| Summary: | Gill pathologies, especially the Amoebic Gill Disease (AGD), present one of the main health concerns for marine aquaculture worldwide. In Ireland alone, Atlantic salmon (Salmo salarL.) production in fish farms was 12,000 tonnes worth €114.5 millionin 2018, but the mortality of the livestock in marine farms due to AGDreaches an average between 10-20% every year. As of yet, the most common means to reduce AGD is to control the abundance of its first aetiological agent, the free-living amoebaNeoparamoeba perurans, that typically produces white mucoid patches on infected gills. There are two main ways to diagnose AGD: i)by scoring gills based on the abundance of white patches onthem; ii)quantifying N. peruransabundance ongillsusing quantitative-PCR assays. However, these diagnosis toolsare only useful in confirming the amoeba colonisation on gills, being unable to determine the vulnerability to AGD prior to the colonisation.Indeed, our understanding of AGD is far fromcomplete; specifically, the role of the gill microbiome from seawater farmed salmon and how it responds to anAGDepisodeis limited. The present thesis mainly aimed to characterise the prokaryotic gill microbiome from farmed Atlantic salmon (Salmo salarL.) before and during an AGD episodeusing high-throughput sequencing approaches. Afirst sampling campaign was carried out in a single Irish fish farm, where gill and mucus from gills were sampled from Atlantic salmonfrom May to October in 2017. A novel DNA extraction procedure was optimised and used to get the microbiome DNA from entire gill arches, with the objective to avoid under-sampling and taxa under-representation that could happen as a result of characterising the gill microbiome from part of a gill arch. On the other hand, the microbiome DNA in mucus samples was extracted and isolated aiming to test the efficacy of mucus sampling as a suitable alternative source to gills for AGD microbiome analyses. A set of variables, such as AGD gill scores, N. peruransabundance on gills, fish condition factor, ...
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