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.