Saving Oxford’s Wetland Wildlife eDNA Surveys

As part of Saving Oxford’s Wetland Wildlife we have undertaken environmental DNA (eDNA) surveys to collect baseline data on freshwater fish, amphibians and other species in the area.

As part of the project, we surveyed new sites specifically for Great Crested Newt using eDNA surveys around Oxford, including ponds at Science Oxford Centre.

What is eDNA?

Environmental DNA, or eDNA for short, is nuclear or mitochrondrial DNA that is released by an organism into its surrounding environment. Sources of eDNA include shed skin and hair, faeces, urine, mucous, gametes (sex cells) and carcasses. In ponds, lakes, rivers, streams and ditches, eDNA can persist for up to one month, depending on environmental conditions, leaving a unique trace of the plant or animal in the water.

Advances in DNA technology mean it is now possible to detect freshwater animals and plants by collecting and analysing a simple water sample.

Survey Types

There are two different types of eDNA survey available at present. They use different DNA analysis methods and are suited to different things.

The first type, which uses an analysis method called qPCR (quantitative Polymerase Chain Reaction) is useful for detecting a single target species, and gives us a ‘yes’ or a ‘no’ as to whether or not our target species was detected in our sample. We use these single-species kits at Freshwater Habitats Trust for our country-wide annual Great Crested Newt survey, PondNet

A Great Crested Newt eDNA kit. Once the water sample has been collected, it is pipetted into test tubes filled with ethanol to preserve the DNA before being sent to the lab.

The second type of eDNA kit is able to detect lots of different species at once (a ‘multispecies kit’). It uses an analysis method called DNA metabarcoding, which allows us to get lots of species data at once. This technique records many species at once, but is less sensitive than single qPCR analysis, so must be interpreted in a different way when trying to build up species lists for individual sites.

The surveyor must choose a particular target taxonomic group for analysis, for example fish, freshwater mussels or vertebrates (otherwise the data would be completely overwhelmed with the DNA of microorganisms like bacteria). The metabarcoding analysis provides you with a list of all of the different species detected in your sample, within your target group. 

For the multispecies eDNA kits, the water sample is pushed through a plastic-encased filter (see picture) and this traps the DNA. It is then sent to the lab for analysis.

We have used both of these eDNA kit types as part of Saving Oxford’s Wetland Wildlife.

In summer 2019, our wonderful volunteers undertook 28 multispecies vertebrate eDNA surveys in and around the proposed Oxford Flood Alleviation Scheme area. They detected some notable species including Water Vole, Water Shrew and one of our three species of lamprey, most likely to be the Brook Lamprey in the Oxford area (at present the kits can’t distinguish between these three species). You can read the full report by clicking on the picture below.

In July 2020, Project Officer Ellie Mayhew undertook 12 Great Crested Newt surveys around Oxford, the results of which are coming soon.

eDNA: Revolutionising the recording of freshwater biodiversity?

Environmental DNA surveys have the potential to revolutionise monitoring of freshwater biodiversity worldwide. Many aquatic species are elusive and difficult to identify, and surveys are costly and time-consuming, often requiring highly-trained specialists.

eDNA kits are simple to use and make surveying freshwater biodiversity vastly more accessible, as volunteers are able to collect samples and no specialist training is required. This means data can be collected on a much larger scale than was previously possible.

Additionally, eDNA surveys allow landscape-level surveying of freshwater habitats, which has, until recently, been very challenging. Most fish records, for example, were previously obtained from a subset of the water environment by anglers and electrofishing surveys.

eDNA surveys have the potential to make the monitoring of the water environment easier, cheaper and more accessible, and Freshwater Habitats Trust is excited to be at the forefront of pioneering the use of this novel survey technique. 

Great Crested Newt eDNA Kit