Optimization of environmental DNA collection and extraction techniques for early detection of aquatic invasive species
In my thesis, I focused on improving environmental DNA (eDNA) detection sensitivity for aquatic invasive species (AIS) through methodology optimization. I compared two eDNA storage and extraction techniques to detect three common AIS. One method involved storing samples in ethanol and extracting DNA using a Qiagen DNeasy Powersoil Pro Kit. The other method used cetyl trimethylammonium bromide (CTAB) for storage and phenol-chloroform-isoamyl (PCI) DNA extraction. CTAB-PCI yielded significantly more detections across species compared to ethanol-Qiagen. Additionally, I discovered that using 1µl of DNA template in qPCR reactions was equally effective as 3µl. Furthermore, I investigated the effect of crayfish molting on eDNA detectability and particle size distribution, observing higher detectability before molting but a significant increase in detections over time post-molt and a predominant DNA particle size >5µm. These findings provide insights for eDNA-based monitoring and highlight the need for further research to optimize methods for different species and environments.
