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Aquatic species monitoring using eDNA: ecological detective work

By Francis LeBlanc, Aquatic Science Biologist

eDNA sampling for the detection of Brook Floater in New Brunswick rivers. Photo credit: Francis LeBlanc/DFO

Aquatic species do not always need to be seen to be detected. This is because all organisms, including whales, fish and lobsters, release DNA into their environment by shedding cells and other biological material. This trail of DNA is known as environmental DNA, or eDNA, and species can be identified from their unique DNA signature.

It’s unique and oh-so-easy

In the same way grocery items are assigned unique barcodes, biologists can identify various species based on their DNA “barcodes.” Specific sections of DNA can be used as barcodes because they are specific to individual species. Atlantic salmon, for example, have a different DNA barcode than brook trout. By collecting DNA from the environment and looking at the DNA barcodes that are present, we can determine the species that live within an ecosystem.

The eDNA sampling method isn’t complicated and can be as simple as filtering a litre of water using a filter paper to collect cells, microscopic organisms and even free-floating DNA. Inexpensive equipment and a small handheld vacuum pump that can fit in your backpack is all you need. The filters with the trapped DNA can then be sent to a DNA laboratory for testing. Alternatively, some companies now offer handheld devices that work as portable DNA detectors that can be used in the field to tell you what species are present.

Did you know?

  • The idea of a standardized DNA region for species identification, or DNA barcode, was started in Guelph, Ont., in 2003.
  • Different sections or regions of DNA are often used to identify different branches of the tree of life. For example, part of the COI gene is used to identify most animals; 16S is used for bacteria; and rbcl and matK are used for most plants.

Why it’s helpful

At Fisheries and Oceans Canada in the Gulf Region, we use eDNA to detect rare and endangered species such as the Brook Floater, a type of freshwater mussel, in order to identify critical habitat. Another important eDNA application is as an early detection and monitoring tool for aquatic invasive species that might cause significant damage to native species and their habitats. Identifying aquatic invasive species as early as possible enables us to put in place mitigation measures to minimize their spread and potential harm to native species.

More recently, we started evaluating the use of eDNA concentrations to estimate the abundance of fish species, including Atlantic salmon and striped bass. Using eDNA in this context could provide an additional tool to help with species stock assessments, which are crucial to making sound management decisions.

The continued use of eDNA for these various applications and anticipated advances has the potential to revolutionize the way aquatic species are monitored, as well as to provide crucial information for the conservation and management of our important aquatic resources. Given the ease of eDNA sampling and the fact that you do not need specialized training, this technique allows us to involve and engage citizens and community groups in the monitoring of aquatic species that are important to Canadians.

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