Using eDNA to uncover clues from invasive animals

Detection is a crucial part of any biosecurity strategy – finding a new invasive species early can mean the difference between being able to eradicate it, and having to live with its presence and effect on native ecosystems. But how do you find a fish in a murky creek or an ant a few millimetres long across the vastness of northern Australia?

Every living organism sheds tiny, DNA-containing traces of itself – such as skin cells, scales, or fur – into its surroundings. This environmental DNA, or eDNA, can linger in water or soil, and may be carried far from the animal that left it.

This makes eDNA a powerful tool in species detection for both biosecurity and conservation – instead of having to find the animal or plant itself, you can take environmental samples and test them for the presence of DNA.

Dr Cecilia Villacorta-Rath, from JCU’s TropWATER and Centre for Tropical Biosecurity, says eDNA detection methods can provide evidence for better targeting of biosecurity investigation.

“You can take water samples from 20 creeks instead of having to check them each on foot,” she says. “If three creeks show DNA from your target species, you send people to only those three creeks or their catchments, which saves time and money.”

The most common way to collect eDNA samples is by filtering water, which is very easy when the water is clear, such as in rainforest streams or around coral reefs.

“However, most of our tropical creeks and rivers are really turbid for at least part of the year, which clogs the filters and makes it challenging to collect samples,” Villacorta-Rath says.

“We developed a method for field sample collection where water is scooped up and poured into a jar loaded with a stabilising buffer to keep eDNA intact until it reaches the lab.

“Our trials show this preserves the eDNA for at least three months at ambient temperature, and at least six weeks at 60 degrees, allowing us to process samples from remote places like the Gulf of Carpentaria, the Great Barrier Reef and Western Australia.”

The simplicity of collection allows eDNA sampling to be conducted by anyone working in remote Australia, whether they have specialist scientific training or not: council officers, government workers, citizen scientists, and Indigenous rangers on Country.

“The usual way to survey for invasive fish and turtles is to catch them, by electrofishing or netting – this takes a lot of time, people and permits, which makes it expensive,” Villacorta-Rath says.

“Using eDNA opens opportunities to cut costs and engage with the people on the ground.”

Rangers in Queensland use eDNA kits as part of routine surveillance against cane toads or tilapia. Villacorta-Rath has used eDNA to survey rivers across northern Queensland and compare the results with electrofishing surveys, helping to identify where tilapia is present and where sentinel monitoring may be needed after flooding.

Once samples are back in the lab, Villacorta-Rath’s team can use one of two analysis approaches.

“Metabarcoding casts a wide net, giving us the full picture of all the species present in a sample, while targeted eDNA is specific to one or a few species,” she says.

“A new infestation of an invasive species may only involve a handful of animals, so we usually recommend a targeted approach for biosecurity scenarios because the eDNA signal won’t be swamped by that of other species that are more abundant.”

As powerful as eDNA is in the search for invasive species, selecting where to sample in the first place requires a different type of expertise.

“The first rule of thumb when you’re using eDNA is to work alongside an ecologist who can share all the factors around species biology and behaviour that you need to take into account to plan sampling design,” Villacorta-Rath says.

“We’re really lucky at JCU to have expertise from ecologists working with insects, fish, frogs and vertebrates in general.”

One such ecologist is Villacorta-Rath’s colleague from the Centre for Tropical Biosecurity, CTB Director Professor Lori Lach.  The two researchers joined forces to tackle the issue of yellow crazy ants.

These insects, which have gained footholds in Queensland, are recognised as one of the world’s most invasive species by International Union for the Conservation of Nature.

Villacorta-Rath took soil samples from areas where ants were crawling around to confirm her test would detect yellow crazy ant eDNA. But back in the lab, their DNA was not showing up in the analysis.

Lach explains that the ants were probably only transiting through the sampling area, so weren’t shedding much DNA.

Villacorta-Rath took more samples, this time at suspected nest entrances where the ants were engaging in activities such as moving babies and dead bodies. Sure enough, these samples yielded more accurate detections.

But detecting target ant eDNA in soil required sampling to be done in proximity to nests, which is not practical to detect new ant incursions.

Yellow crazy ants often nest beside creeks, so Villacorta-Rath took water samples following rainfall events to see whether yellow crazy ant eDNA could be detected in the waterway – and showed that it was.

It was the first time in the world the eDNA of a terrestrial invertebrate had been detected in a natural waterway, and resulted in a more effective method for monitoring large areas against yellow crazy ant incursions.

As climate change and increased trade ramp up biosecurity threats, Villacorta-Rath sees eDNA continuing to play a role in combating invasive species.

“With eDNA, it’s all about creativity,” she says. “You can collect a soil sample or a water sample or an air sample, or you can swab trees, as long as that gives you the answer to your research question – which means thinking about the target species and where its DNA is likely to end up.”

That versatility is opening new frontiers.

“I think in future years, we’re going to be able to use eDNA to give us more insights into infestations, so not only detecting the presence of an invasive species, but potentially also to trace the source of an incursion, without having to catch the invader,” Villacorta-Rath says.

Being able to trace the origin of an infestation helps biosecurity teams understand how the species spreads and where prevention efforts should focus.

Another frontier is sampling the air itself, which could provide new ways of detecting invasive plants – one of the most under-explored areas for eDNA – through catching pollen carried on the breeze.

For Villacorta-Rath, who began her career extracting DNA from animal tissue in the lab, the shift remains a marvel.

“Being able to collect a water or air sample to find DNA – it still blows my mind.”