Environmental DNA: Tracking the traces
Environmental DNA analysis provides a more efficient way to monitor wildlife presence than traditional surveying methods – making it easier for developers to protect and boost biodiversity, says Catherine Early
Biodiversity has typically been a tick-box exercise for business, if it is given any thought at all – but that is starting to change. Internationally, the issue has come to prominence as scientists warn that one million species are facing extinction, while the World Economic Forum this year listed biodiversity loss and ecosystem collapse as a top risk to business.
In the UK, the Environment Bill is bringing in requirements for developers to prove a net gain of biodiversity on development sites, while the new payment system for farmers will be based on environmental improvements – including to wildlife habitats. Landowners such as water companies now have a legal responsibility to restrict the spread of invasive species such as zebra mussels, which clog pipes and cost millions to remove.
As regulation places more obligations on the private sector to tackle biodiversity, there has long been a lack of precise data for monitoring it. The difficulty of locating and identifying species in an ecosystem, and the time and expense of collecting the data, means that biodiversity knowledge can be patchy at best.
However, new technology that promises to change this is being developed. Analysis of environmental DNA (eDNA) – unique animal cells left in the environment through shedding, sweating, urinating and salivating – can provide the same or better information than traditional biodiversity surveying, at a fraction of the time and cost.
Quick and easy
eDNA is collected from water samples using a simple kit, and is far quicker than traditional methods. A fish survey in Sweden by research institute Aquabiota, using the conventional method of catching them in nets, took around 200 hours in the field; a survey of the same area using eDNA took around 15 hours, including travel. It also found 24 species of fish, whereas net fishing found only 16.
Another eDNA testing benefit is that it is very simple – anyone can collect the samples, which vastly increases the number of places that can be monitored. People living in remote areas, or workers already on a site, can easily send the samples off to specialist labs for analysis.
eDNA can remain in water for an average of 48 hours after an animal has moved on, meaning that eDNA testing can pick up all species that have been present during a particular timescale, rather than only those that were there at a brief moment in time. Though some studies have shown that it can persist in particular environments for as much as 300 hours, it does not linger long enough for long-gone species to be detected.
eDNA can be used to monitor biodiversity in two ways – single-species monitoring and metabarcoding. Single-species testing tells you only whether a particular species is present or not. In the UK, it has gained ground in the surveying of development sites for great crested newts. The species, infamous in ecology and development circles, is the UK’s most heavily protected amphibian. Their habitats cannot be disturbed or destroyed without permission, and developers are required to survey potential breeding ponds to establish if newts are present on development sites.
Natural England approved the use of eDNA to survey for great crested newts in 2014. Testing water samples for newt eDNA has a 99.3% detection efficiency, significantly better than the more conventional methods of bottle trapping (76%), torch surveys (74%) and egg searches (44%).
Since then, eDNA surveying has led to a “transformation” in great crested newt conservation, according to Jeremy Biggs, director of campaign group the Freshwater Habitats Trust. Previously, every great crested newt habitat had to be protected, which resulted in some “very silly projects, such as ponds in the middle of an industrial estate, which were never going to be habitats,” he says.
eDNA monitoring has led to a new way of conserving great crested newts while allowing developments to take place. Under district licensing, currently being rolled out across the country by Natural England, developers pay to join a district-level licensing scheme, removing the need for them to carry out surveys on development sites. Compensatory habitat is created in nearby locations where it has a better chance of being effective than in the middle of the new development.
“Because we can now check where the newts are much more easily, we’re taking the money from development and putting it into habitat where it will stay in good condition for the long term, and we can check more quickly whether it’s working or not,” Biggs says.
Metabarcoding is a second type of eDNA analysis that has emerged more recently; it is now a rapidly growing field of research. By sequencing the DNA from all species present, metabarcoding enables the identification of multiple species from a single water sample. Comparison with traditional findings from conventional surveys has again been favourable.
Nature Metrics, a specialist in analysis of eDNA, has been testing a site near Sunbury-on-Thames over 12 months. The samples have revealed a total of 19 species, including lamprey and European bullhead, both protected species. The Environment Agency has surveyed the same site over 14 years using electrofishing – an expensive method under which fish are caught after being stunned with electric currents. The agency’s tests identified many of the same species, but far less consistently and at much higher expense.
There are a few drawbacks. Metabarcoding of eDNA tells you what species are present, but cannot quantify the population. However, Biggs points out that some species are so rare or hard to survey using conventional methods that it’s hugely beneficial that eDNA can tell you they are there at all. “It’s such powerful information that people will stop caring that you can’t count them all,” he says.
“eDNA is collected from water samples using a simple kit, and is far quicker than traditional methods”
Dr Kat Bruce, co-founder and chief executive of Nature Metrics, says: “Every single method we use for measuring biodiversity has its own set of biases and limitations; the important thing is to understand what these are so you can make an informed decision about what to use in a certain context.”
For this reason, those wishing to use eDNA will still need the advice of specialist ecologists who understand the environment being sampled and the species being targeted, to make sure the samples are collected in the right place at the right time to provide the information sought, she adds.
eDNA cannot be used for all species – for example, hard-bodied invertebrates with exoskeletons leave less eDNA than softer species. “A lot of water quality monitoring under the Water Framework Directive is based on benthic macroinvertebrate surveys,” explains Bruce. “There’s been a lot of interest in whether you can get the same data from eDNA analysis of water samples as you can from netting, but that is challenging, because a lot of these types of species don’t leave DNA. At the moment, it doesn’t look like eDNA sampling is going to replace conventional monitoring for invertebrates.”
The applications of eDNA metabarcoding are varied. Nature Metrics is already working with some infrastructure developers to generate baseline data for environmental impact assessments (EIA), which can then be compared with future data to assess the impact of a development on biodiversity.
Samples of insects or soil can also be sequenced using metabarcoding, enabling identification of species that have typically been too small and difficult to identify, Bruce says. “You can get much better information about how an ecosystem is changing in a general sense and whether it’s becoming more or less healthy. You need a lot of baseline data to build the foundations to use the technology in that way, but if the will is there, it has a lot of potential,” she says.
eDNA metabarcoding could appeal to businesses that want to go above and beyond compliance and be leaders in biodiversity protection, she says. “If they really want to understand what’s happening in the habitats they’re impacting and tell that story, then this will give them the information to do that in a better way.”
Catherine Early is a freelance journalist