Evaluating ecological health of the Chishui River using a multi-taxa index of biological integrity (IBI)

Understanding the biodiversity and ecological status of aquatic ecosystems is critical for riverine conservation and management. However, spatiotemporal patterns of biological integrity remain unclear, and single-taxon assessments often yield inconsistent or biased results due to divergent responses of different biotic communities to environmental change. In this study, we used eDNA metabarcoding to investigate phytoplankton, invertebrate, and fish communities in the upper Chishui River across four seasons and three longitudinal sections (BJ, ZT, RH). We developed taxon-specific biological integrity (BI) indices using four core metrics: taxon richness, dominance, network density, and phylogenetic distance. We further constructed a comprehensive index of biological integrity (IBI) by calculating the unweighted arithmetic mean of the three BI values, enabling a holistic evaluation of ecosystem health. Our results showed clear spatiotemporal variations in community composition and diversity. BI values exhibited asynchronous responses among taxa and differed from diversity patterns. Phytoplankton BI was generally good or moderate; invertebrate BI was stable but poor at some sites in summer; fish BI increased longitudinally from poor to good (except summer). Correlation analysis showed that community diversity and BI were driven by different environmental factors, whereas the integrated IBI showed no significant correlation with individual environmental variables, indicating greater stability. The asynchronous responses among single taxa confirm the limitations of relying on single taxon-based BI. In contrast, the multi-taxa IBI provided a comprehensive assessment of overall ecological health, which was generally good to moderate in the upper Chishui River. This study demonstrates that integrating multiple biological communities improves the reliability of bioassessment, supporting more effective river management and conservation.