Estimating Rapid Diversity Changes During Acute Herbicide Contamination Using Environmental DNA

The biodiversity of freshwater ecosystems globally is facing severe threats due to various anthropogenic stressors, such as habitat degradation, introduction of invasive species, and pollution. Assessing the effects of human-induced environmental stressors on population and community persistence requires accurate biodiversity estimates. While environmental DNA (eDNA) metabarcoding has emerged as a promising tool, its effectiveness in capturing rapid biodiversity responses to acute stressors across levels of biological organization (community, population, and intra-specific levels) remains to be investigated. In this study, we tested the efficacy of eDNA metabarcoding in assessing rapid changes in aquatic zooplankton and insect communities by conducting a two-month mesocosm experiment with pulses of glyphosate-based herbicide under contrasting nutrient levels (mesotrophic and eutrophic). We examined the effects of treatments on community assemblages, family richness, and intraspecific diversity, and compared our findings with those obtained through a microscopy approach. Metabarcoding revealed partially congruent ecological findings with microscopy, indicating its potential in assessing rapid community changes. The herbicide induced shifts in community composition and differentially impacted zooplankton and insect family richness (increase in insects, and decrease in crustaceans and rotifers), suggesting a gradient of tolerance to the herbicide among taxa and potential top-down regulation by insect larvae that may counteract the advantage gained by herbicide-tolerant zooplankton. Finally, we showed that nutrient enrichment exacerbated the negative effects of the herbicide on intraspecific diversity, highlighting concerns about genetic erosion. Our findings underscore the complexity of responses to herbicide and nutrient enrichment in freshwater ecosystems. We conclude that eDNA metabarcoding can not only be used to estimate rapid changes in invertebrate communities but also provides additional value by offering a broader perspective on diversity dynamics and potential cascading effects at different scales of biological organization.