LAUSR

Abstract Management of microbial communities in aquaculture systems to maximize and increase productivity has been gaining interest in recent years. A first step towards the development of aquaculture microbial management strategies is to understand the dynamics of microbial communities in these systems. Here we applied an in-depth 16S rRNA gene based high-throughput sequencing approach to study seasonal variation over a one-year period (with samples collected every two months) in the structure of bacterioplankton communities of a semi-intensive European seabass (Dicentrarchus labrax) aquaculture system and surrounding estuarine water. Despite seasonal variation, the aquaculture waters maintained a distinct bacterioplankton community throughout the year, characterized by a lower richness and a dominance of OTUs mainly assigned to the Rhodobacterales and Flavobacteriales orders. The overall analysis of bacterioplankton community dynamics showed an increased dominance of potential fish pathogens in estuarine water in September along with shifts in water pH, temperature, total organic carbon (TOC) and a reduction in the relative abundance of putative antagonistic bacterial groups, namely, the Roseobacter group and the Actinomycetales order. Interestingly, disease outbreak and fish mortality was observed during the following sampling event. This study emphasizes the importance of a better understanding of the influence of environmental variables and the dynamics of fish pathogens and naturally occurring putative antagonistic bacteria in order to develop pathogen control strategies in semi-intensive aquaculture systems.