Improving freshwater ecosystem assessment via the integration of eDNA-based multitrophic biotic groups

Global freshwater ecosystems are experiencing widespread ecological degradation and biodiversity loss, creating an urgent need for robust ecological health assessment frameworks. Traditional assessment approaches typically rely on a single taxonomic group, limiting their ability to capture ecosystem degradation because different biological groups exhibit taxon-specific responses and temporal lags to environmental changes. Based on environmental DNA (eDNA) metabarcoding, we developed a multitrophic index of biotic integrity (IBI_m) to assess ecological health by integrating bacteria, fungi, eukaryotic algae, and invertebrates of 40 shallow lakes in the Yangtze-Huaihe River basin, China. The effectiveness of the IBI_m was supported by its strong associations with environmental gradients and its sensitivity to declines in β-diversity. Compared to single-taxon IBIs, the IBI_m showed stronger correlations with multiple physicochemical variables, including dissolved oxygen and ammonia. In addition, lower IBI_m values were associated with reduced local contributions to beta diversity (LCBD) across multiple biological groups, indicating a loss of local community uniqueness under degradation. Lake health assessments based on IBI_m were more stringent than those based on the water quality index (WQI): only 37.5% of lakes were classified as "Good" by IBI_m, compared with 82.5% by WQI. The IBI_m framework bridges practical biomonitoring with ecological interpretation of freshwater degradation and provides a promising tool for ecosystem monitoring and management under global change.