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Environmental DNA and Fish Detection

Monitoring resident and juvenile freshwater salmonids with waterborne DNA

Project Leads and Contributors: Jeff MacAdams, Morgan Hocking, Ben Koop, Amber Messmer, Peter McCully, Brian Starzomski 



Conventional monitoring of stream fish requires methods that are often harmful to the animal, as well as considerable investments of time and taxonomic expertise. New methods have recently emerged that allow detection of aquatic animals simply from collecting stream water and extracting their DNA that has been shed to the environment (eDNA). Our objective is to determine if this method can be applied quantitatively to monitor freshwater fish populations, specifically salmonids. The key questions are: what is the detection threshold of eDNA? How do detection threshold and abundance estimates from eDNA methods compare with those made by conventional methods? What effect do hydrologic and biogeochemical factors (eg, stream discharge, DOC, acidity) have on the dispersal and deterioration of eDNA in streams?


Background: Environmental DNA is an emerging technique for biodiversity monitoring and detection of cryptic and elusive species by identifying the DNA that animals have shed to the environment. In freshwater systems, it entails collecting water samples directly from a stream or lake, and trapping the eDNA that remains in suspension. The technique minimizes time and effort required for conventional field methods, as well as associated stress and mortality from unnecessary handling. It has also proven more sensitive for detection at low densities than conventional methods. Streams on Calvert and Hecate Islands span the physiological limits of Salmon and therefore, extremely low Salmon densities are found in several of these streams. Developing eDNA methods for Pacific Salmon could be instrumental in an expansion of monitoring capacity.

Methods: After collecting 2L water samples, vacuum filtration through a very fine membrane (<1µm) captures the DNA. It can then be isolated following common DNA extraction protocols. Taxon or species specific target DNA fragments are then amplified using PCR. Post-amplification product is sequenced to confirm species identities and community composition. eDNA can be quantified with real-time PCR, which then can offer abundance estimates by comparing eDNA quantity with a fish density ~ eDNA model in development with field experiments.

An element of the Kwakshua Watershed Program: Environmental conditions can be primary drivers of aquatic community composition and ecosystem productivity. Research in aquatic biogeochemistry of nutrient and organic matter cycling can reveal watershed level effects on stream communities. Biogeochemical and hydrologic effects are also known to influence the persistence of eDNA in aquatic systems due to DNA degradation, and dilution and dispersal with high stream flows. Monitoring these stream characteristics can inform eDNA monitoring of aquatic communities. 

Progress Updates:  In 2013 we completed fish and invertebrate community inventories, stream habitat assessments in Kwakshua watersheds, and comparison of watershed productivity with invertebrate size spectra. In 2014 we had successful eDNA fish detections in several Kwakshua streams, finding high correlation of fish detections between eDNA and conventional methods. We documented juvenile salmon and other fish species in higher reaches of Big Spring Creek and watershed 1015.

Related Programs
Kwakshua Watersheds Program
With this program we seek to understand and model the flux of terrestrial materials from land to sea.