eDNA water sampling to boost post-bushfire biodiversity analysis

Researchers from Monash University are using environmental DNA to track populations of freshwater species in the waterways of NSW and Victoria, a methodology that could prove life-saving for species following the catastrophic 2019-20 bushfire season.

The technique involves filtering water samples taken from water bodies to capture the DNA that organisms leave behind in the environment. By using species-specific DNA primers and a technique known as the quantitative polymerase chain reaction (qPCR), researchers are able to track whether or not a species has been present at a site.

Reid Tingley, a Lecturer at Monash University’s School of Biological Sciences, said this type of data will be used to help decipher the impact that the 2019-20 bushfires have had on populations of freshwater species, such as the platypus, which will be important for rehabilitation efforts.

“You just need to determine a short DNA sequence that is unique to your species of interest. Once you filter the water, the DNA gets trapped on that filter. You then extract the DNA from the filter using a blood and tissue kit — essentially the same process that you would use to extract DNA from any sort of biological material,” he said.

“If your species is present in a water sample, the primer will amplify the species’ DNA in a qPCR. This gives us an estimate of the number of copies of DNA in the sample.”

Old technology, new context

While the use of eDNA detection in water samples has been around for a while, Tingley said the field has grown exponentially in recent years and now offered some game-changing insight for biodiversity monitoring and rehabilitation.

“The idea of extracting DNA from water samples first came about in 2008 when a European group realised they could detect frogs by filtering water from ponds. The discovery set off this exponential growth in eDNA research,” he said.

“I started working in this field in 2013 with colleagues at EnviroDNA. We started playing with the eDNA technology after we began working on a European newt that has established in Australia.

“Now we've applied eDNA sampling to newts, cane toads, platypus, to all sorts of fish and amphibians. But the idea that you can extract DNA from the environment has been around for a long time.”

Following the 2019-20 bushfire season, Tingley and his colleagues received a $255,000 grant from the Australian Government’s Wildlife and Habitat Bushfire Recovery Program to apply the method to a post-bushfire biodiversity analysis.

“It’s a 12-month project. We have started sampling already, but our goal is to do two sampling trips. When analysing how species respond to bushfire, there may be differences over time,” he said.

“The first set of sampling will reflect the short-term impact. The second set — taken next autumn — will assess impacts over the medium term.

“Taking the water samples is simply a matter of going to each of the sites. Once you're at the site the work takes 10 minutes, but it's accessing all the sites across such a large area, particularly in New South Wales, that’s the biggest challenge at present.”

The project includes sampling waterbodies in fire-affected river basins, including private land and parks in the Mitchell-Thomson, Snowy, Ovens, Upper Murray, Murrumbidgee, Hawkesbury, Hunter and Shoalhaven catchments, as well as Bega, East Gippsland, and the Clyde-Jervis Bay region.

Future benefits

While it’s hoped that the research will help in short-term rehabilitation efforts, Tingley said there is a lot of potential for the technology to be applied much more broadly.

“One of the main benefits of this technology is the geographic scale over which you can apply it.
We're fortunate to have about 350 sites throughout the bushfire area that we had already sampled in 2018 and 2019,” he said.

“For a species that’s quite cryptic, like the platypus, the traditional approach would involve trapping, which isn’t always successful in detecting animals when they are present," he said.

“But now, over one or two field seasons, we can test thousands of sites and be quite confident that the species is not present if we fail to detect its DNA.”

Tingley said the new bushfire project has opened up the possibility to sample a much larger variety of aquatic species by designing universal primers capable of detecting entire taxonomic groups.

“What's really interesting about this recently funded bushfire project is that we're now not only using species-specific primers to determine how platypus have fared, but also using multi-species techniques that allow us to determine the composition of entire biological communities of vertebrates and crayfish,” he said.

“This is where the real power is: our recent platypus project showed us that, over a relatively large area, you can gather information on a species’ distribution relatively quickly. It's not a perfect technique. There's always the chance that you'll miss the species’ DNA.

“But it’s providing us with an ability to do broad-scale monitoring in a way that hasn’t been this fast or comprehensive before.”