Fisheries management, Invasive species management, Research
Metabarcoding Early Detection and Monitoring Program
Status
Ongoing

States

Illinois, Indiana, Michigan, Minnesota, New York, Ohio, Pennsylvania, Wisconsin

Subject

Fisheries
Fisheries management
Research
Science

The Whitney Genetics Lab and Northeast Fishery Center are partnering to utilize large-scale metabarcoding as another method in the Great Lakes Early Detection and Monitoring program. This initiative is designed to improve the efficiency of the U.S. Fish and Wildlife Service to detect aquatic invasive species invasive species
An invasive species is any plant or animal that has spread or been introduced into a new area where they are, or could, cause harm to the environment, economy, or human, animal, or plant health. Their unwelcome presence can destroy ecosystems and cost millions of dollars.

Learn more about invasive species early in a potential invasion.

What is Metabarcoding?

Metabarcoding eDNA is a method that allows biologists to simultaneously identify many taxa from a single sample. For the Early Detection and Monitoring Program, metabarcoding will allow geneticists to amplify a portion of the mitochondrial DNA to potentially identify the species of fish that had DNA collected in an environmental sample. 

The image shows the process of DNA Metabarcoding from DNA strands in a water sample, extraction of DNA from the sample, PCR amplification of all fish species DNA, and lastly the identification of all fish species DNA found in the sample.
Image Details
Samples are collected and sent to the lab. DNA is extracted from the sample similar to qPCR. The lab uses PCR to amplify all the fish DNA found in the sample. Amplified DNA is then sequenced and compared to a reference sequence database to identify all the fish species that had amplified DNA in that sample.

Benefits of metabarcoding

  • Allows biologists to identify many species with one sample, which is more efficient when looking for multiple species.
  • With the understanding of which fish species might be present from metabarcoding results, field personnel can equip themselves with the appropriate traditional gear tailored to the specific types of fish they are targeting. The success of capturing a live fish is often contingent upon utilizing correct equipment, as the choice of gear varies based on factors such as fish size, habitat preferences, and behavioral characteristics. A targeted approach significantly improves the likelihood of successful species capture.
  • Environmental sampling for metabarcoding can be less time intensive, more sensitive, and less intrusive than traditional sampling techniques.

What stage of development is the Metabarcoding Early Detection and Monitoring program in right now?

  • The Metabarcoding Lab at the Whitney Genetics Lab has just been constructed and is now processing samples.
  • Lab techniques have been finalized and Standard Operating Procedures are being written on lab procedures.
  • We continue to build and improve reference DNA libraries.
  • Field offices and other partners are testing metabarcoding sample collection, standard operating procedures, and reporting protocols.
A pristine lab for metabarcoding
Image Details
The Metabarcoding Lab built in 2024 housed within the Whitney Genetics Lab.

Facilities

PCR machine with blue strand of DNA
Whitney Genetics Laboratory
The Whitney Genetics Laboratory specializes in high-throughput environmental DNA processing for monitoring aquatic invasive species through its Invasive Carp eDNA Monitoring and Genetic Surveillance of Invasive Species programs. Lab staff participate in development of new scientific methods to help...
Conservation Office
Onalaska,WI
A blue sky with clouds as the sun shines on the upper Mississippi River with green bluffs in the distance.
Midwest Fisheries Center
The Midwest Fisheries Center is the region’s Fish Technology Center for the U.S. Fish and Wildlife Service. Fish Technology Centers provide leadership in science-based management of trust aquatic resources through applied research and the development of new concepts, strategies and techniques to...
Conservation Office
Onalaska,WI
A cisco fish with coloring dusky gray to bluish on the back, silvery on the sides, and white on the underside being held laying on its side across two hands.
Northeast Fishery Center
The Northeast Fishery Center (Center), located in Lamar, PA includes the Lamar Fish Health Center and the Lamar National Fish Hatchery and Fish Technology Center. We help guide and conduct the science and technology needed to restore and conserve species and their habitats. Our research helps...
Conservation Office
Lamar,PA

Contact

Initiatives

boat with service employees electrofishing with multiple fish jumping out of water
Aquatic Invasive Species
Aquatic invasive species cause tremendous harm to our environment, our economy, and our health. They can drive out and eat native plants and wildlife, spread diseases, and damage infrastructure. We work to protect our waterways and the communities that depend on them from the threat of invasive...
Initiative
Invasive Species

Programs

A man is fishing in a boat with three young girls. The kids are excitedly pulling a fish out of the water.
The Fish and Aquatic Conservation programs work together to deliver resilient habitats, healthy fish, connected people, and strong partnerships. From habitat restoration to aquatic invasive species prevention, captive breeding to population assessment and monitoring, our programs are driven by the...
Program
Falls Church,VA
Silver Carp Jumping
Aquatic invasive species cause tremendous harm to our environment, our economy, and our health. They can drive out and eat native plants and wildlife, spread diseases, and damage infrastructure. We work to protect our waterways and the communities that depend on them from the threat of invasive...
Program