Finding traces of fish with DNA from water samples

Silje Halvorsen bends down and fills a plastic bottle with water from Gillsvannet lake, a sheltered bathing spot just outside the center of Kristiansand.

This is something she has done many times before. In 2022, she took monthly water samples from fourteen locations in the lake, and then every three months until October 2023.

The goal? To find traces of pike and other species that may be in the lake. Pike don’t naturally belong in Gillsvannet, and the authorities wanted to eliminate them.

Traditionally, researchers have used nets, fishing rods or traps to determine what kinds of fish inhabit a body of water. This approach can be costly and time-consuming, and it may harm the fish.

“Collecting a water sample takes only a few minutes and does not disturb the fish. The method is also the most sensitive. It can provide information about which species were present in a lake or stream at the time the sample was taken,” says Halvorsen.

Her doctoral thesis focused on environmental DNA.

DNA is genetic material found in the cells of all living organisms. It serves as a blueprint for how the individual grows, looks and functions. Every human, fish, or bacterium has its own unique blueprint, but these become more similar the closer they are genetically related.

Environmental DNA is genetic material left by organisms in the environment in the form of cells from skin, hair or other tissues.

Kills everything

Authorities in Kristiansand decided that Gillsvannet should be treated with the toxin rotenone to eliminate the pike. This kills all animals that breathe with gills in the water—not just pike, but also other fish and some insects. It is a drastic treatment that is not carried out often.

As a researcher, Halvorsen wants to observe what happens to wildlife before, during and after the treatment.

“We haven’t found other studies looking at the entirety of how a fish community reacts to such treatment. Typically, only the one species you want to get rid of is examined,” Halvorsen says.

Like a coffee filter

A day in the field is over, and 14 liters of water from Gillsvannet stand on the bench in the laboratory.

To extract all the small particles from the water, Halvorsen pumps the water through a fine-meshed filter—not unlike a coffee filter. The filter captures DNA from all organisms that were near the lake when the sample was taken.

But the filter also captures a lot of irrelevant debris. To extract information from the sample, it must be cleaned. The filter is chopped into small pieces and placed in a tube with a liquid that causes the cells to burst. Halvorsen then adds chemicals and filters the liquid through another small filter to wash out the unwanted particles.

Finally, she is left with a clean DNA sample.

In the ground, in the water and in the air

Using environmental DNA in this way is relatively new. It had already been used to find bacterial communities in soil and sediments, but in 2008 researchers began using it in water. One of the latest developments is that it can also be used with air samples.

“Researchers have examined moist air in zoos with tropical climate exhibits where there are microscopic drops of water in the air, and DNA is present in these droplets,” says Halvorsen.

It may also be possible to estimate the number of animals in an area using this method, but the research is still in its early stages. Halvorsen is among those who have studied this application, which may be useful in dealing with rare species or those just beginning to establish themselves in a new place.

“The limitations of environmental DNA are that you don’t necessarily know if the fish detected in the sample are dead or alive. And even if a species does not appear in a sample, it may still be present. However, the more samples you take, the more certain you can be,” she says.

DNA as a puzzle

Back in the laboratory, after the final filtering, Halvorsen has a sample of pure DNA. But this DNA could belong to pikes, snails or even dead seagulls.

To determine whether the sample contains pike DNA, Halvorsen uses a method called real-time polymerase chain reaction (PCR). This takes place in a white box the size of a kitchen appliance, looking precisely like something you would expect to find in a laboratory.

The researchers have created a puzzle piece that fits exactly with the DNA of pike, but not of any other species. In the PCR machine, the DNA fragments are split in two. If pike DNA is present, the researchers’ puzzle piece will attach to it and emit a fluorescent light that is detected by the machine.

Seeing the bigger picture

“The rotenone treatment worked as intended. Even three years later, we find no traces of pike in the samples,” Halvorsen says.

Some species have re-established themselves in the water. Trout, eel and sticklebacks have returned from the sea or upstream streams. Nevertheless, researchers will continue to monitor the lake to keep an eye on the ecosystem.

“I think it’s important that we don’t view fish and other animals as merely a resource we can exploit. We must not only protect the species we want to harvest and eat but understand that all species have a role that is important for the ecosystem to function. We don’t have the primary right to everything,” she says.