Putting eDNA into action

A round whitefish monitoring program in Lake Ontario

In 2018, Ecometrix participated in a round whitefish monitoring program with NatureMetrics (previously Precision Biomonitoring) to develop a targeted eDNA assay.

Due to the size of Lake Ontario and the potential for a diluted eDNA signal, we tested a variety of collection techniques.

A scientist driving a boat to collect eDNA samples.

These included sampling large volumes along transects as well as in-place collection before, during, and after gillnets were set to capture, quantify, and concentrate the round whitefish.

In doing so, we found that one transect had an eDNA signal 800 times greater than more traditional collection methods, though it’s worth noting there’s a chance this came down to location rather than methodology.

With the collection point situated in a position down-current from the round whitefish habitat, there was a significant positive relationship between samples with the eDNA signal and the number of fish up-current.

With experience in handling both targeted and metabarcoding eDNA strategies, this project allowed Ecometrix to see how different detection methods compared.

With the round whitefish samples assessed using each technique, we ultimately found that the results were similar, but the targeted approach was more sensitive.

A preliminary fish survey to begin fish community characterization

A scientist collecting eDNA using high-throughput eDNA filters and pump.

Ecometrix recently conducted several surveys in an area with minimal prior knowledge.

To complement this information, we used this as an opportunity to determine optimal eDNA detection strategies by testing three key aspects of the eDNA process.

1. Filtration
   Using a new high-throughput filtration system to filter six different volumes of water, from one to 25 litres, in triplicate.
   
2. eDNA isolation and purification
   Tested a popular eDNA extraction method and a newer protocol from existing literature.
   
3. Metabarcoding primers
   Tested three different metabarcoding DNA target locations to ensure all possible fish could be detected.

With this information and the initial fish survey data, we can ensure the future full baseline assessment will be accurate, efficient, and cost-effective.