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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #394200

Research Project: Improving Salmonid Health through Breeding, Vaccination and Microbiome Modulation

Location: Cool and Cold Water Aquaculture Research

Title: A large-scale, multi-year microbial community survey of a freshwater trout aquaculture facility

item GRAF, JOERG - University Of Connecticut
item TESTERMAN, TODD - University Of Connecticut
item BEKA, LIDIA - National Institutes Of Health (NIH)
item REICHLEY, STEPHAN - Mississippi State University
item KING, STACY - Colorado State University
item Welch, Timothy - Tim
item Wiens, Gregory - Greg

Submitted to: FEMS Microbiology Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/30/2022
Publication Date: 9/1/2022
Citation: Graf, J., Testerman, T., Beka, L., Reichley, S.R., King, S., Welch, T.J., Wiens, G.D. 2022. A large-scale, multi-year microbial community survey of a freshwater trout aquaculture facility. FEMS Microbiology Ecology. 98:1-15.

Interpretive Summary: The microbiome found on, in, and around farmed aquatic species strongly influences development, disease, and overall health. This paper describes the microbial communities residing on surfaces and within the water column of a rainbow trout aquaculture facility in Idaho with a specific focus on the indoor hatchery building. Additionally, this paper tracked the localization and relative abundance of an economically-impactful fish pathogen, Flavobacterium columnare. This work is important as it characterizes an understudied environmental space within the aquaculture system and provides information on sources and reservoirs for pathogens in flow-through farm systems.

Technical Abstract: 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.