Environmental DNA (eDNA) monitoring for invasive non-native species to protect marine biodiversity

European oyster (Ostrea edulis) beds were once extensive and wide-spread but are now rare and threatened biodiversity hot-spots. They are important nursery and foraging habitats for many fish and invertebrates and also act to stabilise the seabed and prevent coastal erosion. European native oyster populations have been functionally extinct for 100 years due to overfishing coupled with anthropogenic-driven changes in the marine environment. A major restoration project in the Dornoch Firth (Dornoch Environmental Enhancement Project - DEEP) is currently being undertaken to reintroduce oysters into a Special Area of Conservation (SAC) as a demonstration of European restorative Marine Protected Area (MPA) management. Application of stringent biosecurity protocols for the transfer of oysters into the area is paramount in order to eliminate the risks to biodiversity of invasive non-native species (INNS). INNS are a major global driver of biodiversity loss; competing for food and space and in some cases altering the functioning of whole environments once established. Accidental introduction of INNS into the Dornoch Firth could have long lasting negative consequences for conservation in the SAC and the restoration industry. Due to the shortage of wild native oysters, reintroduced oysters are obtained from selected shellfish farms in Scotland. Movement of shellfish stock has been identified as an important pathway for introduction of INNS and numerous species are known to be associated with aquaculture activities. Recently, two priority invasive species of tunicate, Didemnum vexillum and Styela clava have been identified as high risk invasives. Recent technological advances in DNA sequencing has revolutionised the detection of targeted species and monitoring of whole communities from environmental samples such as water without the need for visual observation. The detection of so-called environmental DNA (eDNA) is currently changing the way biodiversity is captured and described in both aquatic and terrestrial environments. The detection of eDNA has been shown to be a powerful tool for the detection of INNS in aquatic environments, exhibiting potential for successful detection even on occasions when traditional survey methods failed. This project will explore the feasibility of eDNA-based monitoring for the presence of INNS in native oyster stocks and biodiversity assessment of oyster bed restoration in support of DEEP. This highly multidisciplinary project will involve field sampling, aquarium experiments, laboratory-based marker development and validation, bioinformatics and statistical modelling. Field experiments will be conducted to assess the persistence of eDNA and how this varies due to environmental factors such as water temperature, salinity and tidal flow. Site occupancy models will then be used to quantify the presence of eDNA whilst simultaneously accounting for imperfect detection probabilities. The project will also involve conducting experiments in the aquarium to estimate detection probabilities for INNS eDNA and assess the sensitivity and specificity of assays developed in the laboratory. Metabarcoding, using second-generation sequencing platforms is now routinely utilised for describing biodiversity in a variety of ecosystems and has been shown to be a powerful approach for the surveillance of INNS. In addition, the recent development of third-generation sequencing platforms such as the Oxford Nanopore MinION offers a cost-efficient alternative to more traditional HTS platforms and provides an opportunity to develop a portable monitoring platform to analyse samples directly in field.