Disease dynamics in freshwater ecosystems: validation of eDNA for informing exposure risk to wild and farmed fish

所有生物体都会通过脱落的细胞、粘液、排泄物等在环境中留下DNA的痕迹。这种环境DNA （eDNA）可以从水样中提取，用于追踪稀有或入侵物种，或更广泛地表征生物多样性（例如鱼类群落或无脊椎动物分类群的多样性）。寄生虫从宿主身上脱落到水中，也可以与宿主的eDNA同时检测和定量。这种基于edna的寄主和寄生虫分布的同时跟踪有可能极大地帮助了解水生疾病的流行病学。这一点很重要，因为疾病是扩大水产养殖业的主要障碍，而通过dna检测、监测和监测疾病病原体可能是实现可持续水产养殖的重要工具。水产养殖与自然水生系统（湖泊、河流、湖泊或河口）密切相关，自然动物和养殖动物之间的病原体溢出是一种持续存在的风险。eDNA可能对病原体扩散、溢出潜力和养殖动物暴露风险的时间变化提供特别重要的见解。该项目将侧重于在河流中进行dna采样，以跟踪寄生虫及其宿主的分布，并评估寄生虫在河流中的运输如何影响相关养鱼场的暴露风险。该项目是跨学科的（生命科学和地理学的联合），学生将接受以下方面的培训：1a)野外工作（eDNA和无脊椎动物宿主收集）和1b)分子实验室工作（eDNA提取、定量PCR、NGS文库制备和测序以及生物信息学）。2)实验室实验（量化eDNA变异和寄生虫孢子腐烂和释放）。3)空间显式分析/建模（eDNA和孢子运输/衰变）和量化感染热点的环境相关性。现场收集和分子工作：我们之前对鲑科鱼类寄生虫的研究表明，水中寄生虫密度高的热点发生在河网的不同部分。该学生将使用eDNA采样来追踪英国河流中寄生虫的浓度，并将浓度与鱼类和无脊椎动物宿主的存在（通过“元条形码”从eDNA测量）联系起来，以揭示暴露和感染的“热点”。采样地点将包括主要河流系统中养鱼场的上游和下游地点，以评估自然环境和养殖环境之间溢出的可能性。实验室实验：我们的初步工作表明，在水中检测寄生虫比检测宿主DNA更容易变化。学生将在实验室/现场设计并进行实验，以比较宿主自然脱落的eDNA和水中寄生虫孢子中产生的eDNA的检测结果。空间显式模型：了解寄生虫扩散、滞留和检测可能性的变化对于更好地重建受感染宿主的分布和了解网络中孢子的有效感染范围至关重要。学生将接受地理空间分析技术的培训，并使用最先进的遥感技术绘制河流网络和栖息地特征。目的是确定限制或促进传染因子传播的关键特性，以及河网拓扑结构如何修改从eDNA采样获得的物种分布信息。参考文献：Bush， A., Sollmann， R.,Wilting， A., Bohmann， K., Cole， B., Balzter， H., Martius， C., Zlinszky， A., Calvignac-Spencer， S., cobolold, ca .和Dawson， t.p., 2017。将地球观测与高通量生物多样性数据连接起来。自然生态与进化，1(7),p.0176。https://www.nature.com/articles/s41559-017-0176Carraro， L., Hartikainen， H., Jokela， J., Bertuzzo， E.和Rinaldo， A., 2018。利用环境DNA估算河网物种分布和丰度。

All organisms leave traces of DNA in the environment via sloughed cells, mucous, excretions etc. Such environmental DNA (eDNA) can be extracted from water samples and used to track e.g. rare or invasive species, or to characterise biodiversity more broadly (e.g. fish communities or diversity of invertebrate taxa). Parasites shed from hosts into water can also be detected and quantified simultaneously with the eDNA of their hosts. Such eDNA-based, simultaneous tracking of the host and parasite distributions has the potential to greatly aid in understanding the epidemiology of aquatic diseases. This is important because disease is the major obstacle to the expanding aquaculture industry, and detection, monitoring and surveillance of disease agents via eDNA may provide an important tool for achieving sustainable aquaculture. Aquaculture is closely associated with natural aquatic systems (lochs, rivers, lakes or estuaries) and pathogen spill-over between natural and farmed animals is a constant risk. eDNA may provide particularly important insights to pathogen dispersal, spill-over potential and the temporal variation in exposure risk of farmed animals. This project will focus on eDNA sampling in rivers to track the distributions of parasites and their hosts and assess how parasite transport in rivers affects exposure risk on associated fish farms. The project is interdisciplinary (joint between Life Sciences and Geography) and the student will receive training in: 1a) Field work (eDNA and invertebrate host collections) AND 1b) Molecular lab work (eDNA extraction, quantitative PCR, NGS library preparation and sequencing and bioinformatics). 2) Laboratory experiments (quantifying variation in eDNA and parasite spore decay and release). 3) Spatially explicit analysis/modelling (eDNA and spore transport/decay) and quantifying the environmental correlates of infection hotspots. Field Collections and Molecular Work: Our previous work on a parasite of salmonid fish has shown that hotspots of high parasite densities in water occur in different parts of a river network. The student will use eDNA sampling to track parasite concentrations across rivers in the UK, and relate the concentrations to the presence of fish and invertebrate hosts (measured from eDNA via "metabarcoding") to reveal exposure and infection 'hotspots'. Sampling locations will include sites upstream and downstream from fish farms,in key river systems, to assess the likelihoods of spill-over between natural and farmed settings. Lab experiments: Our preliminary work suggests that parasite detection in water is more variable than detection of host DNA. The student would design and conduct experiments in the lab/field to contrast the detection of eDNA naturally sloughed by hosts with the eDNA originating from parasite spores in water. Spatially explicit models: Understanding the variation in the dispersal, retention and detection likelihoods of parasites is crucial for better reconstructing the distributions of the infected hosts and understanding the effective infective range of spores within networks The student will be trained in geospatial analysis techniques and use state-of-the-art remote sensing to map river networks and habitat features. The aim is to identify the key properties that constrain or facilitate the spread of infectious agents and how river network topology modifies the species distribution information gained from eDNA sampling. References:Bush, A., Sollmann, R.,Wilting, A., Bohmann, K., Cole, B., Balzter, H., Martius, C., Zlinszky, A., Calvignac-Spencer, S., Cobbold, C.A. and Dawson, T.P., 2017. Connecting Earth observation to highthroughput biodiversity data. Nature Ecology & Evolution, 1(7), p.0176. https://www.nature.com/articles/s41559-017-0176Carraro, L., Hartikainen, H., Jokela, J., Bertuzzo, E. and Rinaldo, A., 2018. Estimating species distribution and abundance in river networks using environmental DNA.