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Upper Midwest Environmental Sciences Center

Zebra Mussel Control Research and Evaluation in Minnesota Waters (LCCMR) – Assessing the efficacy of zebra mussel eDNA as a control measure prioritization tool

Principal Investigators: Jon Amberg

Impact of UMESC Science

Results from this study will determine the utility of eDNA sampling as a tool to prioritize zebra mussel control efforts.  This will make it easier for resource managers to find the most dense zebra mussel beds of a water body where treatments can be the most efficient.


Currently, environmental DNA (eDNA) is being used to monitor aquatic invasive species (AIS) throughout the Great Lakes and Upper Mississippi regions. To this point, eDNA survey tools have been primarily used for early detection of the presence of AIS. As researchers have continued the development of new eDNA markers for the detection of other AIS species, the utility of eDNA assays has also changed to answer other research questions such as reproduction, movement, and abundance.

Zebra and quagga mussels (Dreissena polymorpha and D. rostriformis bugensis, respectively) are nuisance species that have plagued areas of the Great Lakes and many inland lakes in the Great Lakes basin. Zebra mussels were first discovered in the Great Lakes Basin in Lake St. Clair in 1988. Quagga mussel discovery came a year later in Lake Erie. Since that time, rapidly expanding populations of zebra and quagga mussels have changed the basis of food webs, primary productivity, benthic community structure, spawning habitat, nutrient cycling, and food availability in ecosystems. These impacts threaten the health of native mussels and fish. Besides ecosystem level effects, they have also cost Great Lakes coastal industries millions of dollars due to clogged and infested intake and discharge pipes.

The mussel life-cycle lends them well to distribution to other bodies of water, and as such has been expanding in range ever since their first discovery. The range expansion of dreissenid mussels within Minnesota lakes and rivers continues (e.g. ~27 lakes were added to the list since 2009, bringing the total to about 90 waters with confirmed or interconnected dreissenid populations) while management agencies lack access to effective tools to control dreissenid mussel populations in open waters. Due to the heavy environmental and economic impacts of these mussels, there is a need for safe and effective control measures to reduce their impacts. The development and use of an eDNA survey tool for zebra mussels may greatly improve identification of application sites and effectiveness of zebra mussel control efforts.

This project is a portion of a larger study funded through the Legislative-Citizen Commission on Minnesota Resources (LCCMR) entitled “Zebra Mussel Control Research and Evaluation in Minnesota Waters”. The overall goal of the LCCMR-funded proposed project is to determine the safety and efficacy of sprayed dried powder (SDP, formulated Pseudomonas fluorescens Pf-CL145A product Zequanox®) for control of dreissenid mussels in limited, high-value Minnesota waters. Detailed maps of two Minnesota lakes, or portions thereof, (1 high and 1 low level infestation) will be prepared using a combination of bathymetric (using high-resolution sonar systems to characterize habitat), physical (to determine zebra mussel densities) and molecular surveys. The maps will be used to correlate zebra mussel populations within the lake to bathymetric and substrate data. Prior to implementation of an eDNA survey and treatment prioritization tool, zebra mussel specific-markers will be developed and a pilot sampling will be conducted to identify the depth of water to be sampled for eDNA collections.  Samples will be collected at several depths including water surface samples and sediment surface samples over multiple established mussel beds. The depth that produces the greatest rate of detection will be used in sampling eDNA for mapping. 

Physical (e.g. divers) surveys will be completed to determine the potential for eDNA as a treatment prioritization and evaluation tool. Transects selected from the bathymetric maps will be used to select sampling location for the eDNA and physical surveys. Samples for eDNA will be collected in the summer while divers are present and the following winter, after freeze over, to evaluate efficacy of winter eDNA detection surveys for zebra mussel infestation.  After the summer sample collection of the eDNA water samples for each location, a ground truthing physical survey will be conducted to determine the abundance of zebra mussels at that location. eDNA detections and quantities will then be correlated to ground-truth physical surveys to establish the efficacy of using a molecular survey tool and collection of water samples as a treatment prioritization method for control of zebra mussels.


  • Design primer and probe sets (i.e. markers) that can distinguish zebra mussels from native mussels.
  • Determine appropriate sampling depth for maximizing detection of zebra mussel eDNA.
  • Determine if a correlation exists between substrate type and zebra mussel density with eDNA Ct values, copy number, and detection rate.


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