eDNA: Decoding Our Waterways

Most people aren’t thinking about the skin cells, mucous and faeces of fish when they look at a creek or ocean. But it has become the norm for a group of researchers and citizen scientists taking eDNA samples across the Wet Tropics to find out more about fish populations and water quality.

eDNA is a new go-to for scientists. It’s being used to detect the pest fish tilapia, to monitor elusive and critically endangered largetooth sawfish, to find coral-destroying crown-of-thorns starfish at larvae stage and to assess whether polluted waterways are becoming healthier.

Scientific advances have made eDNA sampling much easier. In the Wet Tropics, CSIRO is partnering with Terrain NRM to trial a new method of sampling, using fine filter papers, to see its potential for citizen science projects and to better understand the impacts of pesticides, nutrients and sediment on freshwater and estuarine ecosystems.

Mamu Indigenous rangers, volunteers from the Cairns and Far North Environment Centre and Terrain NRM and Wet Tropics Waterways scientists are sampling at three different spots in each of the Mossman, Barron, Johnstone and Tully River catchments.

Volunteer Stacey Buchanan says the project has been an eye-opener.

“It’s a hands-on project that our kids are loving too. We’re sampling at the same location over 18 months. I’ve grown up in Redlynch and we swim in Freshwater Creek all the time. It’s great to be helping with research looking at the effects of water quality on fish species.”

CSIRO researcher Sharon Hook says eDNA is an emerging science.

“When animals are in a habitat, they normally shed some DNA. By sampling it, we can quickly and accurately determine the number of species using an area. And with newly developed devices we can sample in more places more often.

“It’s more about the presence of species than populations because we are working with variability – from different animals shedding at different rates to their sizes and the persistence of DNA. But that’s still a huge advancement. North Queensland can be a difficult place for field work with its terrain, crocodiles and the big difference between wet and dry seasons. eDNA sampling can give us answers much more quickly and safely.”

Aquatic ecologist and Wet Tropics Waterways executive officer James Donaldson says eDNA sampling could be particularly useful in estuarine areas.

“As the interface between fresh and saltwater, estuaries are the breeding and nursery habitat for many fish species. It’s hard to monitor fish communities in tropical estuaries because we often can’t use traditional sampling methods like nets and snorkelling because of crocodiles, or electrofishing because of the high conductivity of sea water, or cameras because of poor water clarity. The impact of eDNA, for this knowledge gap, is potentially massive.”

Starfish seekers
eDNA sampling is helping to reduce crown of thorns starfish outbreaks. Scientists at the Australian Institute of Marine Science can now detect the larvae of these starfish in small seawater samples. An adult crown-of-thorns starfish can eat a dinner plate-sized chunk of coral every day, so the sooner outbreaks are detected the better.