eDNA to measure fish abundance in a lake

Environmental DNA (eDNA) allows us to detect the presence of organisms without direct observation. Plants and animals shed cellular material in their surrounding environment, and this material can be collected and analyzed. Traces of DNA extracted from environmental samples can be used to determine if a target species has been in the vicinity of a sampling site.

As a consequence an increasing number of studies applies methods using eDNA to identify and track organisms in various aquatic ecosystems, such as lakes/ponds, rivers, and oceans. However, a major challenge is to develop a technique to quantify eDNA concentrations and thereby determine not only an organisms presence but also its abundance.

A team of researchers of the Université Laval and supervised by an old friend, Louis Bernatchez, tested the capability of eDNA techniques to measure abundance with some lake trout populations in 12 southern Quebec lakes. For comparisons with traditional methods the colleagues used lake trout population estimates obtained by their colleagues at Quebec's Ministry of Forests, Wildlife and Parks. This method consists of estimating entire lake populations by extrapolating from the number of fish captured using nets deployed in different parts of the body of water. This method is often time and labor intensive, in addition to having a potentially negative effect on fish populations.

To measure the concentration of lake trout eDNA, the researchers took approximately 10 one-liter samples of water from different areas of each lake studied. They then filtered the water and subjected the particles retained to qPCR analysis of a small COI Barcode fragment in order to accurately measure the quantity of lake trout DNA.

The results showed a strong correlation between population estimates obtained using the traditional approach and those based on eDNA concentration. Variations in eDNA abundance in different parts of each lake are also similar to those reported for net catches.

Our results indicate that eDNA may additionally be used to quantify fish relative abundance in lakes. From a fisheries management perspective, such eDNA analyses represent a new step towards improving spatial and temporal coverage of population assessment and monitoring while being less invasive, less time-consuming and less expensive. While resources generally support the survey of only a few lakes per year using the gillnet method, here eDNA sampling covering southern Québec was achieved in seven sampling days and required two technicians working on average <2 h to cover an entire lake.

The colleagues are continuing their work to extend their method to other target species that are of interest for fishing, such as walleye, sauger, brook trout, Arctic char, and northern pike, but also for a number of rare or threatened species as well as invasive exotic species.