Comparison of Environmental DNA Detection Using qPCR and ddPCR
Detection of environmental DNA from marine invasive species can be done using quantitative Polymerase Chain Reaction (qPCR) and droplet digital Polymerase Chain Reaction. Here we compare these two platforms for 17 very different organisms and show that ddPCR provides higher precision and can reduce sample analysis time.
About the project
Detection of environmental DNA (eDNA for short) can be done with qPCR and ddPCR, where ddPCR for detection of DNA from viruses or bacteria in human pathological studies has been demonstrated to be more accurate compared to qPCR-based detection of eDNA. In this study, the aim is to elucidate whether such increased precision also applies to the detection of eDNA from marine non-indigenous (invasive) species. Here, the same 48 extractions of eDNA from filter water samples collected in 2021 are analysed with both qPCR and ddPCR for the presence of 17 different non-indigenous marine species. It can be concluded that for the rare marine invasive species, the ddPCR platform has a better chance of detecting very low levels of eDNA. For 17 out of 19 tested species-specific detection systems on the ddPCR platform, eDNA detection was as accurate as on the qPCR platform if sufficiently high levels of eDNA are present in the water sample. For low levels of eDNA, the ddPCR platform was better at assessing uncertainty in eDNA concentration than qPCR. With reduced labour time for ddPCR setup compared to qPCR, it is recommended to use ddPCR for future monitoring of eDNA from marine invasive species to achieve better precision and reduce labour time.