Optimizing eDNA Monitoring for Multiple AIS: Phase I

Little information exists to guide the development of widespread, multi-species eDNA monitoring for AIS. This project will answer critical questions regarding the optimal amount of sampling effort, timing, sample location, as well as field and laboratory methods for detecting AIS across a range of lake types and AIS abundances. Results will guide the development of protocols and guidelines for widespread monitoring to establish statistically valid estimates of AIS prevalence, and for early detection efforts.

This project will optimize field and laboratory methods for maximizing the detection of AIS from water samples. The project will also take into account the individual lake characteristics and sampling season on AIS detection probability. Researchers will develop protocols for sampling multiple AIS species using environmental DNA (eDNA) and provide recommendations for sampling multiple species simultaneously. The final product will make recommendations about which eDNA sample methods and strategies are optimal when detecting our target aquatic invasive species in Minnesota. This will give managers, AIS specialist, and non-government organizations guidance and confidence when using eDNA as a monitoring strategy. 

Researchers will visit 21 lakes which span a range of abiotic characteristics. These lakes will be sampled repeatedly over the open-water season. They will be able to determine how lake characteristics and species life history interact to influence optimal timing of eDNA sampling for simultaneous detection of multiple AIS. Researchers will also conduct paired tests of filter materials, pore sizes, sample collection locations, and water volumes among five lakes to determine which methods are most efficient at capturing eDNA. Lastly, they will also compare molecular and extraction methods upon a subset of samples.


1) Determine the effects of lake characteristics and sampling season on AIS detection probability, and to

2) optimize field and laboratory methods for maximizing detection probability of AIS from water samples. Researchers will validate and optimize eDNA methods for early detection of zebra mussel, spiny water flea, rusty crayfish, and common carp. Researchers will develop protocols for sampling each species using eDNA, and provide recommendations for sampling multiple species simultaneously. The products will benefit resource managers, lake associations, researchers, and others.


The team created an outreach flier to distribute to interested agency personnel and citizens which describes our project, goals, and PI contact information (view flier here). The flier has made it much easier to describe what the team is doing and gain acceptance by Bands, lake owners, and agency personnel. Dr. Larson (team member at U IL) developed a probe for previously primer-only eDNA assay for rusty crayfish, which will improve specificity for rusty crayfish among populations of other crayfish species. Dr. Larson also traveled to Duluth and St. Paul, MN for hands-on training of NRRI and UMN teams when collecting eDNA water samples, filtering samples, and laboratory practices. In 2021, the researchers visited 15 Minnesota lakes, collecting over 1,500 water samples using various protocols designed to identify method combinations which work best, including what time of year to sample. The samples will be analyzed over the winter for their accuracy in detecting four invasive species known to be present in study lakes (zebra mussels, spiny water flea, rusty crayfish, and common carp). The team will visit an additional eight lakes in 2022.

Project manager: Joshua Dumke

Funded by: Environment and Natural Resources Trust Fund as recommended by the Legislative-Citizen Commission on Minnesota Resources

Project start date: Jan. 2021

Project end date: Dec. 2022

Phase II: Volunteer surveillance of AIS using eDNA