Environmental DNA applications: developing species-specific qPCR assays for New Brunswick freshwater fishes

Background/Question/Methods

Canadian freshwater fishes are a highly diverse group of vertebrates that have experienced catastrophic population declines. To monitor and protect declining populations, conservation efforts have been made through traditional capture-based methods. However, these techniques are often labour-intensive, time-consuming, and invasive to the environment. The use of environmental DNA (eDNA) has emerged as a new monitoring tool for Canada's freshwater fishes. eDNA is deposited in the environment by target organisms through skin, scales, faeces, or mucus. The molecular tool used to analyze eDNA is quantitative polymerase chain reaction (qPCR). It relies on the use of short DNA sequences called primers and probes, together known as assays, to bind to DNA unique to each fish species. There is currently a lack of robust, specific, and sensitive qPCR for Canadian freshwater fishes. This project has two objectives to address this gap. The first is to develop species-specific qPCR assays to detect 20 Canadian freshwater fishes found in New Brunswick. The second is to test the assays on eDNA samples from freshwater systems where the species is known to occur to prove efficacy and utility as a monitoring tool.

Results/Conclusions

We present species-specific qPCR assays that have been developed thus far during the two year project. These results include assay development techniques, qPCR protocols, primers, and TaqMan MGB probe sequences. These assays strongly amplified DNA from target species and produced no off-target amplification of DNA from other commonly found species in New Brunswick. We discuss further initiatives regarding the testing of these assays on eDNA samples taken at Fundy National Park in New Brunswick. This project aims to create a set of eDNA tools for sensitive, non-invasive, and practical monitoring of Canadian freshwater fishes found in New Brunswick. Through the creation of qPCR assays, this project will significantly complement traditional surveying methods to allow for more robust and accurate assessments of these freshwater fish species. These resources will not only allow for improved monitoring practices in New Brunswick, but also throughout the broader geographic ranges where these species are found. The use of eDNA has and will continue to enhance the ways in which we monitor freshwater fishes. These enhancements will further promote the sustainability of fish populations as it extends to the health of freshwater ecosystems locally and globally.