eDNA and the fight against invasive non-native species (INNS)
Invasive non-native species (INNS) are one of leading causes of biodiversity loss worldwide and there is a demand for more...
APEM Group - Case Study
Yorkshire Water asked APEM Group to consider the reliability of eDNA as a species detection method and how it could be employed within their future environmental plans.
The aim of these plans is to protect and improve the ecological status of freshwater ecosystems. Innovation and technology are key drivers for water companies, so they were keen to explore the prospect of using eDNA as an innovative monitoring method.
Method
APEM Group scientists considered the reliability of commercially available (in the UK) eDNA assays for the detection of two high profile freshwater INNS, signal crayfish and killer shrimp. APEM also co-ordinated a series of field investigations to assess the comparability between eDNA and conventional monitoring for fish and aquatic macroinvertebrates.
During the work, APEM Group:
- Worked with Cardiff University to conduct a series of laboratory experiments where samples for eDNA analysis were collected from signal crayfish and killer shrimp housed under controlled conditions.
- Arranged the collection of eDNA samples in tandem with conventional monitoring for fish and aquatic macroinvertebrates using electro-fishing and kick-sampling respectively to compare the results.
- Collected samples from different habitats (lotic, or flowing, and lentic, or still), on varying spatial scales and used multiple sampling regimes (different levels of subsampling) to assess how eDNA results for fish (lotic only) and invertebrates were affected.
- Worked with multiple eDNA companies who provided the molecular analysis.
APEM Group field scientist holding up a Signal Crayfish
‘‘
Within the Water Research Institute at Cardiff University, we appreciate the opportunity to work on real-world problems with our stakeholders.
– Prof Jo Cable, Head of Organisms and Environment Division and Water Institute theme lead for Health
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A Signal crayfish
What they found
- Both signal crayfish and killer shrimp were detected by eDNA, but the results of the trials varied between the species.
- Signal crayfish were detected down to a density of 1 per 1,000 L but detection was only reliable at a density of 1 per 10 L.
- Killer shrimp could only be confirmed at a density of 1 per 1 L and even this was unreliable (confirmation was only possible for one of three replicates).
For the field investigations, the results, in terms of species detected, were comparable between eDNA and conventional methods for fish. All the species detected by electro-fishing were confirmed by eDNA. Additional taxa were detected by eDNA including those that are less likely to be picked up through electro-fishing due to their small size or low population density. Compared to some aquatic taxa, such as crustaceans, fish release larger amounts of DNA into the environment and are therefore one of the groups for which eDNA methods are best established.
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It has been incredibly rewarding working on this project with Yorkshire Water and Cardiff University. On behalf of the APEM Group I would like to thank Yorkshire Water for initiating this work and for making sharing the results a priority. This will enable industry-wide discussion around the role of eDNA in ecological monitoring. Thanks also to Cardiff University for undertaking the laboratory trials, the eDNA companies who provided the molecular analyses, and to everyone across the APEM Group who contributed to making this project a success.
– Dr Jo James, Principal Scientist, APEM Group
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Unlike for fish, results from the field investigations were not comparable between eDNA and conventional methods for aquatic macroinvertebrates. More individual species were detected with eDNA, but the number of families identified was lower compared to kick-sampling at all sites. For macroinvertebrates, eDNA assays are more proficient at detecting more abundant, smaller, free-floating taxa and taxa that release more DNA into the environment (e.g. filter feeders as opposed to hard-bodied taxa). Therefore, for macroinvertebrates, eDNA could currently be a complementary method of species detection but not a replacement.
eDNA results varied significantly between sampling locations within lentic but not lotic sites. In lentic systems, no significant difference was detected between samples comprising of different numbers of subsamples. In lotic systems, the effect of subsampling was taxa specific. For invertebrates, more taxa were detected in samples consisting of three compared to one subsample, whereas for fish the reverse trend was observed.
How useful is eDNA as a species detection method?
eDNA has somewhat been touted as a silver bullet that could replace conventional monitoring methods. Our findings are that, currently at least, it is a useful complementary method which appears to be reliable for the detection of some taxa. However, eDNA surveys need to be bespoke for species and habitats, for example, to account for differences in the propensity of species to shed DNA or for the reduced movement of DNA in still waters.
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This project has helped us shape how we deliver efficient, evidence-based monitoring to benefit Yorkshire’s Rivers. Yorkshire Water is pleased to see the results from this project shared with our catchment partners and wider industry and would like to thank all involved in this project.
– Dr Steph Bradbeer, Lead Ecologist, Yorkshire Water
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Both of the scientific publications related to this project are openly accessible using the following links:
- James J, Moore EM, Naden R, Aston B, Bradbeer SJ, Masud N, Cable J, Stebbing PD (2024). Using eDNA to detect freshwater invasive non-native species under controlled conditions. Management of Biological Invasions, 15: 41-50.
- James J, Moore EM, Naden R, Aston B, Bradbeer SJ, Stebbing PD (2024). The use of environmental DNA for biodiversity monitoring in lentic and lotic ecosystems. Ecological Solutions and Evidence, 5: e12361.
You can read summaries of these publications on our Science & Quality page or to contact Dr Jo James, Dr Paul Stebbing or Dr Emily Moore, use the form here.
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