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Environmental DNA: What is it and how can it help nature recovery?
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.
What is eDNA?
When an organism, say a fish, moves through the environment it’s constantly shedding bits of itself. A creature can shed anything from dead skin cells to mucus to faeces as it moves through its surroundings.
The DNA in this organic matter is known as environmental DNA (eDNA). If someone tested a sample of the water, these pieces of DNA could indicate the recent presence of the fish, even if no fish is seen.
The benefits of studying eDNA
DNA can be collected from a whole range of environments, including water, soil and air. It 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.
In fact, for some species groups, such as bacteria, the only realistic way to identify their presence is by searching for their DNA.
Dr John Tweddle, the Head of the Angela Marmont Centre for UK Nature, leads several projects looking into how eDNA approaches can support biodiversity discovery and nature recovery in the UK.
‘Current conservation monitoring tends to focus on just a few species groups such as flowering plants, birds, mammals and butterflies,’ explains John. ‘But eDNA allows us to consider the whole range of life, including extremely species-rich groups such as invertebrates and rarer species that may be overlooked by conventional surveys.’
DNA sampling methods are radically extending the way we monitor biodiversity. They can be faster, cheaper, easier to scale up and more accurate than traditional survey approaches.
It is a rapidly advancing field of science, but there remain a number of questions to resolve. For example, one of the key differences between eDNA sampling and visually or acoustically observing wildlife is that when you find some DNA, you can’t always tell if that species still occurs there now, or if the DNA was shed at some time in the past.
John adds, ‘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.’
As technology advances, the applications of DNA in studying and protecting nature have ballooned over recent years.
How we sample eDNA
Looking for eDNA starts with taking a sample from the environment we are studying. Often this will be soil, water or air, but eDNA can also be sampled from a huge range of places: from insect traps, or the gut or faeces of an animal, or even the petals of a flower.
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 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.
Another way is to sequence the DNA directly in the field, using a small DNA sequencing device that can be easily carried to the sampling site. The researcher simply takes a small sample from the soil, for example, shakes it in reagents that extract the DNA and then adds the resulting solution to the sequencing kit. The resulting DNA sequence data can then be run through software on a laptop to find which species match to that DNA.
How are we using eDNA in our research?
The use of eDNA in uncovering the hidden diversity that surrounds us is astounding, as every year researchers figure out yet more applications for the technology.
Our scientists are looking at eDNA in the deep oceans, the tropics and even the Arctic, to understand the diversity of life and why it’s changing.
‘DNA-based methods complement rather than replace traditional surveys,’ says John. ‘The use of eDNA allows us to ask different questions and has the potential to broaden and deepen the evidence base. Traditional surveys will though always have significant scientific benefit, as well as giving huge enjoyment to those of us that carry them out.’
One of the most common current uses of eDNA is to sample water. Taking a sample of water from the bottom of the ocean can, for example, give a rich picture of what lives down in the inaccessible depths, revealing the presence of deep diving whales, fish or crustaceans.
But over the years its applications have ballooned. There are even ways to sample the air we breathe and then condense it down to extract any DNA that it contains.
Scientists are also thinking about how other animals could act, in effect, as DNA collectors. Research has already shown that as sponges filter huge volumes of water, they also filter out pieces of eDNA which can then be sequenced. One study was able to identify 31 different species, including penguins and seals, by sampling pieces of sponge.
Here at the museum, we are using eDNA in a community science project called GenePools, where people collect samples of ponds in urban areas and send it in to us to be sampled, to better understand how beneficial our garden ponds are for wildlife
As technology continues to advance and ideas expand, eDNA has the potential to open up really exciting and creative ways to learn about and help to protect the wildlife around us.
Studying eDNA data and other biodiversity data in a ‘data ecosystem’
Here at the Museum, we’re developing a new public-facing biodiversity and environmental monitoring system to help capture, share and interpret data about the UK’s biodiversity. Sponsored by AWS, it’s called the data ecosystem.
The DNA sequence data that we generate through our research will be stored in this data ecosystem, which will then help us combine this information with visual, acoustic and potentially even video observations of wildlife.
Our work with the data ecosystem will explore why the UK’s biodiversity is changing, with a particular focus on urban nature.
‘We can look at the breadth of life in an area, from bacteria through to birds, and study how that changes through time,’ says John.
This work includes baseline studies of what’s found where, such as the Urban Nature Project. The data ecosystem can also be used for longer-term investigations of how whole ecosystems respond to change, such as climate change or to a positive action that we take, such as habitat repair or the creation of new spaces for nature.
The data ecosystem will allow us to bring different kinds of data together, gathered from community scientists and research partners across the UK.
‘The idea is that it will capture wildlife and environmental data from many different projects,’ says John. ‘This will allow us to really understand the UK’s ecosystems in a way we couldn’t before,’ he adds.
As well as sharing data with researchers, the information will also be accessible in a public-friendly way so that anyone from a community gardener to a teacher will be able to access and use this data to support practical actions for nature.
This little wasp is one of 25,000 species of insect in the UK alone, but advancing DNA techniques are already helping in our understanding of this hugely diverse group.
Uncovering hidden biodiversity in UK grasslands
As part of a study investigating how threatened UK grassland habitats can be restored, our scientists here at the Museum have sampled less than a cup of soil from across a network of London chalkland grasslands for its DNA and eDNA. From this tiny amount of soil, they detected the presence of DNA from an extraordinary 7,000 different types of organisms. This incredible diversity of hidden life spans earthworms and fungi, to unicellular algae, nematode worms and a vast array of microscopic protists (non-bacterial organisms that are not animals, plants, or fungi).
Many of these organisms play important roles in maintaining healthy soils and plant communities, but are not normally surveyed. Complementary DNA studies of above ground diversity identified a further 1,000 species of flying insect, including 26 rare and threatened species that were not previously known from the sites.
‘With careful targeting of the right selection of DNA barcodes, eDNA studies can help us to observe most forms of life,’ explains John. ‘A group we still have much to learn about is the invertebrates. This is unsurprising as there are over 25,000 species of insect alone within the UK - and no one person can be expected to identify them all! eDNA studies are already improving our understanding of some of these more challenging to identify species groups, and will become ever more useful as the DNA reference libraries, which map a DNA sequence to the species that it came from, become ever more complete.’
