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

Authors: SCHMIDT, VICTOR - Marine Biology Laboratory; AMARAL-ZETTLER, LINDA - Marine Biology Laboratory; DAVIDSON, JOHN - Freshwater Institute; SUMMERFELT, STEVEN - Freshwater Institute; GOOD, CHRISTOPHER - Freshwater Institute

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/21/2016
Publication Date: 4/29/2016
Citation: Schmidt, V., Amaral-Zettler, L., Davidson, J., Summerfelt, S., Good, C. 2016. The influence of fishmeal-free diets on microbial communities in Atlantic salmon Salmo salar recirculation aquaculture systems. Applied and Environmental Microbiology. doi: 10.1128/AEM.00902-16.

Interpretive Summary: The stability of bacterial populations in recirculation aquaculture systems (RAS) is highly important for optimal RAS performance; however, changes in fish diet composition can potentially alter RAS microbiomes, water quality, and overall system performance. Given the movement towards alternative proteins in fish feeds, we tested the influence of a fishmeal-free diet on the microbiomes in replicated RAS, specifically examining microbial communities in RAS water, biofilters, and fish microbiomes (gill and intestine) as Atlantic salmon (Salmo salar) were grown to market-size, and compared these microbiomes to those in RAS provided traditional fishmeal feeds. Our results indicate that diet has a clear influence on microbiome structure of the salmon intestine, particularly within the order Lactobacillales; however, we observed an overall strong stability of taxa likely involved in RAS water quality processing irrespective of diet type, and therefore our results suggest that changes in diet composition may not significantly impact RAS biofiltration performance.

Technical Abstract: The 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 promoting price instability. Advances in 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, we know less 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 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 adult market-ready intestines and gills, 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. We conclude that strong stability of taxa likely involved in water quality processing (e.g. Nitrospira) regardless of diet, may further alleviate concerns regarding the use of alternative feeds in RAS operations.