Inter-domain microbial collaboration drives sulfamethoxazole in situ biodegradation in lake sediments

Sulfonamide antibiotics (SAs) are pervasive contaminants in aquatic ecosystems and substantially contribute to the dissemination of antibiotic resistance. Microbial degradation represents the primary pathway for SA removal in aquatic environments, which depends on synergistic interactions between bacteria and eukaryotes. However, how these inter-domain interactions govern SMX degradation processes remains unclear. Here, an integrated approach combining DNA-stable isotope probing (DNA-SIP), high-throughput sequencing, and molecular ecological network analyses pipeline (MENAP) was employed to investigate the functional microorganisms and biodegradation processes of sulfamethoxazole (SMX) in lake sediment microcosms. After 30 days of incubation, SMX mineralization rates ranged from 5.2% to 19.2%. DNA-SIP identified diverse functional bacteria and eukaryotes, primarily including Burkholderia-Caballeronia-Paraburkholderia, Lysobacter, BOLA868, and Scenedesmus. During incubation, the inter-domain network exhibited increased in complexity, the proportion of positive correlations, and the proportion of bacterial-eukaryotic links. Furthermore, the subnetworks average degree was significantly and positively correlated with the SMX mineralization rates (P < 0.001). Path analysis indicated that bacteria, fungi, and algae were directly involved in SMX degradation, whereas metazoans and protozoa indirectly promoted the degradation via top-down predation. UPLC-MS/MS analysis revealed that microbial degradation of SMX occurred via hydroxylation, acetylation, deamination, nitrosation, and cleavage of N-O and S-N bonds. Overall, this study highlights the pivotal role of inter-domain bacterial-eukaryotic cooperation in the in situ SMX degradation and provides valuable insights for the bioremediation of SMX contaminated aquatic environments.