Overlooked yet Critical: Unveiling the Impacts of Emerging Contaminants on the Phytoplankton Community Structure and Function in an Urban River System

Abstract Urban river ecosystems are confronting increasing pressures from emerging contaminants (ECs), yet their in situ impacts on phytoplankton communities remain poorly understood. This field-based research in an urban river system, employing amplicon and metagenomic sequencing, provides the first quantitative evidence that ECs are dominant drivers shaping the phytoplankton community structure and metabolic functions. Phytoplankton community exhibited seasonal shifts, characterized by deterministic assembly and Ochrophyta dominance in spring, transitioning to stochastic processes and Cyanobacteriota/Chlorophyta dominance in summer. ECs accounted for 20.8–30.6% of the variance in both composition and functions, fundamentally rivaling or exceeding the impacts of basic water quality parameters and metals. Metagenomic functional profiling revealed that ECs may disrupt key metabolic pathways involved in carbohydrate, energy, lipid, amino acid, glycan, and cofactor/vitamin metabolism. Crucially, phytoplankton exposed to elevated antibiotic or herbicide levels showed enrichment of genes related to photosynthesis and oxidative phosphorylation, suggesting a potential compensatory functional response under stress. This study highlights the overlooked yet critical role of ECs in shaping the phytoplankton community structure and function, advocating for the integration of ECs into holistic aquatic ecological assessment and urban river management frameworks.