Testing the methodology and usability of eDNA for detecting fish, crayfish, and mussels

Last changed: 04 March 2025

Water contains fragments of DNA from fish, crayfish and mussels. Can a water sample show which species live in a lake? We test and develop the eDNA method as a complement to traditional environmental monitoring.

What is eDNA?

eDNA, short for "environmental DNA", refers to DNA fragments from organisms present in, for example, water. This DNA can come from living organisms or their parts, such as eggs, sperm, and larvae, as well as from dead materials like feces, mucus, fish scales, or free-floating DNA molecules. In recent years, technology for analyzing eDNA and identifying organisms in water samples has advanced rapidly.

eDNA as a Complement to Environmental Monitoring

There is strong justification for developing eDNA methodology due to its simplicity, accuracy, and cost-effectiveness. This approach can significantly enhance environmental monitoring, particularly for freshwater fish, freshwater crayfish and mussels.

The following areas of environmental monitoring can be supported by eDNA:

  • Species inventory: eDNA can help inventory specific species, such as large mussels, which currently require considerable resources, including expertise, materials, and time. This also applies to diving inventories of species like wels nests.
  • Rare and elusive species: eDNA can detect rare species or those that are underrepresented in traditional monitoring methods.
  • Challenging environments: It can be used in difficult-to-sample locations, such as deep watercourses with poor visibility.
  • Invasive species: eDNA can detect alien species in their early invasion phases, often before they are established. Early detection can help manage control measures before the species become widespread, making management both more cost-effective and easier.
  • Early life stages: Fry and eggs, which are often difficult to identify using conventional methods, can also be detected through eDNA.

eDNA sampling from water is a non-destructive method, both for the environment and for the species involved, making it an increasingly important tool for the future.

The hunt for the pumpkinseed sunfish (Lepomis gibbosus)

In the summer of 2018, the invasive sun perch, or pumpkinseed (Lepomis gibbosus), was discovered in a pond in Kungsbacka, Halland County. A local resident found dead sunfish in a dried-up stream on July 16. Two days later, on July 18, the County Administrative Board of Halland, in collaboration with SLU (Swedish University of Agricultural Sciences), conducted electrofishing at several locations in and downstream of the pond. They discovered large numbers of reproducing individuals in the pond, as well as a live sunfish near the outlet at Lillån River, indicating an increased risk of the species spreading to nearby waters.

Shortly after, the Department of Aquatic Resources (SLU Aqua), was contacted by the Swedish Agency for Marine and Water Management to track the sun perch using eDNA. SLU Aqua led the project, which was completed with the assistance of SeAnalytics in Gothenburg. A few weeks after the discovery, the pond was drained by the landowner under the supervision of the County Administrative Board of Halland County.

Tracking Sun Perch Spread Using eDNA

eDNA technology was employed to track the spread of the sunfish around the Kungsbacka area. Sampling was conducted in Kungsbackaån River, Lillån River, and nearby waterways (Skårsjöån River, Rolfsån River, and the canal connecting Kungsbackaån River and Rolfsån River) during the summer of 2018. The water samples were then analyzed using "ddPCR" (droplet digital PCR), a highly accurate and specific method for detecting low levels of DNA in water samples.

Analysis Results

The analysis results indicated that sunf perch were not present in the sampled waters or enclosures. However, it is important to note that during an electrofishing survey in September 2018, several sun perch were captured approximately 1.5 km downstream from the stocking dam. This suggests an increased risk of the species spreading further downstream into Lillån River/Kungsbackaån River.

Publications

The project is detailed in SLU Aqua's report series (Aqua reports 2018:21 Jakten på solabborren (Lepomis gibbosus) - En eDNA-studie i Kungsbackaån).

For more information about the sunfish, visit the SLU Swedish Species Information Centre.

Tracking Fish, Crayfish, and Mussels in Freshwater with eDNA

Check out the report Water Sampling of DNA from Fish, Crayfish, and Mussels – a comprehensive guide that explains how to effectively track various species in freshwater using water samples.

Facts:

What is eDNA?

  • eDNA, short for environmental DNA, refers to genetic material collected from environmental samples such as water, soil, or air. It includes DNA from living organisms or their parts — such as eggs, sperm, and larvae — as well as from deceased material like urine, feces, mucus, or fish scales.

  • By analyzing the eDNA present in lakes and waterways, it’s possible to track the species of fish, mussels, and crayfish in a given area.

  • Advantages of eDNA: Provides quick and accurate species identification, non-invasive to species and sampling environments, capable of detecting even a small number of individuals in a body of water

  • Disadvantages of eDNA: Does not provide information about population structure (e.g., size, age, sex, or health status), cannot estimate biomass, cannot distinguish between individual organisms or hybrids

Related pages:

Contact

Patrik Bohman, Environmental Monitoring and Assessment Analyst
Department of Aquatic Resources, Institute of Freshwater Research, SLU
patrik.bohman@slu.se, +46 10 478 42 17