Large-Scale, Multi-Year Microbial Community Survey of a Freshwater Trout Aquaculture Facility

Aquaculture is an important tool for solving growing worldwide food demand, but infectious diseases of the farmed animals represent a serious roadblock to continued industry growth. Therefore, it is essential to understand the microbial communities that reside within the built environments of aquaculture facilities to identify reservoirs of bacterial pathogens and potential correlations between commensal species and specific disease agents. Here, we present the results from three years of sampling a commercial rainbow trout aquaculture facility. The sampling was focused on the early-life stage hatchery building and included sampling of the facility source water and outdoor production raceways. We observed that the microbial communities residing on the abiotic surfaces within the hatchery were distinct from those residing on the surfaces of the facility water source as well as the production raceways, despite similar communities in the water column at each location. Within the hatchery building, most of the microbial classes and families within surface biofilms were also present within the water column, suggesting that these biofilms are seeded by a unique subgroup of microbial taxa from the water. Lastly, we detected a common fish pathogen, Flavobacterium columnare, within the hatchery, including at the source water inlet. Importantly, the relative abundance of this pathogen was correlated with clinical disease. Our results characterized the microbial communities in an aquaculture facility, established that the hatchery environment contains a unique community composition, and demonstrated that a specific fish pathogen resides within abiotic surface biofilms and is seeded from the natural source water. ImportanceThe complex microbial consortium residing in the built environment of aquaculture facilities is poorly understood. In this study, we provide a multi-year profile of the surface- and water-associated microbial communities of this biome. The results demonstrated that distinct community structures exist in the water and on surfaces. Furthermore, it was shown that a common and economically impactful bacterial pathogen, F. columnare, is continually introduced via the source water, is widespread within surface biofilms in the hatchery environment, and is likely amplified within these raceways but does not always cause disease despite being present. These results advance our understanding of pathogen localization at fish farms, show the interplay between host and environmental microbiomes, and reveal the importance of microbial community sequencing in aquaculture for identifying potential beneficial and harmful microbes. This study adds to the aquaculture microecology dataset and enhances our ability to understand this environment from a "One Health" perspective.