Measuring eDNA concentrations

Evaluations of species distribution and biomass are fundamental in studies on the population dynamics and community structure of an ecosystem. Recently, methods using eDNA were used to identify and track organisms in various aquatic ecosystems, such as lakes/ponds, rivers, and oceans. However, no quantitative eDNA technique has been fully established, because there are methodological limitations to quantifying eDNA concentrations.

A group of Japanese researchers now claim that they used a recently developed new PCR technology to quantify eDNA concentration in eDNA studies. 

Droplet digital PCR (ddPCR), also known as a “third-generation” PCR, is an emerging DNA detection method that provides absolute quantification of target DNA without a standard curve of the reference. DNA is partitioned into approximately 20,000 droplets, some of which ideally contain one or few copies of the target DNA. The PCR occurs in each droplet, and end-point PCR amplification is detected using fluorescence probes.

The colleagues used eDNA from mesocosm experiments with different numbers of common carp to evaluate the quantification accuracy of qPCR and ddPCR when estimating species abundance and biomass. They found that ddPCR quantified the concentration of carp eDNA relative to carp abundance and biomass more accurately than qPCR, especially at low eDNA concentrations. In addition, errors in the analysis were relatively lower with ddPCR than with qPCR. 

The researchers conclude that in the future this technique could be applied for habitat research on rare or non-native species in the field, because the eDNA recovered for target species from field samples typically occurs in very low concentrations. 

We showed that the relationship between carp abundance and eDNA concentration was higher than that between biomass and eDNA using both ddPCR and qPCR. Therefore, ddPCR can be used to quantify eDNA concentration in water. However, ddPCR is currently more expensive and time consuming compared to qPCR and in natural habitats, eDNA estimation for organism abundance is more complex. Therefore, by using multiple technologies, we can develop better eDNA methods to evaluate the distribution and abundance/biomass of species and communities.