Environmental DNA (eDNA) method has been applied to evaluate species distribution, and it has the potential to estimate species abundance/biomass by quantifying the target DNA concentrations in the sampled water. We addressed the applicability of eDNA method to estimate fish abundance/biomass in the field (stream) and mesocosm experiment.
In a stream, we investigated the eDNA concentration of ayu, Plecoglossus altivelis, using quantitative real-time PCR (qPCR) and their abundance/biomass by a snorkeling survey. We evaluated the relationship between eDNA concentrations and the abundance/biomass estimates by snorkeling.
In a mesocosm experiment, we compared the quantification accuracy of a new quantitative PCR technology, droplet digital PCR (ddPCR), to a conventional qPCR. ddPCR partitions PCR reactions into thousands of droplets and detects the amplification in each droplet, thereby allowing direct quantification of target DNA. Both PCRs were applied to quantify eDNA concentrations in mesocosm tanks involving different numbers of common carp, and the quantification accuracy to estimate carp abundance/biomass was compared.
We found significant positive correlations between the eDNA concentration of the fish and their abundance/biomass estimates in the stream across the three seasons, from spring to autumn. This suggests the eDNA method can be used to estimate the species abundance/biomass even in lotic environments (current velocity; 0.43 to 1.09 m s-1).
In the mesocosm study, we found that ddPCR quantified the concentration of the carp eDNA along with their abundance/biomass more accurately than qPCR analysis. Thus, ddPCR is a suitable method to estimate eDNA concentration in the water, and it may provide more accurate results for the fish abundance/biomass than qPCR.