Merging eDNA and ecological network analysis to assess aquatic ecosystem status

• Network parameters improve the efficiency of watershed ecological status assessment. • Combining network parameters and diversity indices effectively reflects ecological status. • The new method can predict ecological status based on environmental monitoring data. • Network parameters enhance the model’s applicability across various watersheds. Aquatic ecosystems are essential for human environments, however, are highly sensitive to external disturbances, making accurate assessment crucial. This study evaluates the ecological composition and integrity of the Yangtze River Basin using environmental DNA (eDNA) sequencing and network analysis. A comprehensive index of biological integrity (CIBI) was developed based on 63 key metrics selected from 477 candidates, revealing notable seasonal variation in ecological status. By focusing on diversity indices and network parameters, the assessment model avoids the complexity of traditional indicator selection and biological analysis, instead capturing core ecosystem characteristics and reliably predicting the ecological condition of the basin. A structural equation model was used to further refine the model by reducing the number of evaluation indicators, demonstrating that ecological status is affected by physical and nutrient factors, with biodiversity serving as a mediating variable. Overall, ecological status was highest at the river’s source, declined downstream, and exhibited pronounced seasonal variation. This study presents a comprehensive framework for aquatic ecosystem assessment, integrating eDNA and network metrics to enhance understanding and prediction of ecological dynamics in the Yangtze River Basin.