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Is there pike here? The answer can be found in a litre of water

Researchers find traces of fish using DNA from water samples.

Silje Halvorsen takes a water sample from the freshwater lake Gillsvannet.
COMMUNICATIONS ADVISER
Presented by: University of Agder
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Silje Halvorsen bends down and fills a plastic bottle with water from Gillsvannet lake, a sheltered bathing spot in southern Norway. 

This is something she has done many times before. In 2022, she took monthly water samples from 14 locations in the lake. Then, every three months until October 2023.

The goal? To find traces of pike and other species that might inhabit the lake. 

Pike does not naturally belong in Gillsvannet, and the authorities wanted to eliminate them.

Cheaper and better than traps

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

“All organisms leave traces of DNA where they live,” says researcher Silje Halvorsen.

“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.

She researches environmental DNA.

DNA is genetic material found in the cells of all living organisms. It serves as a blueprint for how an individual grows, looks, and functions. 

Every human, fish, or bacterium has its own unique blueprint, but they become more similar the closer they are 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. Rotenone 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 used 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,” says Halvorsen.

Like a coffee filter

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

To extract all the small the particles from the water, Halvorsen pumps it through a fine-meshed filter – similar to a coffee filter. The filter captures DNA from all organisms that were near the lake when the sample was taken.

However, 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, which removes the unwanted particles.

Finally, she is left with a clean DNA sample.

In the ground, water, and 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 in 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 become possible to estimate the number of animals in an area using this method, but that research is still in its early stages. 

Halvorsen is among those who have studied this application. It can be useful in dealing with rare species or those just beginning to establish themselves in a new area.

“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 doesn't appear in a sample, it could 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 filtration, Halvorsen has a sample of pure DNA. But this DNA could belong to pike, snails, or even dead seagulls.

To determine if 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. It looks exactly like something you would expect to find in a laboratory.

The researchers have created a puzzle piece that fits precisely with the DNA of pike, but not with any other species. In the PCR machine, the DNA fragments are split in two. If pike DNA is present, the 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,” says Halvorsen.

Some species have re-established themselves in the water. Trout, eel, and stickleback 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.

Reference:

Halvorsen, S. Exploring freshwater challenges for conservation efforts: Insights into threatened and invasive fish species using environmental DNA, Doctoral dissertation at the Universitetet i Agder, 2024.

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Read the Norwegian version of this article on forskning.no

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