Dynamic Gill and Mucous Microbiomes Track an Amoebic Gill Disease Episode in Farmed Atlantic Salmon

Background Amongst gill disorders in Atlantic salmon, amoebic gill disease (AGD) is currently one of the most common and virulent, resulting in large losses for the aquaculture industry. However, our understanding of the role of the gill microbiome during AGD development is limited. Thus, we undertook a longitudinal study with the main objective of characterising the microbiome of gill, and mucous, samples from farmed Atlantic salmon before, and during, an AGD episode. Using a newly optimised DNA extraction protocol, we sequenced rRNA genes from 90 Atlantic salmon gill microbiomes from a fish farm (West coast of Ireland) over the course of a summer season. The first aetiological agent of AGD, Neoparamoeba perurans , was quantified using PCR targeting 18S rRNA genes. The same analyses were done using mucous samples as suitable, non-lethal alternatives to gill samples. Microbiome features across the sampling campaign were distinguished, focusing on patterns before and during the AGD episode. Results The richness and balance of the prokaryotic community on gills were trending upwards prior to the first appearance of AGD symptoms. The microbiome changed significantly, with reduced diversity and balance, after the AGD episode was confirmed, and the changing bacterial community was driven by competitive exclusion. However, this trend was reversed with the application of a first, and a second, freshwater bath treatment. Mucous samples behaved similarly. The variance of the entire prokaryotic community from both gill and mucous samples was significantly affected by the abundance of N. perurans . Rubritalea sp. were abundant in every gill and mucous sample; however, other genera ( Dyadobacter, Shewanella and Pedobacter ) were maximally abundant in gill and mucous samples 12 days prior to the first detection of AGD symptoms. Conclusions Gill and mucous microbiomes changed significantly after the first AGD symptoms were evident, correlating with N. perurans concentrations and supporting a connection between the development of the AGD and the gill microbiome. Those changes, however, were reversed by the application of multiple freshwater treatments, which returned gills to a more healthy state. Despite differences between microbiome features from gill and mucous samples, the data establish mucous scrapings as suitable, non-lethal substitutes for partial characterisation of the whole prokaryotic community from fish gills. The genus Shewanella was widely present, and significantly more abundant, immediately before the first AGD symptoms than during the AGD episode, marking this out as a feasible, putative target in identifying proxies for early detection of AGD.