Environmental DNA Metabarcoding Reveals Divergent Patterns of Biodiversity, Community Assembly, and Environmental Sensitivity Across Taxa in Adjacent Rivers

The differentiated responses of biological groups to environmental change are central to river ecosystem management; however, the shared and distinct environmental selection processes that shape their spatial patterns remain understudied. We investigated two adjacent rivers with contrasting environmental conditions and applied eDNA metabarcoding to characterize the eukaryotic plankton and fish communities. The alpha diversity showed no significant river-to-river difference for either group, but beta diversity differed strongly, indicating high spatial turnover. Both groups exhibited distance-decay relationships, which were stronger in plankton, whose community assembly was mainly stochastic; in contrast, fish assembly was predominantly deterministic. Community variation in both groups was significantly associated with physical and chemical factors-electrical conductivity (EC), the potential of hydrogen (pH), water temperature (WT), dissolved oxygen (DO), chemical oxygen demand (COD), and biochemical oxygen demand (BOD5)-while plankton also responded to nutrient variables, including total phosphorus (TP), total nitrogen (TN), and ammonium nitrogen (NH4-N). Collectively, our results emphasize differential environmental selection across biological groups and provide a basis for designing targeted river restoration and water quality improvement strategies.