Linking Bacterial r/k Ecological Shifts to Spatiotemporal Nitrogen Removal Dynamics in Recirculating Aquaculture Systems

The composition and function of bacterial communities in recirculating aquaculture systems (RAS) vary significantly across operational phases and treatment units. Yet the causal links between these bacterial dynamics and nitrogen removal mechanisms remain obscure. In this study, we demonstrated dynamic shifts in bacterial community composition and nitrogen removal function within RAS throughout cultivation and in each unit, by water quality monitoring, 16 S rRNA gene sequencing, metagenomics, 15N isotope tracing and kinetic modeling. Bacterial community composition shifted temporally, marked by a decline in r-strategists and increases in both α- and β-diversity from the start-up to the culture phase, a succession primarily driven by salinity, total dissolved solids, and conductivity. Ecologically, this transition is indicative of a shift in dominant life-history strategies, from an r-selected pioneer community to a K-selected, more stable and resilient community. Denitrification, anammox, and nitrification dominated nitrogen removal pathways, collectively representing 45.2% of the nitrogen-cycling functional genes. In addition, there was significant spatiotemporal heterogeneity in bacterial nitrogen removal. Spatially, aquatic bacteria exhibited higher denitrification activity, while biofilm-attached anammox bacteria of K-strategist demonstrated disproportionately high metabolic activity relative to their low abundance; this was probably regulated by biofilm-associated quorum sensing. Temporally, the ammonia-oxidizing bacteria (AOB) enabled an initial rapid ammonia degradation, whereas nitrite-oxidizing bacteria (NOB) and denitrifiers dominated later-stage decreases in nitrite and nitrate, indicating that the bacterial nitrogen removal function responded to nutrient dynamics. This study demonstrated the coupling mechanisms between ecological adaptation strategies of bacterial communities and nitrogen removal function in RAS, thereby establishing a basis for precision management technologies targeting functional bacteria. Diagram of bacterial dynamics and nitrogen removal function in RAS. Spatially, variations in nitrogen removal functions between aquatic and biofilm-attached bacteria were demonstrated. Temporally, shifts of water quality, bacterial community composition and nitrogen removal functions in fish culture tank across the culture cycling were revealed.