Prokaryotic diversity in marine and freshwater recirculating aquaculture systems

Abstract Intensive aquaculture food production has been continually increasing over the past decades. Recirculating aquaculture is an innovative technology which relies on water reuse and removal of toxic metabolites by utilizing specific prokaryotic groups such as nitrifiers, settled in special biofilters. Focused on recent next generation sequencing‐based studies on the microbiome of recirculating aquaculture systems, this review highlights dominant genera and families, and investigates their possible metabolic function in key niches within recirculating aquaculture systems (rearing water, biofilters and fish mucosal microbiome), while aiming to identify core prokaryotic groups across studies. A total of 136 genera belonging to 77 families and 13 phyla have been characterized as dominant or functionally important in relevant studies, mainly isolated from nitrification biofilters, system water and intestinal samples of the farmed species. Proteobacteria is undoubtedly the most abundant phylum, followed by Bacteroidetes, Firmicutes and Actinobacteria, while Rhodobacteriaceae and Flavobacteriaceae are the common dominant families. Nitrosomonadaceae and Nitrospira members are enriched in biofilter samples and serve as the most common ammonium and nitrite oxidizers, respectively. Composition of dominant genera appears system specific due to unique characteristics of individual RAS designs, although faint community patterns emerge when examining RAS by their salinity level. Considering the number of ribosomal RNA operon copies, 75% of genera are likely slow growers, dominating biofilter and water communities, whereas the few fast‐growing opportunists are mainly associated with the intestine of farmed species. Finally, this review stresses the lack of information regarding archaeal and microeukaryotic communities in recirculating aquaculture systems and prokaryotic–protist interactions.