Data from: Reduced sampling intensity through key sampling site selection for optimal characterization of riverine fish communities by eDNA metabarcoding

Effective conservation management of river systems requires a
comprehensive understanding of local and regional biodiversity,
necessitating accurate characterization of species communities.
Environmental DNA (eDNA) metabarcoding has emerged as a pivotal tool for
assessing aquatic organisms, especially fish communities. However, optimal
sampling resolution and site positioning to obtain robust fish diversity
indices across heterogeneous river systems remain inadequately understood.
This study empirically evaluates the optimal number of eDNA samples needed
to accurately capture diversity both locally and stream-wide across three
distinct river systems, comparing eDNA metabarcoding results to
traditional electrofishing data. Habitat and landscape factors were
characterized to interpret the localisation of key sampling sites
contributing most to the overall species richness. We detected 30 fish
species via eDNA metabarcoding, compared to 28 species by electrofishing,
with eDNA requiring fewer sampling sites per river system. To reach ≥95 %
of the estimated species richness, eDNA analyses required between one and
nine sites across three river systems spanning ten kilometres each. In the
most diverse river, a single eDNA sampling site even achieved a higher
species richness (n = 20 species) compared to the nine required sites to
reach ≥95 % of the estimated species richness via electrofishing (n = 9
species). To account for eDNA particle dilution and degradation over
larger distances (>1 km), sampling at both upstream and downstream
sites may be crucial, with strategic site selection further refined by
factors like adjacent stream inflows, substrate type, and river discharge
rate, all of which influence species-specific habitat occupancy. On a
smaller scale, the location of key sampling sites only moderately differs
within 100-meter transects therewith informing on the precise placement of
those sampling sites. Our work highlights the robustness and
cost-effectiveness of eDNA analyses for riverine biodiversity assessment,
demonstrating strong potential for enhancing various conservation
practices.