Högskolan i Skövde

The invasive Chinese Mitten Crab, Eriocheir sinensis, poses an increasing ecological risk in Swedish waters, prompting the need for effective detection methods. This study aimed to detect E. sinensis using environmental DNA extracted from controlled aquarium setups and field sediment samples from Lake Vänern, employing both qPCR and Nanopore sequencing. Effectiveness of water and sediment as matrices for recovery and detection of E. sinensis eDNA was evaluated. Aquarium experiments revealed unpredictable variability in DNA concentrations due to complex DNA dynamics likely influenced by both biotic and abiotic factors. Water samples consistently showed higher DNA concentrations, potentially influenced by the sediment type and the agitation performed before sampling, and better qPCR detection rates compared to sediment samples. Although sediment yielded less DNA here, it remains promising as a complementary matrix because DNA can adsorb to particles and persist, potentially integrating signals over longer periods; with optimized extraction and inhibitor mitigation, sediment may improve site-level detectability. Although Nanopore sequencing demonstrated substantial potential for eDNA analysis due to its portability and PCR-free approach, limitations were observed, including low data output, classification errors, and dependency on high-quality, comprehensive reference databases. The qPCR approach emerged as a more reliable, practical, and cost-effective method for targeted E. sinensis detection. Field sampling, performed in known hotspots during the low-activity spring season did not yield any definitive detections with either method. Future research should focus on optimizing sample processing, improving reference databases, and exploring more sensitive and specific molecular detection technologies.