Experts can tell what lives in lakes and rivers from floating DNA

Scientists can now tell what fish live in lakes and rivers by simply testing DNA in the water

  • Aquatic creatures leave DNA traces in water as they shed cells, blood and waste
  • Comparison with reference DNA sequences can identify the animals responsible
  • Analysing shed DNA is cheaper and less harmful than directly capturing animals
  • The UK Environment Agency will begin widespread use of the method next year 

Scientists can now check which varieties of water dwelling creatures live in lakes and rivers can now be to the shedding of DNA.

Experts can compare genetic material from blood, bodily waste and cells left in a body of water to tell which species left them behind. 

The UK Environmental Agency, which began exploring the potential of the technique seven years ago, will be rolling out DNA-based monitoring programmes in 2020. 

It will be used to track the spread of non-native species driven by rising temperatures — such as the highly invasive demon and killer shrimp.

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Researchers can determine which aquatic species live in a given body of water from just a water sample — all thanks to the shedding of DNA (stock image)

The UK Environment Agency is responsible for monitoring the health of rivers, lakes and other bodies of water in the UK.

Keeping count of the number of species living in a given one of these environments can offer a good proxy for the health of the water both.

Seeking efficiency savings, the organisation began to investigate the potential of applying environmental DNA — or ‘eDNA’ — to their work in 2012.

This DNA is left floating in lakes and rivers after animals leave behind cells, blood and waste in the water.

Advances in rapid DNA sequencing technologies, along with our growing catalogue of reference genomes, have now made it possible to use these chemical footprints.

Comparing DNA samples from water bodies to known DNA sequences, researchers can determine which species left the signals behind. 

Their findings suggest that eDNA analysis is now not only viable, but can also be the most accurate way to determine the presence of aquatic species.

‘eDNA is no longer a concept,’ Environment Agency researcher Kerry Walsh told the New Scientist.

To monitor aquatic life, scientists have conventionally relied on capturing organisms in order to study them directly.

This is achieved, for example, by using nets or scraping underneath boulders. 

The problem with these methods, however, is that they are extremely time-consuming, require considerable training before researchers can undertake them and can also have the potential to harm the species being studied.

For example, the capture of fish is often achieved by using electricity to stun them, which sometimes can accidentally kill the animals. 

The use of environmental DNA offers a cheap, quick and simple alternative that does not require marine life to be disturbed at all.

In fact, the pervasiveness of eDNA means that the technique can capture information on animals that other techniques, like the use of nets, might miss. 

‘Some fish become aware of nets and stay away. Whereas with eDNA it’s in the water, it’s mixed,’ said Dr Walsh.

A recent eDNA analysis undertaken in Windermere, Cumbria (pictured, stock image)  succeeded in detecting 14 of the 16 fish species ever recorded in the lake

In fact, a recent eDNA analysis undertaken in Windermere, Cumbria, succeeded in detecting 14 out of the 16 species of fish that have ever been recorded in the lake — including eel and pike.

This is around three times the number of species that are typically detected in one sitting using conventional monitoring approaches. 

‘Fish are great because they are slimy and releasing eDNA all the time,’ she added Walsh. 

Dr Walsh and her Environment Agency colleagues hope that environmental DNA will help the organisation monitor the presence of invasive species within UK waters.

Scientists expect that rising temperatures will help these intruders spread.

‘If we’ve got the tools to detect them early before they’re established, it’s much easier to deal with them,’ said Dr Walsh.

The Environment Agency is devising procedures to spot four priority non-native species: the demon shrimp, killer shrimp, quagga mussel and zebra mussel.

These monitoring efforts are expected to begin in 2020.

Dr Walsh and her Environment Agency colleagues hope that environmental DNA will help the organisation monitor the presence of invasive species (such as the Demon Shrimp, pictured)

Environmental DNA analysis does have its limitations, however.

The technique may be well-suited to determining the number of species to be found in a body of water, but it cannot provide reliable information on the abundance of the given species detected, UK Centre for Ecology and Hydrology expert François Edwards told the New Scientist.

In addition, floating eDNA can outlive the animals that shed it.

Given this, it can be hard to tell whether DNA detected in a lake, for example, has come from creatures that are still present in the water, or those that were there a year ago and have now died off.

The same longevity causes different issues in rivers, Dr Edwards added, where eDNA can end up travelling downstream and ultimately be detected far away from where the actual animals are living.

A recent eDNA analysis undertaken in Windermere, Cumbria (pictured, stock image) succeeded in detecting 14 of the 16 fish species ever recorded in the lake

WHAT IS AN INVASIVE SPECIES?

An invasive species is one – be it animal, plant, microbe, etc – that has been introduced to a region it is not native to.

Typically, human activity is to blame for their transport, be it accidental or intentional.

Hammerhead flatworms have become invasive in many parts of the world. They feast on native earthworms, as shown

Sometimes species hitch a ride around the world with cargo shipments and other means of travel.

And, others escape or are released into the wild after being held as pets. A prime example of this is the Burmese python in the Florida Everglades.

Plants such as Japanese knotweed have seen a similar fate; first propagated for the beauty in Europe and the US, their rapid spread has quickly turned them into a threat to native plant species.

Climate change is also helping to drive non-local species into new areas, as plants begin to thrive in regions they previously may not have, and insects such as the mountain pine beetle take advantage of drought-weakened plants, according to NWF.

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