Environment-driven shift of the microbial community in a flow-through rainbow trout farm across a reoccurred Viral Hemorrhagic Septicemia outbreak. Environment-driven shift of the microbial community in a flow-through rainbow trout farm across a reoccurred Viral Hemorrhagic Septicemia outbreak

The adaptation of Viral Hemorrhagic Septicemia virus (VHSV) to various aquatic environments puts both wild and farmed fish at great risk. To solve the problem, a better understanding of VHSV ecology is necessary, especially its potential relationship with other microorganisms. In the present study, we encountered a reoccurred VHS outbreak at a flow-through rainbow trout (Oncorhynchus mykiss) farm using untreated natural surface water. Before the outbreak, as well as during the early and late phase of the outbreak, we conducted metagenomic analyses of the upstream water, gill mucus and biofilm on submerged surface. Results indicate that the microbial community of gill mucus was similar to upstream water, while the biofilm microbial community differed from both. The temporal shift of the microbial community in upstream water directed similar changes in both gill mucus and biofilm. Potential correlation was discovered between the gill mucus-abundant bacteria and the VHS outbreak. The possibility of the ciliate Euplotes as potential intermediate vector of VHSV is proposed, hence a sudden increase of the symbiotic bacterium Polynucleobacter necessarius on fish mucosal surface may serve as an early warning sign. Evidence of distant environmental migration of extracellular VHSV is presented and apoptotic bodies from infected fish as a possible viral carrier is discussed. Biosecurity via water disinfection with peracetic acid (PAA) showed a non-selective and concentration-dependent effect on planktonic and biofilm bacteria. With periodic applications at a strong antibacterial concentration (1 mg/L), PAA can reduce fish mortality probably through inhibiting bacterial co-infections but not prevent viral infections.