Using eDNA as a viable fish monitoring approach in Northern Gulf estuarine habitats

Abstract

Environmental DNA (eDNA) has become an important tool for studying fish presence or absence in aquatic systems. eDNA metabarcoding has been shown to produce fish diversity results comparable to traditional surveys. Environmental factors may influence the detection of fish species and estuarine applications of eDNA methodologies are more limited relative to studies in freshwater systems. In this study, we adapt existing approaches to evaluate the effectiveness of eDNA metabarcoding of fish species in two estuarine systems located in the northwest Florida Panhandle and southwestern Alabama. Sites were located in four distinct estuarine habitats for optimum representation of species present within the study area. In November 2022, mid-water samples were collected using aseptic protocols. Water samples were filtered at the end of the collection day and stored at -70 °C until filtered DNA was extracted, amplified, and sequenced. A set of universal primers was used to amplify DNA material in collected samples. The reference DNA library was amassed using contributed fish species data from national and local resource management programs. Results yielded the identification of 58 fish species, 10 distinct genera, and 13 distinct families. Greater than 80% of identified taxa were characteristic species of the estuarine systems. Eighteen of detected species were freshwater fish known to periodically inhabit tidal marshes. Unexpected species represented less than 5% of all detected species and their presence was found plausible. While more research is needed, findings suggest that an eDNA metabarcoding approach may be adequately generalizable for measuring the prevalence of fish communities in estuarine environments.

Keywords: Environmental DNA; Environmental monitoring; Estuary; Fish communities; Fisheries; Restoration.