Performance, metabolism, and resistance of an SMX-stressed continuous-flow AGS-MBR system: Microscopic mechanism of macroscopic instability phenomena.

To clarify how long-term sulfamethoxazole (SMX) pressure converts macro-scale performance loss into micro-level mechanistic change, a continuous-flow aerobic granular sludge membrane bioreactor (AGS-MBR) was operated for 140 days at SMX concentrations ranging from 0 to 5 mg L⁻¹. At 0.2-1 mg L⁻¹, the system remained resilient: TN and TP removal stabilized at 90 % and 72.8 %, respectively, and the volume-mean granule diameter remained 282 µm. Metagenomics revealed significant up-regulation of the glycogen-metabolising gene glk and the polyphosphate gene ppk, which fuelled an energy-compensation pathway that supplied ATP and precursors for TB-EPS synthesis and reinforced granule scaffolding. When influent SMX rose to 5 mg L⁻¹ this compensation collapsed: EPS dropped 45 %, Dv shrank 38 %, granules disintegrated, TN removal fell to 70 % and TP to 44.8 %. The community shifted to a filamentous bacteria dominated state with Thiothrix >25 % relative abundance. Concurrently, the non-pathogen Rubrivivax became a shared host for antibiotic resistance genes (sul1, sul2) and multiple transposases; mobile genetic elements mediated the co-transfer of resistance and virulence genes and eroded functional redundancy. LC-MS further showed that the major transformation products P4 and P6 exhibited 2.3 folds higher chronic toxicity than the parent compound and imposed additional chemical stress on the already impaired granule microbiota. SMX dose dictated a cascade in which metabolic compensation was followed by selection of filamentous hosts prone to gene mobility and finally by chemical toxicity, progressively dismantling granule structure, nutrient removal services and ecological safety. These results elucidate the dose-dependent macro-to-micro cascade under SMX stress and provide insights for mitigating ecological risks in antibiotic laden wastewater.