Introduction
There is a growing interest in the gill health of economically important species such as Atlantic salmon ( Salmo salar) as this organ is central to many physiological functions and overall fish performance. As a mucosal surface , gills can be colonised by pathogens and act as a site of pathogen entry . Numerous pathogens and environmental factors contribute to the gill inflammation, but the underlying response mechanisms to the disease are poorly understood. The terms “c omplex g ill disorder” (CGD) and “p roliferative g ill disease” (PGD) reflect the complexity and multifactorial aetiology of gill inflammation. Microbiota associated with the gill mucosal surface that remain in homeostasis are believed to be an essential part of the gill immunity and health. Over the last decade, the interaction between microbiota and mucosal immunity has become an active field of research, aiming to improve understanding of gill health. The main objective of this study is to further our understanding of gill health in Sea farmed Atlantic salmon.
Materials and methods
We sampled Atlantic salmon from three different marine production sites in Scotland (A on Isle of Mull and B and C in Shetland) and examined the gills at three different levels of organization: gross morphology with the use of PGD scores (macroscopic examination), histopathology (microscopic examination) and microbial community composition (samples and other parameters fully described in Król et al. 2020) . Gill mucus swabs were taken from 75 fish in total and used to extract DNA. Gill microbiota composition was evaluated by sequencing the V3/V4 variable region of the bacterial 16S using an Illumina MiSeq platform, followed by analysis of a mplicon sequence variants (ASVs) with a DADA2 pipeline
. Functionality was inferred using Piphillin (Iwai et al. 2016).
Results
Fish from the three different sites (A, B and C) had significantly different gill microbiota composition (p < 0.001, Fig. 1) . The dominant gill microbial phyla were Actinobacteria , Bacteroidetes , Firmicutes and Proteobacteria, which is consistent with other salmonid studies (Brown et al., 2019) . Site C, which had lower gill histopathology scores than sites A and B (Król et al. 2020) , was characterised by significantly higher alpha diversity indices. All three sites were clearly separated by beta diversity . Despite the differences, all fish had a core gill microbiota that was shared between the sites. The functional analysis of the gill microbiota composition revealed the differences associated with the metabolic pathways.
Discussion and conclusions
The d iversity of the gill microbiota composition was predominantly associated with the origin of fish (sites A, B and C) , suggesting the importance of spatial and temporal drivers in shaping gill microbiota and gill health . Gill microbiota diversity was the highest in the fish with the lowest histopathology scores (site C), although the causality of this observation remains unknown. Oppositely , fish with the decreased gill microbiota diversity had higher gill histopathology scores (sites A and B). The relationship between gill microbiota composition and gill histopathology as well as their impacts on gill health require further studies.
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