Community-based eDNA metabarcoding for monitoring fish biodiversity and food webs in the Peace-Athabasca Delta

The Peace-Athabasca Delta (PAD) is the largest freshwater inland delta in North America. It holds Outstanding Universal Value (OUV) as part of the Wood Buffalo National Park (WBNP) World Heritage Site (UNESCO). The health of the PAD and its OUV was questioned by the Mikisew Cree First Nation in a petition to UNESCO in 2014. In response, UNESCO directed Canada to take a series of actions to determine if WBNP should be listed as a World Heritage in danger. Canada created the WBNP Action Plan (2018), which included a key action to assess the condition of WBNP's OUV with local First Nations. The waters of the delta have been and remain the habitat of essential fishery resources for the Indigenous Communities in the area. There is, however, limited scientific data available concerning the abundance and distribution of fish, their health, and the structure of the food webs that support them within the PAD. Thus, innovative molecular techniques, such as environmental DNA (eDNA) metabarcoding, can enhance existing capture-based sampling methods for assessing and monitoring freshwater ecosystems. A pilot project was conducted in the summer and fall of 2021 to evaluate the potential utility of molecular tools in addressing key knowledge gaps regarding fish diversity, distribution, and contributing to the collaborative Integrated Research and Monitoring Program's assessment of PAD health. In this context, eDNA metabarcoding methods were employed to assess community diversity from traces of DNA that organisms shed into the aquatic environment or release during digestion (prey DNA). Samples were collected in collaboration with local Indigenous Governments, specifically the Athabasca Chipewyan and Mikisew Cree First Nations' Community-Based Monitoring (CBM) technical staff and the Mikisew Cree Land-Users Advocacy Network (LUAN), Parks Canada, and the Genomic Network for Fish Identification, Stress and Health (GEN-FISH). Using two mitochondrial markers (COI and 12S), eDNA metabarcoding studies detected a combined total of 15 fish species known to inhabit PAD waters, with distinct distributions across the 15 sampling locations. Differential performance in fish detection was observed between the molecular markers used, with 12S providing greater specificity for fish and COI providing broader taxonomic coverage, detecting a diversity of birds, mammals, and invertebrates from the region. Similarly, DNA metabarcoding analysis of stomach contents of Lake Whitefish (Coregonus clupeaformis) detected nine of 19 previously reported diet items, including all the primary known diet items for Lake Whitefish, except Sphaeriids and Pontoporeia. The above results highlight the utility and readiness level of the molecular tools developed by GEN-FISH for conducting fish surveys and assessing food webs in freshwater at sites surrounding Fort Chipewyan.