Research and analysis

Operationalisation of eDNA methods for crayfish monitoring: summary

Published 16 December 2024

Applies to England

1. Chief Scientist’s Group report summary

This research project tested and validated the use of a new species-specific monitoring method that analyses genetic material in the environment (eDNA) to detect white-clawed crayfish, signal crayfish, and crayfish plague in English waterbodies. This method proved to be effective in detecting crayfish species and crayfish plague, therefore supporting its use for crayfish monitoring by the Environment Agency.

1.1 Background

White-clawed crayfish are a native species found in English rivers. They play an important role in river ecosystems and the delivery of ecosystem services. However, the white-clawed crayfish population has declined dramatically in recent decades, and they are now classified as ‘endangered’. This is due to the introduction of signal crayfish, an invasive, non-native species that outcompetes white-clawed crayfish. Signal crayfish also carry the pathogen, crayfish plague, which infects and is fatal to white-clawed crayfish.

The Environment Agency is responsible for monitoring crayfish populations and their health in England. Crayfish monitoring is currently reliant on resource intensive trapping and visual field surveys that are conducted in the summer months when crayfish are more active. However, developments in technologies for analysing eDNA from water samples has led to the development of a new, more sensitive method for detecting and tracking white-clawed crayfish, signal crayfish, and crayfish plague without the need to see or trap them.

1.2 Approach

A protocol was developed to collect eDNA samples. To test the eDNA crayfish method, 72 samples were collected from six waterbodies in northern England on a minimum of four occasions between November 2021 and February 2023. Four waterbodies with known target species present were selected for testing and two with no target species thought to be present acted as controls.

1.3 Results

Most results (67 of a total 72 eDNA tests undertaken) matched expectations regarding the presence or absence of the target species at the sampling location. This gives us confidence in the accuracy and specificity of the eDNA method. All three target species were detected at sites outside the traditional sampling window, meaning this method also enables year-round monitoring. There were 2 sampling instances at one location where target species were not detected, despite being expected to be present. Conversely, white-clawed crayfish and crayfish plague were unexpectedly detected on several occasions at another location; this is probably due to downstream transport of genetic material from white-clawed crayfish populations present in the river’s tributaries. This highlights that the transport of genetic material along rivers needs to be considered when interpreting results.

During the trial a crayfish plague outbreak was detected at a site using eDNA methods, and later confirmed by visual surveying. This led to the declaration of an incident in January 2023 and action to conserve healthy, white-clawed crayfish was taken. Using the eDNA method meant the crayfish plague outbreak was detected much earlier and enabled healthy, white-clawed crayfish to be relocated to plague-free sites, ready to be reintroduced once the crayfish plague burnt itself out. Had eDNA not been used the outbreak would not have been detected until the annual crayfish survey later in the year or when there were sightings of dead crayfish at the site.

1.4 Conclusions

This research showed that the sampling protocol was effective in collecting eDNA and minimising contamination, and staff reported that it was easy to follow. We demonstrated that a positive eDNA detection is strongly correlated with crayfish presence, meaning this method is suitable for operational use in crayfish monitoring. This study demonstrates the value of eDNA-based monitoring method, and we suggest that exploring the use of similar methods for monitoring other plant and animal species of interest could be of benefit to the Environment Agency.

1.5 Publication details

This summary relates to information from the following project:

• Title: Operationalisation of eDNA methods for Crayfish monitoring
• Project manager: Kerry Walsh, Chief Scientist’s Group

This project was commissioned by the Environment Agency’s Chief Scientist’s Group, which provides scientific knowledge, tools and techniques to enable us to protect and manage the environment as effectively as possible.

Enquiries: [email protected].

© Environment Agency