Using environmental DNA research to trace endangered - or invasive - species

Reliable surveying techniques are essential to aid the protection of endangered species and chart the spread of invasive species. Using environmental DNA (eDNA), researchers at the University of Derby are transforming the way different species can be detected, monitored and quantified, opening up avenues for the conservation of rare species and for the effective management of non-native species which are invading and colonising various freshwater habitats worldwide.

Finding the correct method

Environmental DNA assessment methods developed and validated by the University’s Aquatic Research Facility, within the Environmental Sustainability Research Centre (ESRC), have already been transferred to industry for commercial use and adopted by leading national and international organisations working in the field of wildlife and habitat conservation and management.

Capable of detecting very small numbers of individuals or populations, the eDNA approach is a more accurate, cost-effective, and time-efficient method of surveying that causes less damage to vulnerable habitats and does not require expert staff to collect samples.

The research team’s success lies in improving the way these methods can be used in freshwater environments, where eDNA is diluted and distributed by water movement and affected by environmental factors such as temperature and salinity. Their work has therefore involved rigorous validation for each new eDNA assay produced.

Our current findings

So far, they have devised specific eDNA assays for species like the white-clawed crayfish and the freshwater pearl mussel, both classified as endangered by the International Union for Conservation of Nature. The same methods have also been used to chart the presence of highly invasive species such as the demon shrimp and marbled crayfish which threaten native populations.

In one of its most important advances, the team partnered with forensic analysis specialists SureScreen Scientifics who have adopted and released assays for the white-clawed and signal crayfish as a new commercial service. This has allowed the company to diversify into ecological surveying markets and create new revenue streams. The impact of the collaboration was highlighted by the National Centre for Universities and Business in its State of the Relationship annual report for 2019.

Where our research has been used

The novel eDNA techniques have also been adopted for species-distribution surveys by a range of governmental, charitable and scientific organisations. The researchers were commissioned by:

• The Environment Agency to survey for crayfish as part of a weir removal project in Derbyshire
• Dorset Wildlife Trust to check for crayfish and disease outbreak in a river where traditional survey methods had failed
• Natural Resources Wales for a state-of-the-art survey, combining eDNA assays with a double droplet PCR technique, to detect a critically endangered stonefly.

International developments

Similar surveys have taken place at international locations through the team’s collaborations with researchers at the Hellenic Centre for Marine and Inland Waters Research in Greece, the Research Institute for Nature and Forest in Belgium, and the German Cancer Research Institute.

Funders

• Surescreen Scientifics
• Natural Environment Research Council (NERC)
• Environment Agency
• Natural England
• Centre for Environment, Fisheries and Aquaculture Science (Cefas)
• Department for Environment, Food and Rural Affairs (Defra)
• Marine Scotland
• Canal River Trust
• Dorset Wildlife Trust
• Zoological Society of London 

Researchers

• Dr Michael Sweet, Associate Professor in Aquatic Biology (2013-present)
• Dr Mark Bulling, Senior Lecturer in Ecology (2010-present)
• Dr Andrew Ramsey, Head of Environmental Sciences (2012-present)
• Dr Alfred Burian, Postdoctoral Researcher (2017-present)

Research papers:

• Influence of accuracy, repeatability and detection probability in the reliability of species-specific eDNA based approaches
• Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys
• The development of an eDNA based detection method for the invasive shrimp Dikerogammarus haemobaphes