Unsupervised multitrophic eDNA index captures seasonal variation and nutrient controls of coastal ecosystem integrity

Environmental DNA (eDNA) metabarcoding has become an increasingly effective tool for assessing biodiversity and ecosystem health in aquatic environments. This study applied an eDNA metabarcoding strategy to evaluate the biological integrity of five key taxonomic groups, including algae, bacteria, protists, zooplankton, and fish, in the coastal waters of Wenzhou. By integrating four core ecological metrics, namely species dominance, phylogenetic distance, co-occurrence network density, and taxon richness, a composite Biological Integrity Index (IBI) was developed. The results revealed pronounced seasonal shifts in community structure and integrity, with generally higher IBI scores in summer and marked declines in autumn, particularly for algae and protists. Spatial variability was also evident. Sites located in the eastern island and offshore sector exhibited relatively high IBI values, whereas lower scores were observed in nearshore bays and estuarine regions. Nitrate, phosphate, and ammonium were identified as the primary environmental factors associated with integrity across trophic levels. Overall, the study highlights the ecological relevance and practical value of an eDNA-based multi-trophic assessment framework for coastal monitoring and underscores the importance of nutrient control for maintaining ecological integrity.