The influence of fishmeal-free diets on microbial communities in Atlantic salmon Salmo salar recirculation aquaculture systems

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Reliance on fishmeal as a primary protein source is among the chief economic and environmental concerns in aquaculture today. Fishmeal-based feeds often require harvest from wild fish stocks, placing pressure on natural ecosystems and causing price instability. Alternative diet formulations without the use of fishmeal provide a potential solution to this challenge. Although the impact of alternative diets on fish performance, intestinal inflammation, palatability, and gut microbiota has been a topic of recent interest, less is known about how alternative feeds impact the aquaculture environment as a whole. The recent focus on recirculating aquaculture systems (RAS) and the closed containment approach to raising food fish highlights the need to maintain stable environmental and microbiological conditions within a farm environment. Microbial stability in RAS biofilters is particularly important, given its role in nutrient processing and water quality in these closed systems. If and how the impacts of alternative feeds on microbial communities in fish translate into changes to the biofilters is not known. We tested the influence of a fishmeal-free diet on the microbial communities in RAS water, biofilters and salmon microbiomes using high-throughput 16S rRNA gene V6 hypervariable region amplicon sequencing. We grew Atlantic salmon (Salmo salar) to market-size in six replicate RAS tanks, three with traditional fishmeal diets and three with alternative protein, fishmeal-free diets. We sampled intestines and gills from market-ready adult fish, water and biofilter media in each corresponding RAS unit. Our results provide the first data on how fish diet influences the RAS environment, and corroborates previous findings that diet has a clear influence on microbiome structure of the salmon intestine, particularly within the order Lactobacillales (lactic acid bacteria). We conclude that strong stability of taxa likely involved in water quality processing regardless of diet (e.g. Nitrospira) may further alleviate concerns regarding the use of alternative feeds in RAS operations.
© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Applied and Environmental Microbiology 82 (2016): 4470-4481, doi:10.1128/AEM.00902-16.
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Applied and Environmental Microbiology 82 (2016): 4470-4481
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