Protists show high resilience and thrive under multiple chemical stressors

Impact statement Protists are an underexplored but functionally important component of aerobic‐activated granular sludge under pollution stress. Using metagenomics, we profiled protistan responses to ciprofloxacin, triclosan, and Cu 2+ (alone or in combination). Protists remained a stable 6.35%–7.88% of the bacterial community, and the consumers were the most abundant groups. Ciprofloxacin showed little effect on protist abundance, while Cu 2+ increased protist abundance, especially consumers. Stress conditions also strengthened predominantly positive protist–bacteria associations, suggesting cross‐domain interactions that may enhance community resilience. These results demonstrate that protists are key determinants in stabilizing microbial communities under multiple stressors.