The widely utilized TiO
2 nanoparticles (NPs) tend to accumulate in wastewater and affect microbial growth. This work investigated the impacts of prolonged TiO
2 NP addition to filamentous aerobic granular sludge (AGS) using two identical sequencing batch reactors (SBRs, R1 and R2). R1 (the control) had no TiO
2 NP addition. In this reactor, filamentous bacteria from large AGS grew rapidly and extended outward, the sludge volume index (SVI
30) quickly increased from 41.2 to 236.8 mL/g, mixed liquid suspended solids (MLSS) decreased from 4.72 to 0.9 g/L, and AGS disintegrated on day 40. Meanwhile, the removal rates of COD and NH
4+-N both exhibited significant declines. In contrast, 5–30 mg/L TiO
2 NPs was added to R2 from day 21 to 100, and the extended filamentous bacteria were effectively controlled on day 90 under a 30 mg/L NP dosage, leading to significant reductions in COD and NH
4+-N capabilities, particularly the latter. Therefore, NP addition was stopped on day 101, and AGS became dominant in R2, with an SVI
30 and MLSS of 48.5 mL/g and 5.67 g/L on day 130. COD and NH
4+-N capabilities both increased to 100%. Microbial analysis suggested that the dominant filamentous bacteria—Proteobacteria, Bacteroidetes, and Acidobacteria—were effectively controlled by adding 30 mg/L TiO
2 NPs. XRF analysis indicated that 11.7% TiO
2 NP accumulation made the filamentous bacteria a framework for AGS recovery and operation without NPs. Functional analysis revealed that TiO
2 NPs had stronger inhibitory effects on nitrogen metabolism compared to carbon metabolism, and both metabolic pathways recovered when NP addition was discontinued in a timely manner. These findings offer critical operational guidance for maintaining the stable performance of filamentous AGS systems treating TiO
2 NP wastewater in the future.
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