Microbial succession and dominance patterns in modular RAS and their implications for effluent-based Phaeodactylum tricornutum cultivation

Microbial communities are central to water quality, fish health, and operational stability in modular recirculating aquaculture systems (M-RAS). The composition and succession of microbial communities in the main production tank and the effluent were investigated during an Atlantic salmon grow-out period using 16S rRNA gene sequencing. Effluent from the aquaculture system was further reused for cultivation of Phaeodactylum tricornutum, enabling assessment of how effluent-derived microbial communities respond to algal growth conditions. In the main production tank, microbial communities showed an early shift from Rhodobacterales toward increasing dominance of Flavobacteriales, followed by a community assemblage with strong contributions by taxa of Thiotrichales and Chitinophagales. Operational disturbances, including reduced feeding and salinity adjustment, coincided with increased relative abundances of ASVs affiliated with Arcobacteraceae, Weeksellaceae, and Pseudoalteromonadaceae, taxonomic groups that include species described as opportunistic or pathogen-associated in marine fish systems. The effluent harboured a temporally variable microbial community throughout the grow-out period, characterized by fluctuations in the relative abundances of dominant orders such as Flavobacteriales, Enterobacterales, and Bacteroidales. Microbial communities in effluent studied during a two-week cultivation of P. tricornutum shifted toward taxa typical of algal phycospheres, including Caulobacterales and Rhodobacterales, which are often linked to mutualistic functions between algae and bacteria such as vitamin provision and nutrient remineralization. However, the effluent also harboured Bacteroidetes taxa (e.g., Maribacter , Zobellia , Aurantivirga ), some of which have been reported in other systems to compete with diatoms for resources. Their presence during algal cultivation may therefore warrant consideration if the resulting biomass is intended for use in aquafeeds. These findings suggest that microbial community composition in M-RAS responds to operational adjustments, and that effluent reuse for algal cultivation not only enables resource recovery but also reshapes downstream microbial community assembly. • Long-term monitoring revealed temporally stable microbial communities in modular RAS, with episodic shifts during operational disturbances. • Aquaculture effluent from M-RAS served as cultivation medium for Phaeodactylum tricornutum and was accompanied by microbial community shifts toward taxa commonly associated with algal systems. • Potentially opportunistic taxa (e.g., Arcobacteraceae , Weeksellaceae , Pseudoalteromonadaceae ) increased during periods of reduced feeding and salinity adjustments, highlighting biosecurity considerations. • Integrating microbial community monitoring with operational data supports early detection of system disturbances and informs management of microbial stability and nutrient reuse strategies.