Conventional fish monitoring requires considerable investments of equipment and labour, and often harmful techniques. Emerging methods allow detection of aquatic animals by collecting water and extracting DNA that has been shed to the environment (eDNA). Present knowledge gaps include minimum densities necessary for consistent detection, and persistence of eDNA after a target species has left a site.
We conducted two experiments at a salmon hatchery in British Columbia to answer these questions. Water samples were taken from flow-through tanks with juvenile coho salmon densities ranging from 35.7g/kL to 0.5g/kL. To simulate field surveys in recently abandoned habitats, we sampled water from tanks after removing fish, at flow-through volumes ranging from 20kL to 160kL (effective fish densities of 1.2g/kL-0.2g/kL). Water samples were filtered and the eDNA trapped, isolated, and analyzed for presence of coho DNA by PCR and gel electrophoresis.
We also undertook a field validation of the method at five streams in the Great Bear Rainforest of BC. Water samples were taken from each stream and tested for presence of coho salmon and salmonid (coastal cutthroat trout) eDNA. Results were compared to those from conventional monitoring techniques for consistency of detection, as well as sampling effort.
Results/Conclusions
In the tank experiments, water samples from tanks containing one or more fish tested positive for coho DNA at least 70% of the time, increasing at higher densities. Samples taken after removing the fish had detection probabilities of 66% and 40% at respective flow-through volumes of 20kL and 40kL. Coho detection failed at flow-through volumes greater than 40kL (effective density lower than 0.6g/kL).
In stream samples, all sites with coho or salmonid presence confirmed by traditional trapping also tested positive for target species’ eDNA. One site tested positive for coho eDNA where conventional methods failed, indicating a possible higher sensitivity of eDNA sampling. We also mapped the distribution of juvenile coho salmon through multiple tributaries of a productive salmon system with conventional and eDNA detections.
This study improves on an emerging method with a new species by addressing existing uncertainties regarding eDNA detection threshold, and signal persistence through dilution in a simulated freshwater habitat. It also demonstrates that eDNA methods can be used to assess coastal streams for juvenile salmonid presence.