The role of the microbiome in the gill health of farmed Scottish Atlantic salmon

The mucosal gill microbiome of finfish, in particular those of commercial importance such as farmed Atlantic salmon (Salmo salar) is a growing area of research, with notable gaps in knowledge on the composition and structure of the gill microbiomes. It is recognised that mucosal microbiomes can play important roles in the health and immunities of host organisms, as may the mucosal gill microbiome with gill disease. Complex Gill Disease (CGD), in which non-specific pathological changes occur, possibly in conjunction with one or more types of distinct gill diseases, is now a major threat to the health and welfare of farmed Atlantic salmon. To investigate the role of the gill microbiome in the gill health of farmed Atlantic salmon, two cohorts were tracked from input till harvest by sampling every two or four weeks. Characterisation of these microbiomes from marine stocking until harvest shows that gill microbiomes are dynamic in nature, constantly changing in structure and composition during the production cycle. Both cohorts exhibited a degree of uniqueness in their microbiomes when compared, presenting multiple genera in different abundances across time. Environmental factors such as salinity and surface temperature were found to drive the variation in beta diversity over time, with evidence of seasonal linked temporal changes. Moreover, while gill disease status may drive variance in the microbiome of salmon, environmental factors and the presence of putative pathogens also drive microbiome changes during these times.

硬骨鱼类的鳃黏膜微生物组（microbiome），尤其是具有商业养殖价值的种类（如养殖大西洋鲑（Salmo salar）），是当前日益受到关注的研究领域，但学界对鳃微生物组的组成与结构仍存在诸多认知空白。学界已达成共识：黏膜微生物组对宿主的健康与免疫功能发挥重要作用，鳃黏膜微生物组亦与鳃部疾病的发生发展密切相关。复杂性鳃病（Complex Gill Disease, CGD）以非特异性病理变化为特征，可能伴随一种或多种特异性鳃部疾病，目前已成为威胁养殖大西洋鲑健康与福利的主要问题。为探究鳃微生物组在养殖大西洋鲑鳃部健康中的作用，本研究对两批养殖群体开展了从入池到收获的全程追踪，每2或4周采样一次。对从海水放养至收获阶段的微生物组进行表征分析后发现，鳃微生物组具有动态变化的特性，在整个养殖周期内其结构与组成始终处于动态调整中。两组养殖群体的微生物组均表现出一定的个体特异性，随时间推移，不同菌属的丰度呈现出差异化分布。研究发现，盐度、表层水温等环境因子是驱动β多样性随时间变化的主要因素，且存在与季节相关的时间序列变化特征。此外，尽管鲑鱼的鳃部疾病状态可影响其微生物组的变异，但环境因子与潜在病原体的存在同样会在此阶段推动微生物组发生改变。