Antiviral defense systems drive persistence but limit the transfer of antimicrobial resistance genes in anaerobic digestion

Phage-bacteria interactions critically shape antimicrobial resistance (AMR) dynamics in environmental reservoirs, yet their ecological roles remain poorly understood. Using swine manure anaerobic digestion as a model system, we integrated short- and long-read metagenomics, meta-transcriptomics, and high-throughput chromosome conformation capture (Hi–C) data to investigate how the phage-bacteria arm race impacted the transfer of antimicrobial resistance genes (ARGs). We identified 6,210 viral OTUs, of which 26 vOTUs carried ARGs, with Hi-C and historical infections revealing 45 transduction events but 1,524 ARB lytic events (57.7% of infections); notably, vOTUs driving lysis exhibited significantly higher abundance than those carrying ARGs or involved in transduction (p < 0.001), with no expression of phage-borne ARGs, challenging their role as ARG vectors. Antiviral defense systems (ADS), widely present in antimicrobial-resistant bacteria (ARB) (4.5 per genome) and actively expressed, exhibited a dual role: CRISPR-Cas spacer-based immune networks showed expressed spacers protecting ARBs from lysis, while spacers targeting ARG-carrying contigs suppressed HGT, as confirmed by conjugation assays with developed antiviral defense strains. Our findings elucidate the dual nature of ADS caused by phage-bacteria arm race in AMR dynamics, and offer a framework to harness phage lysis and ADS for global AMR mitigation across environmental systems.