Cleaning the cleaner fish: managing the microbiome of lumpfish in hatcheries

清洁更干净的鱼：管理孵化场中肿块鱼的微生物组

• 批准号: 1939244
• 金额: --
• 依托单位: University of Bath
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2017
• 资助国家: 英国
• 起止时间: 2017 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-1939244
• 关键词: Cleaning; cleaner; fish; managing; microbiome

The salmon farming industry is worth almost £2 billion in Scotland alone, but in recent years the salmon louse (Lepeophtheirus salmonis) has become a widespread commercial problem leading to a 10% reduction in salmon production in 2016. The ectoparasites cause damage to fins, gills, and skin, and can disrupt ionic homeostasis in smolts, leaving the fish vulnerable to secondary infections. The salmon louse can lay thousands of eggs during its brief lifespan which increases the risk of infection to both farmed salmon and wild stock. Increasing resistance to pesticides and the misuse of Thermolicers, causing mass mortality events in salmon farms, has led the industry to turn to biocontrol. In particular cleaner fish have been successfully deployed to salmon cages to remove the lice from the salmon. The species most commonly used as cleaner fish are wrasse (Labridae) and lumpsuckers (Cyclopterus lumpus L.). Wrasse have been used to delouse salmon for almost thirty years and consequently commercial production is well developed. However, in recent years attention has moved to lumpfish as they continue to feed at temperatures as low as 4 degrees C and are ready for deployment to cages much earlier than wrasse. Lumpfish have traditionally been caught from the wild but this is an unsustainable approach and there is now a push to develop lumpfish as an aquaculture species in the UK. There has been a high mortality rate of lumpfish both pre- and post- deployment to salmon farms which is largely due to bacterial pathogens, including Pasteurella spp., Aeromonas salmonicida and other common aquaculture pathogens. A mounting body of evidence points to a central role for the microbiome in the development of the immune system and in providing direct protection against pathogens. An understanding of these interactions therefore holds great promise for improving fish husbandry. Currently, however, the microbiome of C. lumpus is completely uncharacterised. The main aim of the PhD is to characterise the microbiome of C. lumpus during the vulnerable early life stages (eggs, larvae, fry). By combining both genotypic (metagenomic) and phenotypic (experimental) approaches the project will aim to further understand the role of the microbiome in lumpsucker development, immunity and general health, and ultimately develop novel probiotics or prebiotics. Whole genome sequencing will be used to profile the bacterial communities at the level of species abundance and down to the level of individual genes. This will inform on community structure and function and give an insight into how different conditions the lumpfish are exposed to e.g. diet, water temperature and stocking density can impact on the microbiome. Antagonistic interactions will be examined between individual isolates and whole communities to identify likely pathogenic or protective species and the genes underpinning these reactions. Recent studies in other organisms have shown the microbiome can influence host behavior, including feeding patterns, which can be manipulated to increase the salmon cleaning efficiency. This project fits with the BBSRCs strategic research priority of agricultural and food security as the overall aim is to reduce the sea lice burden of salmon, thus increasing salmon production.

鲑鱼养殖业仅在苏格兰就价值近20亿英镑，但近年来鲑鱼虱（Lepeophtheirus salmonis）已成为一个普遍的商业问题，导致2016年鲑鱼产量减少10%。体外寄生虫会对鳍、鳃和皮肤造成损害，并破坏小鲑鱼体内的离子平衡，使鱼容易受到继发感染。鲑鱼虱在其短暂的生命周期内可以产下数千个卵，这增加了养殖鲑鱼和野生鲑鱼感染的风险。对杀虫剂的抗药性增加和Thermolicers的滥用，导致鲑鱼养殖场的大规模死亡事件，导致该行业转向生物控制。特别地，清洁鱼已经成功地部署到鲑鱼笼中以从鲑鱼中去除虱子。最常用作清洁鱼的物种是濑鱼（Labridae）和圆鳍鱼（Cyclopterus lumpus L）。濑鱼被用来去除鲑鱼的虱已有近30年的历史，因此商业化生产也得到了很好的发展。然而，近年来，人们的注意力已经转移到圆鱼身上，因为它们继续在低至4摄氏度的温度下进食，并且比濑鱼更早地准备部署到笼子里。块状鱼传统上是从野外捕捞的，但这是一种不可持续的方法，现在英国正在推动将块状鱼作为水产养殖物种。在部署到鲑鱼养殖场之前和之后，块状鱼的死亡率都很高，这主要是由于细菌病原体，包括巴氏杆菌属，杀鲑气单胞菌和其他常见水产养殖病原菌。越来越多的证据表明，微生物组在免疫系统的发育和提供针对病原体的直接保护方面发挥着核心作用。因此，了解这些相互作用对改善渔业大有希望。然而，目前，C. lumpus是完全没有特征的。博士学位的主要目的是研究C的微生物组。在脆弱的生命早期阶段（卵、幼虫、鱼苗）出现肿块。通过结合基因型（宏基因组）和表型（实验）方法，该项目旨在进一步了解微生物组在圆斑吸盘发育，免疫和一般健康中的作用，并最终开发新型益生菌或益生元。全基因组测序将用于从物种丰度水平到单个基因水平对细菌群落进行分析。这将为群落结构和功能提供信息，并深入了解圆鱼暴露于不同条件下的情况，例如饮食，水温和放养密度对微生物组的影响。将检查单个分离株和整个群落之间的拮抗相互作用，以确定可能的致病性或保护性物种以及支持这些反应的基因。最近对其他生物的研究表明，微生物组可以影响宿主行为，包括摄食模式，可以通过操纵来提高鲑鱼的清洁效率。该项目符合BBSRC农业和粮食安全战略研究优先事项，因为总体目标是减少鲑鱼的海虱负担，从而增加鲑鱼产量。