Amoebic gill disease (AGD) and complex gill disease (CGD) are recurrent gill disorders in Atlantic salmon, resulting in significant aquaculture losses. The role of gill microbiomes in gill disease development is unclear. We undertook a longitudinal study to characterise the gill tissue and gill mucus microbiomes of farmed Atlantic salmon before, and during, a gill disease episode. Using a newly optimised DNA extraction protocol, we sequenced rRNA genes from microbiomes of gill samples taken from 105 individual salmon on a farm, over a summer season. The AGD aetiological agent, Neoparamoeba perurans, was PCR-quantified targeting 18S rRNA genes. Similar analyses were carried out on mucus samples. Mucus scrapings were suitable, non-lethal substitutes for characterisation of the gill prokaryotic community in this study. Gill tissue and gill mucus microbiomes changed during the campaign, correlating with N. perurans concentrations. Time explained 35% of the gill tissue and gill mucus microbiome variance, while N. perurans concentrations explained 5%. Genera including Dyadobacter, Shewanella and Pedobacter were maximally abundant in gill and mucus samples at the timepoint prior to the the detection of gill disorder signs, at T3. Shewanella was significantly more abundant before than during the gill disease episode, and we suggest this genus could be considered in future studies addressing relationships between gill disease and the gill microbiome.

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.

S designed the experiments. K.N.D collected and maintained amoeba isolates and performed the protein extractions. K.N.D and O.S analysed and processed the raw mass spectrometry data. E.D provided statistical input on the mass spectrometry analysis. N.B provided the N. perurans protein database. V.B extracted N. perurans DNA, developed the OTU graph and aided in the results interpretation. K.N.D and O.S wrote the manuscript and critical revision was provided by A.T, I.O.C, E.MC, N.B and E.D. "The original Article and the Supplementary Information file that accompanies the article have been corrected.