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.