Amoebic gill disease (AGD) affects many different species across a broad geographical range within the context of commercial finfish mariculture. Associated with high economic losses, 100 million USD from two outbreaks alone, considerable scientific endeavour has been undertaken to identify and mitigate the impact of this disease. Caused by the ectoparasite Neoparamoeba peruran s, significant effort has been made to understand the disease and inform approaches to control outbreaks and reduce loss. Currently, freshwater treatment is the method of choice for the treatment of AGD in Atlantic salmon farms however little is known about the impact of freshwater treatment on gill health and microbiome dynamics .
In this study , we sought to examine the impact of freshwater treatment of AGD on gill health. Several m ethods were used to characterise gill health and response to freshwater treatment including a detailed examination of the gill surface for microparasites using both histology and qPCR and targeted expression analysis of key markers of the Atlantic salmon gill immune response. Additionally, we analysed the bacterial communities present on the gill surface using a non-invasive sampling approach. Microbiome analysis was performed by developing a novel quantification protocol that included a titration step before building 16S rRNA amplicon libraries in this challenging tissue .
Results showed freshwater treatment of AGD had a notable impact on the Atlantic salmon gill microbiome and inflammatory responses. Gill bacterial community structure changed significantly after freshwater bath application (Figure 1). Our data indicated that the freshwater treatment not only decreased levels of N. perurans but also decreased the bacteria related to AGD. Parallel analyses of gene expression revealed that MHCII, IL-1β and TNF-α mRNA transcripts were downregulated after freshwater treatment, whereas TGF- β and IL-10 mRNA abundance was not impacted.