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

欧洲牡蛎(Ostrea Edulis)曾经分布广泛，但现在是稀有的，威胁到生物多样性的热点。它们是许多鱼类和无脊椎动物重要的育苗和觅食栖息地，也起到稳定海床和防止海岸侵蚀的作用。由于过度捕捞和人为驱动的海洋环境变化，欧洲本土牡蛎种群已经在功能上灭绝了100年。目前正在多诺克湾(Dornoch Environmental Enhulation Project-DEEP)进行一项重大修复项目，将牡蛎重新引入特别保护区(SAC)，作为欧洲恢复性海洋保护区(MPA)管理的示范。应用严格的生物安全协议将牡蛎转移到该地区，对于消除外来入侵物种(INN)的生物多样性风险至关重要。客栈是全球生物多样性丧失的主要驱动力；它们争夺食物和空间，在某些情况下，一旦建立就改变了整个环境的功能。意外地将客栈引入多诺克湾可能会对SAC和修复行业的保护产生长期的负面影响。由于野生本土牡蛎的短缺，重新引入的牡蛎是从苏格兰精选的贝类养殖场获得的。贝类种群的移动已被确定为引入INN的重要途径，已知许多物种与水产养殖活动有关。近年来，两种重要的被囊类入侵物种被确定为高危入侵种，即毛球海鞘和柄海鞘。DNA测序方面的最新技术进步使从水等环境样本中检测目标物种和监测整个群落的工作发生了革命性的变化，而不需要肉眼观察。对所谓环境DNA(EDNA)的检测目前正在改变在水生和陆地环境中捕获和描述生物多样性的方式。EDNA的检测已被证明是检测水环境中INN的有力工具，即使在传统调查方法失败的情况下，也显示出成功检测的潜力。该项目将探讨以EDNA为基础监测土著牡蛎种群中是否存在Inns的可行性，以及对支持深海牡蛎养殖场的牡蛎床恢复的生物多样性评估。这一高度多学科的项目将涉及实地采样、水族馆实验、基于实验室的标记物开发和验证、生物信息学和统计建模。将进行实地实验，以评估EDNA的持久性，以及这种持久性如何因水温、盐度和潮汐流量等环境因素而变化。然后将使用站点占用模型来量化EDNA的存在，同时考虑到不完美的检测概率。该项目还将涉及在水族馆进行实验，以估计Inns Edna的检测概率，并评估在实验室开发的分析的敏感性和特异性。元编码，使用第二代测序平台，现在被常规用于描述各种生态系统中的生物多样性，并已被证明是监测客栈的一种强有力的方法。此外，最近开发的第三代测序平台，如牛津纳米孔MINION，为更传统的高温超导平台提供了一种经济高效的替代方案，并为开发便携式监测平台提供了机会，可以直接在现场分析样品。

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.