Quantitative monitoring of diverse fish communities on a large scale
combining eDNA metabarcoding and qPCR
Abstract
eDNA metabarcoding is an effective method for studying fish communities
but allows only an estimation of relative species abundance (density /
biomass). Here, we combine metabarcoding with an estimation of the total
abundance of eDNA amplified by our universal marker (teleo) using a qPCR
approach to infer the absolute abundance of fish species. We carried out
a 2850 km eDNA survey within the Danube catchment using a spatial
integrative sampling protocol coupled with traditional electrofishing
for fish biomass and density estimation. Total fish eDNA concentrations
and total fish abundance were highly correlated. The correlation between
eDNA concentrations per taxon and absolute specific abundance was of
comparable strength when all sites were pooled and remained significant
when the sites were considered separately. Furthermore, a non-linear
mixed model showed that species richness was underestimated when the
amount of teleo-DNA extracted from a sample was below a threshold of
0.65.106 copies of eDNA. This result, combined with the decrease in
teleo-DNA concentration by several orders of magnitude with river size,
highlights the need to increase sampling effort in large rivers. Our
results show a comprehensive description of longitudinal changes in fish
communities and underline our combined metabarcoding/qPCR approach for
biomonitoring and bioassessment surveys when a rough estimate of
absolute species abundance is sufficient.