Exploring the secret lives of underwater creatures through DNA

Mobile science aboard Achiever to learn more about coastal waters.

With our Conservation Genetics Lab up and running at the Pacific Science Enterprise Centre, we are excited to begin working on projects that connect our programs at Raincoast. From our Wolf Conservation program, Healthy Waters program, and more, we are working on projects that can glean important information through the use of environmental DNA (eDNA). 

Through fecal material we are beginning to explore the diet of coastal wolves, and our Healthy Waters program is using genetics to identify the source of potentially harmful bacteria in water samples. We piloted the use of eDNA in our lab in 2023 with the help of Achiever and some friends of Raincoast.

Taking samples

Looking over the glassy ocean water of Say Nuth Khaw Yum Provincial Park, Tsleil-Waututh territory, with a view of Granite Falls, it’s easy to forget the plethora of life that lives and flows just below the surface. On a recent journey on our research vessel Achiever, we deployed some hydrophones to test the level of noise that permeates and in some cases dominates the habitat of all the creatures below. Far away from any visible boat we could still distinctly hear the persistent turning of a propeller, louder than any noise we could hear from the torrents of water flowing from Granite falls.

View from the deck of Achiever towards Granite Falls.

It was a sobering demonstration that highlighted the importance of our NoiseTracker project, which will monitor underwater noise along key areas of the BC coast and guide mitigation efforts to lower noise and aid whales and other marine life in a number of meaningful ways.

In the ocean, everything from phytoplankton to whales sheds biological material which can remain in the water column long after they leave. This biological material is full of DNA from the species recently present in the water, and we can capture that to see what has been lurking under the surface. Using a clean disinfected bucket, we scooped water and then used a mobile vacuum pump system to push all that water through a filter with a pore size of less than half a micron. This collected all the DNA and cells containing DNA on the filter. 

Vacuum pump and filter station for eDNA capture.
Filter ready to prep for eDNA analysis.

Analyzing the DNA

Back in the lab we digested a portion of each filter in a solution that helps protect and separate out the DNA for further analysis. We focused on a portion of the DNA that each cell has many copies of (mitochondrial DNA), and we used DNA sequencing to get all of the unique sequences in our samples. The portion of DNA that we focus on is highly diverse between species so we are able to get specific matches to a database with thousands of different DNA sequences. 

Filters digesting to extract DNA.
Purified DNA ready for analysis.

After DNA sequencing the matching process begins, taking every single DNA sequence found in the water samples and matching against the DNA of thousands of species in our database. For some of our DNA sequences, we were able to get an exact match to a known species such as those for Harbour Seal and Blue Mussel. For a small number we got a match that was close but  not exact, which indicates it’s likely a closely related species. A good example of this is our detection of a species with DNA very similar to Nemipterus, a fish found in the Mediterranean. As we build out our database with more analysis this will fill in some of those gaps and identify the true DNA culprit.

With our Genetics Lab fully up and running, we are excited to incorporate eDNA-based studies from our programs at Raincoast to see what else we can uncover from water samples, coastal carnivore fecal samples, salmon samples, and of course more killer whale poop.

You can help

Raincoast’s in-house scientists, collaborating graduate students, postdoctoral fellows, and professors make us unique among conservation groups. We work with First Nations, academic institutions, government, and other NGOs to build support and inform decisions that protect aquatic and terrestrial ecosystems, and the wildlife that depend on them. We conduct ethically applied, process-oriented, and hypothesis-driven research that has immediate and relevant utility for conservation deliberations and the collective body of scientific knowledge.

We investigate to understand coastal species and processes. We inform by bringing science to decision-makers and communities. We inspire action to protect wildlife and wildlife habitats.

Coastal wolf with a salmon in its month.
Photo by Dene Rossouw.