eDNA is becoming increasingly useful in biodiversity research and conservation. But what is eDNA, exactly?
All living things have DNA and regularly shed that DNA via hair follicles, feathers, skin cells, scales, reproductive cells, blood, saliva, biological waste, and more.
When this happens, the DNA enters the surrounding environment and becomes environmental DNA or ‘eDNA’. Scientists can collect eDNA via soil samples, freshwater and marine samples, air samples, and so on.
The eDNA is then isolated and sequenced, and that sequence is then compared to a reference database of known species-specific DNA sequences. If a match is found, the species that shed the eDNA can be identified.
“In principle, if there is eDNA in an environmental sample, when we sequence [it] we’re actually sequencing the DNA of animals living in that environment at the time of sampling,” explains Dr Michelle Guzik, an environmental scientist at the University of Adelaide. Michelle recently joined the bi-monthly TERN Webinar, where she spoke about her work using eDNA. She explained how its use as a non-invasive, low-cost biomonitoring tool is enabling scientists to gain a better understanding of species richness and distribution in a wide range of ecosystems. In particular, she is using eDNA to characterise biodiversity in groundwater systems.
There are many different sources of eDNA (image: Sahu, A. et al (2025) Ecological Indicators Volume 173 creative commons)
The idea of using DNA sequencing to better understand biodiversity has been around for several decades, but this approach has really taken off in recent years with the help of technological advances in DNA detection, genetic sequencing and computational power. Nevertheless, a number of challenges remain.
eDNA stability
DNA is a relatively stable molecule while it’s still part of a living cell in a living organism where it’s protected by tissues and cellular structures and also benefits from repair processes. However, once DNA has been shed and enters the environment, those protections break down.
eDNA is generally found in tissue fragments, in individual cells or it might be entirely extracellular. The decay of those cells and tissues, as well as the degradation of the eDNA itself is influenced by a variety of parameters, including temperature, pH, moisture, salinity, and exposure to ultraviolet light. Microbial activity is major factor, because bacteria, algae, fungi and other microbes are known to scavenge DNA from their surroundings with the help of DNA-degrading enzymes. The more microbes present, the faster eDNA degrades. With all these assaults on its structural integrity, eDNA is continuously breaking down and is often found in small fragments.
The environmental context of the eDNA can have a big influence on how fast it degrades. Animal tracks are a good place to find eDNA, but you’re more likely to collect better quality eDNA if the tracks are in snow than if they’re in warm, microbe-rich mud. Left image: puma print in mud (credit: Zachary Amir). Centre image: wallaby in Tasmanian winter (credit: Florian Rohart licensed as CC BY-NC-ND 2.0 via Flickr). Right image: cockatoo feather shed in flight (credit: Fiona McMillan-Webster)
A needle in a haystack
The amount of eDNA collected in a sample depends on a variety of factors. Once eDNA enters the environment, it can be dispersed by air currents and water flow. It also depends on how much time an organism spends in an area and how much DNA it shed in the first place. Moreover, different species shed their DNA in different amounts and at different rates, and this can also vary across contexts – from a few skin cells to a significant injury – and can also vary across seasons, reproductive cycles and life stages.
It can be challenging both to collect enough eDNA and to determine whether that eDNA was shed nearby or many kilometres away. It’s also tricky to isolate diluted eDNA fragments in environmental samples that are brimming with other molecules and cellular material.
Fortunately, technological advances are making it easier to collect, detect and analyse eDNA. These include specialised filters that allow scientists to select for particles in the size range of eDNA fragments, filtering out larger microbes and smaller nutrients. Meanwhile, researchers are developing ‘molecular magnets’ which are molecules designed to preferentially attract and bind DNA. It’s possible to design molecular magnets that will detect a particular species or wide range of them.
Michelle and her colleagues have been doing just this – they’ve been designing molecular magnets for single and multiple species in subterranean groundwater aquifers in the Pilbara. “We were able to show that we could detect quite a number of the animals that we know live in groundwater at those particular locations,” she says.
Finding a match
A key challenge for such work is that organisms that live in groundwater are quite uncommon and unique. “Most of the fauna are unknown to science,” says Michelle, so their DNA sequences are unknown. That can make it difficult to identify a match.
This raises another important issue in eDNA analysis: once eDNA has been collected, isolated and sequenced, the accurate identification of the species relies on finding a match in a reference database of known DNA sequences. That can only happen if that species’ genome was previously sequenced at some point and stored in that database.
In order for eDNA analysis to be more effective across the board, it will require a concerted effort to genetically characterise as many species as possible and to ensure that data are readily accessible in centralised databases. It’s also important to build local DNA reference libraries for particular ecosystem types as well as specific locations, that way any eDNA found in those places can be quickly and easily compared to what is known to be living there.
Improvements in technology and reference data have important implications downstream, as it were. “Basically, the basis of all our research is that knowledge, evidence and uncertainty determine our confidence in regulatory decision making,” says Michelle. “Any improvements in evidence and confidence in survey data will improve environmental conservation outcomes.”
Something in the air
Scientists in the UK have been collecting eDNA from existing air quality monitoring stations as part of a national wildlife survey. This approach is proving extremely useful for air eDNA monitoring, and shows that existing air pollution monitoring infrastructure could help support large-scale biodiversity monitoring alongside existing tools. In late 2025, TERN Australia joined the study as part of a global expansion of this research. With the help of participating state environmental agencies TERN is coordinating sample collection across Australian states and territories. Beginning this year, used air quality filters will be collected and any trace amounts of eDNA found in the filters will be sequenced and identified using DNA metabarcoding.
The project will serve as a pilot for Australia, testing the use of our existing air quality monitoring infrastructure for biodiversity monitoring, and exploring the feasibility of running national-scale biodiversity monitoring using air eDNA.
