A Comparative Analysis of eDNA Metabarcoding and Field Surveys: Exploring Freshwater Plant Communities in Rivers

While eDNA metabarcoding holds promise as a holistic approach for assessing vegetation changes and community composition across diverse spatial and temporal scales, systematic investigations into its efficacy compared to conventional surveys remain scarce in the literature. The present study explores the differences in plant diversity retrieved with field surveys and that captured with a multi-marker eDNA metabarcoding approach from river water samples. The eDNA approach retrieved 46 aquatic plants (hydrophytes and helophytes) and 245 terrestrial plants, compared to 24 and 127 species identified from the field surveys. On average, eDNA samples collected immediately downstream of the survey sites retrieved 43% and 39% of the observed aquatic and terrestrial species , respectively. Discrepancies were explained by differences in the taxonomic resolution, the stochasticity of retrieving rare and elusive species, and the presence of reference sequences. We found a significant positive correlation between spatial and community distances at scales ranging 2-9 km, and identified turnover as the driving force of these differences. eDNA demonstrated sensitivity to community changes, and both approaches converge on a similar community structure. Interestingly, eDNA samples collected immediately upstream of the survey sites exhibited significant species overlap with the downstream samples (c. 100 m apart). Overall our results demonstrate that, with adequate sampling, eDNA has the potential to approximate catchment gamma diversity while still being informative of the local flora.