Data from: Next-generation freshwater bioassessment: eDNA metabarcoding with a conserved metazoan primer reveals species-rich and reservoir-specific communities

Freshwater habitats are of high conservation value and provide a wide
range of ecosystem services. Effective management requires regular
monitoring. However, conventional methods based on direct observation or
specimen collection are so invasive, expensive and labour-intensive that
frequent monitoring is uncommon. Here, we test whether the evaluation of
environmental DNA (eDNA) from water based on a simple protocol can be used
for assessing biodiversity. We use universal metazoan primers for
characterizing water eDNA across horizontal and vertical spatial
dimensions in two reservoirs with known species diversity for two key
taxa. eDNA obtained directly from 42 samples × 15 ml water
(total = 630 ml) per reservoir yielded DNA signatures for more than 500
metazoan species, of which 105 could be identified to species/genus based
on DNA barcodes. We show that eDNA can be used to assign each water sample
to its reservoir of origin, and that eDNA outperforms conventional survey
methods in single-sample richness comparisons, while revealing evidence
for hundreds of unknown species that are undetected by conventional
bioassessment methods. eDNA also confirms the presence of a recently
discovered invasive snail species and provides evidence for the continued
survival of a rare native species of goby not sighted in that habitat
since 2007. eDNA thus promises to be a useful addition to the
bioassessment toolbox for freshwater systems.