistance genes (ARGs), it is bottlenecked by the selective enrichment of thermophilic antimicrobial-resistant bacteria (ARB), which dominate the residual maturation-phase resistome (∼ 60%). Among 106,387 identified viral operational taxonomic units (vOTUs), lytic interactions (39.5%) quantitatively override transduction (< 0.5%) in driving ARB decline. Correspondingly, the relative abundance of ARG-reducing vOTUs (7.24%) is orders of magnitude higher than that of vOTUs involved in transduction (0.06%) (p < 0.001). However, intense viral predation drives surviving ARB to evolve enriched antiviral defense systems (ADS) against lysis. Intriguingly, this immune shield acts as a genetic firewall, likely restricting the horizontal acquisition of ARGs via transformation or conjugation. Our findings redefine composting as an intense evolutionary arena and suggest that precision strategies targeting the thermophilic reservoir are essential for maximizing ARG mitigation and safer manure recycling.