Complementary strengths of eDNA and morphology in assessing chemical stress on freshwater plankton communities: Evidence from mesocosm experiments

Pharmaceuticals and personal care products, particularly antibiotics and antimicrobial agents, are ubiquitously detected in freshwater ecosystems, yet their community- and ecosystem-level ecological risks remain inadequately understood. Conventional ecotoxicological assessments of chemical stressors in freshwater ecosystems have been limited by narrow taxonomic coverage, often relying on morphology-based identification. To address these limitations, we performed outdoor mesocosm experiments to assess the effects of environmentally relevant concentrations of ciprofloxacin and triclosan on freshwater plankton communities using environmental DNA (eDNA) metabarcoding, compared to traditional morphology-based identification methods. Our results showed that eDNA consistently detected higher genus richness for cyanobacteria and phytoplankton than morphology, despite the relatively limited overlap in genera identified by both methods. The two methods exhibited compound- and taxonomic group-specific sensitivities: eDNA outperformed morphology in detecting changes in taxonomic richness under ciprofloxacin exposure and shifts in community composition under triclosan exposure. In contrast, morphology was more effective in capturing ciprofloxacin-induced shifts in community composition and triclosan-induced declines in taxonomic richness. Collectively, eDNA- and morphology-based assessments yielded partially congruent outcomes, highlighting their complementary strengths in detecting chemical-induced changes in freshwater plankton communities. Overall, our findings suggest that integrating eDNA into regulatory frameworks could substantially enhance the accuracy of risk assessments and strengthen environmental monitoring strategies.