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

淡水生态系统中的疾病动态：验证 eDNA 以告知野生和养殖鱼类的暴露风险

• 批准号: 2434399
• 金额: --
• 依托单位: University of Nottingham
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2434399
• 关键词: Disease; dynamics; freshwater; ecosystems; validation

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.

所有生物都通过脱落的细胞、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，并用于追踪例如稀有或入侵物种，或更广泛地追踪生物多样性（例如鱼类群落或无脊椎动物类群的多样性）。从宿主脱落到水中的寄生虫也可以与其宿主的eDNA同时检测和定量。这种基于eDNA的同时跟踪宿主和寄生虫分布的方法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，通过eDNA检测、监测和监视疾病病原体可能为实现可持续水产养殖提供重要工具。水产养殖与自然水生系统（洛克斯、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个持续存在的风险。eDNA可以提供特别重要的见解病原体的传播，溢出的潜力和时间变化的暴露风险的养殖动物。该项目将侧重于河流中的eDNA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传播如何影响相关养鱼场的暴露风险。该项目是跨学科的（生命科学和地理学之间的联合），学生将接受以下培训：1a）实地工作（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和寄生虫孢子衰变和释放的变化）。3)空间明确的分析/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：我们以前对鲑鱼寄生虫的研究表明，水中寄生虫密度高的热点发生在河流网络的不同部分。学生将使用eDNA采样来跟踪英国河流中的寄生虫浓度，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“热点”。取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，水中寄生虫的检测比宿主DNA的检测更具可变性。学生将在实验室/现场设计和进行实验，以对比宿主自然脱落的eDNA检测与水中寄生虫孢子的eDNA检测。空间显式模型：了解寄生虫的传播，保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内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。其目的是确定限制或促进传染性病原体传播的关键属性，以及河流网络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.，科尔，B，Balzter，H.，Martius，C.，Zlinszky，A.，Calvignac-Spencer，S.，Cobbold，C.A.道森，T. P.，2017.将地球观测与高通量生物多样性数据连接起来。自然生态学与进化，1（7），p.0176。https：//www.nature.com/articles/s41559-017-0176Carraro，L.，Hartikainen，H.，Jokela，J.，Bertuzzo，E. Rinaldo，A. 2018.利用环境DNA估算河网物种分布和丰度。