Community protection of antibiotic biodegradation modulates microbiome succession and stability

Antibiotic residues exert persistent and intense stress on environmental microbiomes, thereby impacting community stability. However, the association between the establishment of antibiotic degradation and community succession remains poorly understood, hindering environmental risk assessment of antibiotic disturbance. Here, the role of antibiotic biodegradation is investigated in community protection by comparing two strategies (natural adaptation and pre-adaptation via antibiotic degrader bioaugmentation) under sulfamethoxazole (SMX) stress in sequencing batch reactors. Pre-adapted communities exhibited higher degrader abundance and improved SMX degradation compared to naturally adapted communities. SMX stress retarded succession in naturally adapted communities while maintaining significantly higher species diversity; whereas more efficient biodegradation in pre-adapted communities alleviated antibiotic stress and restored regular community succession. SMX degraders stabilized microbial interactions by maintaining connectivity under stress, with antibiotic stress and degradation capacity jointly shaping microbiome succession. Naturally enriched SMX degraders exhibited average causal mediation effects that were 1.25-fold higher than the total antibiotic effects, whereas bioaugmented communities exhibited diminished antibiotic sensitivity. These findings highlight the critical role of key degraders in protecting communities and maintaining ecosystem stability under antibiotic stress, providing fundamental insights for developing resilience-based strategies to manage antibiotic risks and conserve ecosystems.