Embracing a new eDNA technology

November 22, 2018 Jake Riley

New sampling approach helps to detect the presence of rare aquatic species—in real time

 

What do human beings, Jefferson salamanders, and Atlantic salmon have in common? They all contain deoxyribonucleic acid—DNA—in each cell. All living organisms expel unique genetic material into their environment. We call this matter environmental DNA (eDNA).

When it comes to fish and other aquatic species, eDNA is shed through the skin, feces, urine, blood, body, eggs, or sperm into the water they inhabit. By sampling the water and analyzing this eDNA, we can detect the presence of a species we’re specifically looking for (also known as the target species).

Right now, our planet is facing a biodiversity challenge and some tough realities with regards to rare and endangered species. Globally, countless numbers of plant and animal species face extinction. Populations of some living organisms have declined at an alarming rate. It’s our job to help our clients monitor where these remaining species are to meet regulatory requirements for protection, as well as help design projects that reduce or avoid impacts to these species.

 

By sampling the water and analyzing this eDNA, we can detect the presence of a species we’re specifically looking for (also known as the target species).

 

A progressive technology

How does eDNA stack up against more conventional methods for observing and detecting aquatic species, such as gillnets and electrofishing? These conventional methods can take a long time, are more expensive, and can harm the target species and their habitat. This is where new eDNA technology provides an advantage. 

Testing for eDNA is by no means a new scientific method—it’s been around for about 10 years in research institutions. What’s new is how we sample and analyze for eDNA. Working together with the University of Guelph and Precision Biomonitoring, we are deploying a hand-held Point of Need tool to sample, extract, and analyze eDNA for the presence of target species in the field. This new tool allows us to produce accurate scientific results, in real time. And now, instead of waiting for eDNA test results to come back from a lab, we can get results live in the field—in less than two hours.

eDNA has proven reliable at detecting rare species at low densities—it helps us in cases where we’re searching for species that are hard to find. The method is also advantageous because, compared with conventional methods, sampling for eDNA is:

  • more sensitive
  • cost-effective
  • safer for both species and field staff
  • less harmful to environment
  • more objective for identifying species

Our hand-held Point of Need tool brings this reliable technology into the field with our biologists. We also combine this with lab-based testing to confirm species identification.

 

Results from the field

Working with our partners, we have developed tests for 20 species for use in the Point of Need tool. Notable studies thus far include the Jefferson salamander, an endangered species in Ontario, and the Atlantic salmon, whose status is endangered under the Endangered Species Act in the US and is also protected in Canada.

_q_tweetable:With the ability to detect rare species without catching or seeing them—the future is in the palm of your hand._q_

In 2017, we tested 10 sites for the Jefferson salamander. 9 out of 10 test sites confirmed historical data of species presence or absence, based on visual surveys in early spring. However, eDNA testing at one site showed that Jefferson salamander was present when past visual surveys indicated that it was absent.

Similarly, we sampled five stream sites for Atlantic salmon in 2018 using eDNA. We didn’t detect Atlantic salmon in the streams; however, we did detect eDNA downstream from our positive field control—a single caged Atlantic salmon—confirming that the eDNA Point of Need tool was working. 

Our work has shown that the Point of Need tool for eDNA is delivering on its promise as a fast, cost-effective, sensitive tool for detecting the presence of rare, threatened, and endangered species at low densities in the environment.

 

Testing for eDNA is by no means a new scientific method—it’s been around for about 10 years in research institutions. What’s new is how we sample and analyze for eDNA. 

 

Key factors for successful results

Detecting eDNA in the aquatic environment depends on several factors when setting up a sampling design. The strength of the eDNA signal will depend on how recent the target species was present and how long the species was there. Population density and lifecycle stage also factor in because they can influence how much eDNA is present in the water body. Water quality can also play a role in degrading eDNA, so filtering and analyzing for eDNA on-site with the Point of Need tool helps manage this issue. Lastly, the flow rate of the aquatic environment plays an important role. Whereas a small pond or lake will likely hold eDNA longer, a running river is more likely to transfer remnant eDNA downstream.

To maximize our probability of success, we take the following into consideration when setting up a sampling plan:

  • Questions that the client needs to address
  • Quality control – positive/negative field controls, and back-up lab eDNA tests
  • Site selection, spatial distribution, sample volume, and sample number
  • Ecology and history of the species
  • Season

Once we have the water samples in hand, we filter onsite. Then we either analyze them ourselves with the Point of Need Tool in the field or preserve the filters and send them off to a lab that is qualified to do eDNA testing. We are setting up relationships with labs in Canada and the US to serve our needs.

 

Our work has shown that the Point of Need tool for eDNA is delivering on its promise as a fast, cost-effective, sensitive tool for detecting the presence of rare, threatened, and endangered species at low densities in the environment.

 

Heading forward

We are moving ahead with more applications of eDNA in the field to address client questions. We are learning, adapting, and embracing eDNA tools to provide reliable services about the presence of rare species in the field. We are using and planning for eDNA tools to detect shortnose sturgeon, bull trout, Arctic grayling, burbot, and striped bass. We’re excited to continue developing tests for other species to expand overall use of eDNA tools for detection of species.

Our goal? To help our clients meet their regulatory requirements effectively and efficiently while reducing costs and avoiding harmful impacts to rare species. Using a cool new sampling method to help detect rare species is just icing on the cake!  

Got an interest in using eDNA? Send a message to eDNA@stantec.com and we’ll get back to you to start planning.

About the Author

Jake Riley

Jake Riley is a project manager and fisheries biologist with over 13 years of experience in endangered freshwater aquatic species and fish habitats. His ability to work collaboratively with stakeholders and agencies of diverse backgrounds enables him to build effective project teams. Jake is an invaluable partner to our clients, as he brings scientific expertise to develop solutions that meet both project goals and agency requirements.

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