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，据报道，由于鳃性能受损，英国鲑鱼在海上的死亡率显著增加。在2019年至2022年期间报告的死亡中，高达70%归因于鳃健康状况，据报道有上升趋势，其中鳃健康不良是英国鱼类死亡的最重要驱动因素。2022年，英国三文鱼行业的鱼类死亡率为1490万(苏格兰鱼类健康监察局)。环境数据表明，在鲑鱼海水生产期间，沿海水域变暖导致海洋环境发生变化。因此，鳃的健康挑战已经成为行业内的一个严重问题，由于阿米巴鳃病(AGD)和/或复杂鳃病(CGD)感染导致的死亡率不断上升，导致气体交换受损、生长不良以及严重的发病率和死亡率。目前的治疗方法是有限的，包括在整个生产周期内对受影响的鱼进行过氧化氢或淡水浴。最近纳入了基于循环水产养殖系统(RAS)的淡水生产，改变了三文鱼的生产周期，与季节变化无关，这对淡季养殖系统的投入有很大贡献。这意味着养殖的鱼类在海上经历了两个完整的夏季时段，导致接触病原体的时间翻了一番，从而导致近些年来该行业内观察到的海水表现不佳和死亡率增加。较差的三文鱼表现并不是某家三文鱼生产商独有的，整个行业都在观察到这一点。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。在鳃上定植的微生物群落统称为鳃微生物群落，对保持良好的鳃健康至关重要，并直接受到水产养殖健康管理干预措施的影响，如申请者所证明的在海水中对AGD进行淡水处理。重要的是，目前的研究还表明，对阿米巴鳃病(AGD)的病原体--Perurans新阿米巴感染的抵抗力具有遗传成分。这表明寄主对AGD的抗性是可遗传的，因此可以通过选择性繁殖来达到目标。目前，鳃健康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养殖计划中确定对AGD的抗性。该项目将直接展示鲑鱼的遗传家族背景与水产养殖环境之间的关系，以及这些相互作用如何在AGD感染期间对鳃健康产生影响，并在多种健康管理干预措施(淡水处理)期间对鳃健康产生影响。该工作方案是利用位于水产养殖研究所的最先进的淡水和海洋水族箱研究以及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、16SrRNA和元基因组DNA测序。该项目将极大地扩展当前的知识，突出鳃微生物组在抗病和鲑鱼健壮方面的作用，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养殖战略，以证明未来英国可持续的鲑鱼养殖。

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.