Impact of husbandry practice on the gill microbiome of Salmo salar and Oreochromis niloticus

The major aquatic interface between host and environment in teleost finfish species is the gill. The diversity of this infraclass, high complexity of the organ and direct exposure to the surrounding environment make it an ideal candidate for furthering our understanding of the intwined relationships between host and microbiome and for monitoring health status in aquaculture practices. Capturing the structure and diversity of bacterial communities from this low biomass, ‘inhibitor-rich’ tissue can, however, prove challenging. Moreover, little is known about the gill microbiome of farmed fish with particular emphasis to the impact of farm husbandry practises, and its potential use as a health and welfare management tool. Through the development of qPCR assay for both host genomic DNA and bacterial 16S rRNA gene, and exploring the community composition using amplicon sequencing, a robust method for sample collection for gill microbiome analysis was developed. The impact of normalising 16S rRNA amplicon sequencing libraries to equal copy numbers of 16S rRNA, starting material concentration, and microbiome DNA enrichment on the recovered microbial diversity were explored. Results showed that the non-invasive approach of gill sampling (swabbing) significantly improved the bacterial 16S rRNA recovery, minimised host DNA, and thereby remarkably increased abundance and diversity of bacteria captured as opposed to the other sampling approaches (surfactant-washed gills and whole gill tissue). Quantifying 16S rRNA and normalising the input to equal copy numbers of 16S rRNA prior to costly library construction showed significant improvements with regards the fidelity of the final data. Utilising the optimised protocol for gill microbiome sampling and analysis, in-depth characterisation of gill and skin microbiomes in co-cultured Nile tilapia (Oreochromis niloticus) and grey mullet (Mugil capito) in semi-intensive pond systems was performed. In addition, the impact of farm practices on the Atlantic salmon (Salmo salar) gill health in terms of microbiome and the associated immune response were investigated. In semi-intensive pond systems, the external autochthonous communities of co-cultured tilapia and mullet were not a passive reflection of their allochthonous communities. The autochthonous bacterial communities of the skin were distinct from those of the gill in both species, indicating that the external microbiome is likely organ specific. Gill autochthonous communities were clearly species specific, whereas skin communities showed higher commonalities between both species. Finally, salmon farm practises including thermal treatment for sea lice, freshwater treatment for amoebic gill disease, and net cleaning had a significant impact on markers of gill immune response and gill microbial community composition. These observations highlight the promising use of gill microbiome as a health and welfare management tool.