eDNA

Page reviewed:  20/05/2025

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?

Water contains fragments of DNA from fish, crayfish and mussels. 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 analysing 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.

In the summer of 2018, the invasive species pumpkinseed (Lepomis gibbosus) was discovered in a pond near Kungsbacka in Halland County. A local resident found dead pumpkinseeds in a dried-out stream bed on 16 July. Two days later, on 18 July, the County Administrative Board of Halland, together with SLU Swedish Species Information Centre, conducted electrofishing at several sites in and downstream of the pond. Numerous reproducing individuals were found in the pond, along with a live pumpkinseed near the outflow at Lillån, which posed an increased risk of the species spreading to nearby waters.

Shortly thereafter, the Department of Aquatic Resources (SLU Aqua) was contacted by the Swedish Agency for Marine and Water Management in an effort to trace the pumpkinseed using eDNA. SLU Aqua led the now-completed project in collaboration with SeAnalytics in Gothenburg. The pond near Kungsbacka was emptied by the landowner under the supervision of the County Administrative Board of Halland a few weeks after the discovery.

eDNA can trace the spread of the pumpkinseed

Using eDNA technology, we are able to trace the movement of pumpkinseed in the Kungsbacka area. Water samples were collected during the summer of 2018 from Kungsbackaån, Lillån, and nearby watercourses (Skårsjöån, Rolfsån, and the canal between Kungsbackaån and Rolfsån). These samples were later analysed using ddPCR. ddPCR stands for 'droplet digital PCR', a highly precise and specific method for detecting very low concentrations of DNA in water samples.

Results of our analyses

The results of our analyses showed no presence of pumpkinseed in the waters and pools sampled for eDNA. However, it should be noted that during an electrofishing session in September 2018, several pumpkinseeds were caught approximately 1.5 km downstream from the original release pond. This indicates an increased risk of the species spreading further downstream into Lillån/Kungsbackaån.

Publications

The project has been published in SLU Aqua’s report series ("The Hunt for the Pumpkinseed (Lepomis gibbosus) – An eDNA Study in the Kungsbacka River, in Aqua reports 2018:21).

Read more about the pumpkinseed at SLU Swedish Species Information Centre.

Recent reports and summaries of current knowledge

  1. The report eDNA i en droppe vatten: vattenprovtagning av DNA från fisk, kräftor och musslor: en kunskapssammanställning  Provides practical guidance on detecting various freshwater species in a water sample.
  2. Jakten på solabborren (Lepomis gibbosus): en eDNA-studie i Kungsbackaån

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