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One of the biggest challenges in wildlife conservation is getting an accurate picture of what species are living where. To protect any environment, scientists and policymakers need to know what is there to begin with.
Normally, surveys involve going out and looking for species of plants, birds or mammals. But in recent decades, the advancement of DNA sequencing technology has given scientists an entirely new way to monitor wildlife. Rather than going out to find the animals themselves, all that is needed is a tiny sample of their eDNA.
When an organism, such as a fish, moves through the environment it is constantly shedding bits of itself, like dead skin cells, mucus, or faeces into 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.
This advance in the use of DNA sequencing technology can be applied to a whole range of environments, not just water but also soil and air. It allows researchers to build up a far more detailed image of which species live in the environment than by simply identifying species on sight.
It also enables scientists to find and identify a whole host of small invertebrates and microorganisms that are ubiquitous in all environments, but very rarely counted due to their small size. These tiny creatures play a vital, if often overlooked, role in healthy environments, yet they are rarely counted due to their small size, sheer diversity and the level of time and expertise required to identify them visually.
Dr John Tweddle, the Head of the Angela Marmont Centre for UK Biodiversity, is involved with leading several projects looking into how eDNA approaches can support biodiversity discovery and practical nature conservation 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 diversity of life, including extremely species-rich groups such as invertebrates and rarer species that may be overlooked by conventional surveys.'
The new methods have the potential to radically change the way we monitor biodiversity - they are faster, cheaper, easier to scale up and more accurate.
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 nature conservation.'
Everything starts with taking a sample of the environment that is to be tested. Usually this will either be soil, water or air. But eDNA can also be sampled from pitfall and malaise traps set up to catch insects that fall or fly into the traps, the gut or faeces of an animal, or even the petals of a flower.
Soil and water samples are then immediately frozen to prevent biological activity breaking down any DNA. The ethanol from the pitfall and malaise traps is also decanted for eDNA extraction.
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. These can then be used to identify, broadly speaking, which types of organisms were, or had recently been, present in the samples.
The resulting DNA-based identifications are often known as Operational Taxonomic Units (OTUs), to signify that the identification is based on analysis of a small piece of genetic code, rather than direct observation of the species itself.
Museum scientists have been testing some of these cutting edge eDNA sampling techniques in the Museum's Wildlife Garden.
The work is part of a long-term programme to develop and refine eDNA sampling and analysis as a conservation tool, and so the researchers have been using their expertise to compare the eDNA results to traditional monitoring – for example, by identifying the whole invertebrate specimens caught in the pitfall and malaise traps.
When Museum scientists sampled less than a cup of soil from central London for its DNA and eDNA, they detected the presence of DNA of an extraordinary 5,672 OTUs, which is roughly equivalent to the number of species that were or had moved through the samples.
This included some 995 different fungi OTUs, 620 types of nematode worms, 296 insects and arthropods, 12 different earthworm species and a huge diversity of unicellular algae and microscopic protists (non-bacterial organisms that are not animals, plants, or fungi). Many of these organisms play important roles in maintaining healthy soils but are not normally surveyed.
'With careful targeting of the right selection of DNA barcodes, eDNA studies can help us to observe most forms of life,' explains John. 'The group we know the least 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 link a DNA sequence to the species that it came from, become ever more complete.'
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. But there are still limitations to it.
'DNA-based methods complement rather than replace traditional surveys,' says John. 'The use of eDNA has the potential to broaden and deepen the evidence base, but traditional surveys will always have significant scientific benefit, as well as giving enjoyment to those of us that carry them out.
'At the moment, DNA testing isn't at a point where we can reliably gather information on population levels and trends, for example, and so we still need traditional surveys to monitor how populations change. We're still exploring how and where DNA-led approaches can best fit within the landscape of conservation monitoring.'
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. Now researchers can sample the soil and reveal the extraordinary diversity found beneath our feet. 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.
A similar technique might also apply to taking swabs from the petals of flowers, which could then be used to build up an idea of what pollinators live in an area.
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.