Temperate Phages Mediate Dual Adaptive Mechanisms That Enhance Microbial Resilience in Antibiotic-Contaminated Wastewater Treatment Systems

Temperate phages play crucial ecological roles in engineered microbial communities, yet their adaptive strategies under antibiotic stress remain unclear. Here, metagenomic analysis was used to investigate how temperate phages facilitate host adaptation in activated sludge acclimated to chloramphenicol (CAP). Antibiotic stress markedly reshaped bacterial and temperate phage communities, with dominant degraders (e.g., Sphingomonas and Caballeronia ) reaching relative abundances of 6.5–42.0%. Temperate phages exhibited specific adaptive responses by significantly enriching antibiotic resistance genes, including multidrug ( arlR and mtrA ) and peptide ( bcrA ) resistance genes, resulting in a 1.56–4.15-fold increase in the phage-derived resistome relative to the control. They also mediated general adaptive responses by encoding auxiliary genes involved in oxidative stress mitigation, DNA repair, biofilm formation, and antiviral defense. Host-phage linkage prediction identified 1045 phage–bacteria interactions, including 11 ARG-harboring viral operational taxonomic units associated with dominant CAP-degrading hosts. Collectively, our findings reveal that temperate phages facilitate microbial resilience in antibiotic-stressed environments by delivering mutualistic genetic traits, encompassing both specific (antibiotic resistance genes) and general (antiviral defense, metabolic, and stress mitigation) adaptive responses, highlighting their ecological significance and potential for enhancing the stability and performance of wastewater treatment systems under pharmaceutical stress.