Environmental DNA – eDNA – is featuring in ever more conversations about natural capital and nature restoration – so we thought we’d ask the obvious question – what is it?
eDNA refers to genetic material, DNA fragments, that are shed by organisms into their surrounding environment through skin cells, mucus, saliva, faeces, urine, or decomposing tissue.
For example a fish sheds mucus and scales as it swims, a deer sheds skin and fur as it runs and a plant sheds cells as it grows.
Scientists can collect and analyse this eDNA from water, the soil or the air to detect the presence of species without directly observing or capturing them.
Josh Davis from the Natural History Museum said, “One of the biggest challenges when working on nature recovery is getting an accurate picture of which species live where. As we seek to restore communities of life and enrich ecosystems, conservationists, scientists and policymakers need to be able to identify the diversity of creatures that live in an area and understand how their populations are changing.
“Until recently, wildlife surveys would involve going out and physically looking for species such as plants, birds or mammals. But now we can also use DNA sequencing technologies to monitor wildlife, and all that is needed is a tiny sample of their DNA.”
Pete Cooper, a Species Ecologist at Restore Nature, explained that, “Every organism on earth is constantly shedding its DNA – skin, leaves, scales, fluid, faeces.” eDNA, he said, has now become a widespread tool for ecologists looking to detect species presence or absence in an ecosystem.
Cooper said that the presence of creatures such as great-crested newts and water voles can be evaluated using this technique. He said, “Whilst it is no replacement for more detailed surveys to assess factors such as abundance and population dynamics, it can be incredibly useful in establishing a foundation of knowledge which would otherwise have cost significant time and money.”
Ancient ecosystems brought back to life
eDNA can also be used to help map historic ecosystems, influencing habitat restoration and management decisions.
Cooper said that, “Samples of eDNA taken from the sediment of the North Sea have revealed clues of the wildlife that once roamed across Doggerland, the sunken land that, until about 8,000 years ago, connected Britain to Europe. And whist it is often difficult to identify ancient DNA to a species level, some fascinating records have been found here, with a diversity ranging from geraniums all the way to wolves.”
Collecting samples
eDNA can be found in water, soil, sediments and air and collection methods vary.
For water testing, samples are collected from lakes, rivers and oceans and passed through a special filter membrane, which traps the eDNA particles. The filter is then preserved, for example in ethanol.
When soil or sediment are sampled, scoops or cores are taken and stored at -20C. DNA is extracted using laboratory methods like CTAB (cetyltrimethylammonium bromide) or commercial soil DNA extraction kits.
Air sampling uses filters that capture DNA shed by animals or plants. The filters are then stored and assessed using processes similar to water and soil.
Davis said that, “In some cases, it’s necessary to immediately freeze samples to prevent biological activity from breaking down the DNA. The samples are then sent for DNA extraction and sequencing in the [Natural History] Museum’s molecular labs. This involves extracting, amplifying and reconstructing the DNA code for specific sections of the DNA fragments found in the samples. Through a computational biology step, so-called ‘barcode regions’ of DNA can then be used to identify, broadly speaking, which types of organisms were, or had recently been, present in the samples.”
DNA can also be sampled directly in the field using a small DNA sequencing device.
What is eDNA used for?
Environmental DNA can be used for conservation and biodiversity monitoring, to detect rare or endangered species and to assess the impact of actions taken to restore nature. It can help to assess ecosystem health, to track populations and to monitor disease presence and movement.
While eDNA is still mostly used to assess water ecosystems, the method can be used anywhere. The Natural History Museum said that in one recent study it found over 7,000 different organisms in a single cup of soil taken from across a network of London chalkland grasslands.
eDNA assessment is non-invasive (there’s no need to capture or disturb wildlife), it’s super-sensitive and cost effective.
Davis explained that eDNA “allows researchers to build up a far more detailed understanding of the species that live in an environment than would be possible if we were to solely rely on identifying species by sight.
“DNA also enables scientists to find and identify a whole host of small invertebrates and microorganisms that are plentiful in most environments. These tiny creatures play a vital, if often overlooked, role in healthy environments, yet they are rarely counted due to their size, sheer diversity and the level of time and expertise required to identify them visually.”
Dr John Tweddle, Head of the Angela Marmont Centre for UK Nature, said, “While there are still some challenges to overcome, DNA-led methods are already enabling us to look for a far greater diversity of species groups and to repeatedly sample over larger spatial areas and longer timeframes than would previously have been practical. We’re now looking at how easy it is to piece together whole wildlife communities and how to tailor and apply these methods for practical nature recovery.”