Hidden Genetic Erosion: eDNA Exposes Chemical Stressors as Silent Drivers of Freshwater Biodiversity Loss

Understanding how synthetic chemicals affect biodiversity is essential for informing ecological risk assessments and supporting global biodiversity targets. Yet, current risk assessments rely mainly on linear extrapolations from laboratory toxicity tests and rarely capture multifaceted biodiversity, particularly genetic diversity, at the watershed scale. We integrated high-throughput mass spectrometry and environmental DNA (eDNA) metabarcoding to assess cumulative chemical stressor impacts on multitrophic communities (protozoa, algae, fungi, invertebrate metazoan, and fish) across streams, rivers, and lakes of the 40,000 km² Tai Lake Basin, eastern China. A total of 132 chemicals were detected, and cumulative ecological risk thresholds were exceeded at >70% of sites, indicating basin-wide chemical stress. Spatial heterogeneity in chemical composition and ecological risk were strongly associated with land-use intensity, particularly agricultural and urban development. eDNA metabarcoding revealed that community composition and sequence diversity mirrored chemical stressor distribution across sites. Sites with higher chemical stressors exhibited reduced sequence diversity and increased community similarity, while taxonomic diversity remained stable. Structural equation modeling showed that chemical effects on beta diversity were mediated through reduced sequence diversity, with no significant direct effects. These findings underscore the need to incorporate sequence-based biodiversity metrics into ecological risk frameworks and develop biodiversity-informed thresholds for freshwater ecosystems.