The astonishing secrets being revealed by the science of environmental DNA (eDNA) are revolutionising the way in which we study and protect biodiversity, from the densest tropical jungle to the deepest ocean trench. But standing beside a ditch in the Gloucestershire countryside with a team from the Wildfowl and Wetlands Trust (WWT), it soon becomes apparent that collecting this biological calling card can still be very rudimentary.
A plastic pot attached to a piece of string is cast into the murky water and, once full, reeled back in, sealed and labelled. A slightly more scientific-looking probe is then sent into the water to measure pH levels before the team moves on to sample the next pool.
Dr Laura Weldon, a principal research officer at the WWT, explains that eDNA is “the bits that are left behind as an individual species moves through an environment”, from faeces and mucus to skin cells, saliva and hair.
The team is searching for evidence that eels may be living in the ditches and farmland ponds of the Severn Vale area, having moved there on purpose, rather than being marooned by floods. While the fields are regularly inundated by the River Severn, the results of a soon-to-be-published 2022 survey of 104 ponds across the area revealed eel eDNA in 37% of them, although only 40% of these were in areas that regularly flooded.
If Weldon and her team can prove that eels are deliberately moving across land to search out these ponds, then more can be done to protect them.
The global population of European eels (Anguilla anguilla) has crashed over recent decades, declining by 95% worldwide since the 1980s. Yet they play a crucial part in the ecosystem as they move in huge migratory waves from the open Atlantic, where they spawn, to fresh water, where they develop and mature.
As well as shifting nutrients from one environment to another, the young eels, which can take up to 20 years to mature, are a source of prey for birds, fish and mammals such as otters, before developing into top predators themselves.
It is then that the eels travel back across the Atlantic to the Sargasso Sea to breed, completing a round trip of up to 10,000km, which they make only once in a lifetime.
The WWT team spends an hour or so surveying various mini-wetlands at the Coombe Hill nature reserve, focusing on patches where wardens have seen herons pulling eels from the weeds. The samples are taken back to the organisation’s headquarters at Slimbridge, where testing the murky ditchwater for signs of the critically endangered fish begins in earnest.
In one litre of river water they have been able to pick up the same information as a decade’s worth of traditional surveying
The process of collecting eDNA was first used in France in 2008 as part of research into an invasive bullfrog. It was subsequently deployed in a groundbreaking survey of the UK’s great-crested newt population, while farther afield it has been used in many ways, from tracking pink river-dolphins in the Amazon to measuring the biodiversity of coral reefs.
As well as testing for a single species, a process called meta-barcoding can reveal everything that has recently passed through an environment, with eDNA hanging around for anything up to a couple of days.
The Guildford-based company NatureMetrics is one of the largest to offer the science commercially. “A challenge of biodiversity has always been that we can’t generate that much data because of the nature of fieldwork,” says its co-founder Kat Bruce. That has now changed, she says. “In one litre of water from a UK river they have been able to pick up the same information as a decade’s worth of traditional surveying. It’s really phenomenal and still blows my mind.”
In Norfolk, NatureMetrics is working with the Rivers Trust to track invasive signal crayfish, which are decimating their native white-clawed cousins, and using the data to ensure that reintroduction sites are intruder-free.
Sequencing technology that once took up a whole room can be carried out on a machine the size of a mobile phone. Easier access to so much data, says Bruce, means that scientists can start to look at things in a more holistic way to “understand what’s going on in an ecosystem [and] how our actions are influencing the natural world”.
It’s not just in water that scientists are capturing eDNA. Sampling soil to find out what microbes and invertebrates it contains is an established way of assessing soil health and a big part of regenerative agriculture. Air is also being tested for traces of eDNA, from studying cave biodiversity to surveying churches to establish the presence of bat colonies. The science is also helping to tackle the illegal wildlife trade by testing the air inside shipping containers for the presence of endangered species. “We are living in a soup of DNA,” says Bruce.
The potential of eDNA has been picked up by businesses, conscious that as more frameworks such as the Taskforce on Nature-based Disclosures are introduced, they need to better understand both their impact and dependency on nature.
Bruce says the next step is to start combining eDNA testing with eco-acoustics – or listening to an ecosystem – with the two methods complementing each other, to provide a more complete picture of what is living there.
Back in Gloucestershire, the water samples from Coombe Hill are being filtered and any DNA extracted and analysed, using a method not dissimilar to the polymerase chain reaction test for Covid-19. Weldon is testing for the short DNA sequence that’s unique to the European eel, but of the eight samples collected today, only one contains the relevant molecular strands.
Weldon is not disheartened. It is all part of the research, she says, another data point that can be used to help save these unassuming watery worlds.
“What we are interested in is the value of wetlands overall, and farm ponds have been overlooked as being valuable in the landscape,” says Weldon. Insectivorous birds, bats and pollinators all rely on them, she adds, but says: “They’re slowly disappearing, and that is having a far bigger impact on biodiversity than we previously thought.”