Environmental DNA Reveals Ecologically Relevant Temporal and Spatial Variation of Fish Community in Silver Carp- and Bighead Carp-Dominant Drinking Water Reservoirs

Environmental DNA (eDNA) metabarcoding was utilized to compare the fish species composition, diversity, and their relationships with environmental factors in four medium-sized drinking water reservoirs (Tongjiqiao, Andi, Shafan, and Jinlan) within the Qiantang River Basin during both wet and dry seasons. A total of 44 fish species belonging to 6 orders, 15 families, and 40 genera were detected, with Cyprinidae being identified as the dominant family (68.2%). Silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) were identified as the most abundant species, representing 81.94% and 99.98% of the relative eDNA abundance, respectively. The fish communities were characterized by river-resident species (59.1%), pelagic species (43.2%), and omnivorous (43.2%) and carnivorous (43.2%) feeding habits. Significant influences of seasonal and reservoir-specific variations on physicochemical parameters, species composition, and ecological traits were observed. However, no significant differences in community diversity (Chao1, Pielou_e, Shannon, and Simpson indices) or distribution patterns were detected between wet and dry seasons. In contrast, Jinlan Reservoir was found to exhibit distinct diversity and distribution patterns compared to the other three reservoirs, which was consistent with the relative eDNA abundance of H. molitrix and H. nobilis. Through a Spearman correlation analysis, the relative abundance of H. molitrix was revealed to be negatively correlated with community diversity, while H. nobilis was shown to have positive correlations (except with Chao1). This suggests that the excessive stocking of H. molitrix may lead to reduced diversity, whereas moderate stocking of H. nobilis could promote diversity restoration. Among physicochemical factors, Chao1 richness was found to be negatively correlated with conductivity, pH, phosphate–phosphorus (PO4-P), and the total nitrogen to total phosphorus ratio (TN/TP), while Shannon and Simpson diversity indices were negatively correlated with nitrate nitrogen (NO3-N) concentrations. A redundancy analysis (RDA) identified NO3-N and permanganate index (CODMn) as the primary physicochemical drivers of fish community structure, indicating that while physicochemical differences were found to influence species composition and diversity, their effects were considered relatively limited. These findings suggest that the overwhelming dominance of H. molitrix and H. nobilis in the reservoirs may reduce the influence of seasonal variations and cross-reservoir physicochemical disparities on fish community dynamics.