Environmental DNA metabarcoding as a powerful tool for monitoring of fish communities in small rivers and large brooks

By use of a longitudinal cage study, using fifteen species known to occur in Belgian waters, we studied the streamreach of eDNA in small rivers and large brooks. Using a high and low source biomass under contrasting river discharge rates, we found strong and significant correlations between the eDNA relative abundances and the relative proportion of biomass per species. With decreasing correlation over distance, the underlying ratios between species remain stable over a distance of 300 m up to 1 km downstream of the eDNA source, depending on the river discharge rate. In both river transects, we found a delayed peak in eDNA relative abundances, which can be explained by a downstream plume-shaped dispersal of eDNA molecules. The strong decrease in similarity between relative source biomass and corresponding eDNA metabarcoding reads over larger distances, might be attributed to variation in species-specific eDNA persistence. Our findings result in a practical approach to eDNA sampling in waters of comparable scale allowing accurate detection of fish assemblages in riverine systems. Sampling distances of 300 m are recommended with subsamples taken every 25 to 50 m. For an approach directed at single-species detection and management, we propose a modified sampling strategy with increased number of subsamples and replicates.