Mitigating salmon gill disease by integrating genotype-environment studies with host-gill microbiome associations

鳃健康是鲑鱼研究的优先领域，由于鳃性能受损，英国鲑鱼在海上的死亡率显着增加。2019-2022年期间报告的死亡率高达70%归因于鳃健康状况，其中鳃健康状况不良是英国鱼类死亡率最重要的驱动因素。2022年，英国鲑鱼行业的鱼类死亡人数为1490万人（苏格兰鱼类健康检查局）。环境数据表明，在鲑鱼的海水生产期间，沿海水域的变暖导致海洋环境的变化。因此，鳃健康挑战已成为行业内的严重问题，由于阿米巴鳃病（AGD）和/或复杂性鳃病（CGD）感染导致的死亡率增加，导致观察到的气体交换受损、生长不良以及严重的发病率和死亡率。目前的治疗方法有限，包括在整个生产周期中对受影响的鱼类进行过氧化氢或淡水浴。鲑鱼生产周期的变化，最近纳入循环水产养殖系统（RAS）为基础的生产，在淡水中，这是独立于季节变化，大大有助于淡季投入到养殖系统。这意味着养殖鱼类在海上经历了两个完整的夏季，导致病原体暴露增加一倍，因此导致海水性能差，死亡率增加，近年来在行业内观察到。Popletin SW的性能并不是一个鲑鱼生产商所独有的，整个行业都在观察。鳃是鱼类最大的外表面，是气体交换的中心，现在也被认为是病原体进入和定居的场所。集落在鳃上的微生物群落统称为鳃微生物组，是维持良好鳃健康的关键，并直接受到水产养殖健康管理干预措施的影响，如申请人证明的海水中AGD的淡水处理。重要的是，目前的研究还显示了对阿米巴鳃病（AGD）病原体Perurans感染的抵抗力的遗传成分。这表明宿主对AGD的抗性是可遗传的，因此可以通过选择性育种来靶向。鳃健康现在被认为是行业内最高的健康挑战，并被视为优先研究领域。促进改善鱼类福利和生存的一个关键研究领域是在大西洋鲑鱼育种计划中鉴定对AGD的抗性。该项目将直接展示鲑鱼遗传家族背景和水产养殖环境对鳃微生物群组成的关系，以及这些相互作用如何影响AGD感染期间的鳃健康和多种健康管理干预（淡水处理）期间的鳃健康。该工作计划是利用位于水族馆研究所的最先进的研究淡水和海洋水族馆，结合一套完善的分析方法，包括一套优化的分子生物学技术，包括基因分型，16 SrRNA和宏基因组DNA测序。该项目将极大地扩展现有知识，突出鳃微生物组在抗病性和鲑鱼健壮性中的作用，重要的是，通过我们的商业合作伙伴，将直接影响商业选择性育种策略，以证明英国未来的可持续鲑鱼养殖。

Gill health is a priority area for salmon research with significantly increased UK salmon mortalities at sea being reported due to compromised gill performance. Up to 70% of mortalities reported between 2019-2022 have been attributed to gill health conditions with an upward trend reported where poor gill health is the most important driver for fish mortality in the UK. Fish mortalities across the UK salmon sector were 14.9 million in 2022 (Fish Health Inspectorate, Scotland). Environmental data indicates a warming of coastal water causing changes to the marine environment during the seawater production of salmon. As a result, gill health challenges have become a severe problem within the industry with increasing mortalities due to Amoebic gill Disease (AGD) and/or Complex Gill Disease (CGD) infections leading to impaired gas exchange, poor growth and severe morbidity and mortality being observed. Current treatments are limited and include hydrogen peroxide or freshwater bathing of affected fish throughout the production cycle. Changes to the production cycle of salmon by the recent incorporation of recirculating aquaculture system (RAS) based production in freshwater, that is independent to seasonal change, contributes significantly to off-season inputs into farming systems. This means that the farmed fish experience two full summer periods at sea leading to a doubling of exposure to pathogens therefore driving poor seawater performance and increased mortalities as observed within the industry in recent years. Poorer SW performance has not been exclusive to one salmon producer and has been observed across the industry. The gills represent the largest external surface of fish and are central to both gaseous exchange and are now also recognised as a site for pathogen entry and colonisation. The microbial communities colonising the gills collectively named as the gill microbiome are central to maintaining good gill health and are directly affected by aquaculture health management interventions such as freshwater treatment of AGD in seawater as demonstrated by the applicants. Importantly, current research has also shown a genetic component to resistance to infection by Neoparamoeba perurans, the causative agent of Amoebic Gill Disease (AGD). This indicates that host resistance to AGD is heritable and therefore can be targeted by selective breeding.Gill health is now regarded to be the highest health challenge within the industry and regarded as a priority area of research. A key area of research to promote improved fish welfare and survival is the identification of resistance to AGD within Atlantic salmon breeding programs. This project will directly demonstrate the relationships between genetic family background in salmon and aquaculture environment on the composition of the gill microbiome and how these interactions impact upon gill health during AGD infection and gill health during multiple health management interventions (freshwater treatments). The programme of work is assembled using current state of the art research freshwater and marine aquaria located at the Institute of Aquaculture combined with a suite of refined analytical methods including a suite of optimised molecular biology technologies including genotyping, 16SrRNA and metagenome DNA sequencing. This project will dramatically extend current knowledge highlighting the role of the gill microbiome in disease resistance and salmon robustness and importantly through our commercial partner will directly impact upon commercial selective breeding strategies to future proof sustainable salmon farming in the UK.