A Recirculating Aquaculture Systems (RAS) are distinctively constructed ecosystems that reduce nutrient pollution discharge to the environment, therefore minimising environmental disturbance. RAS commonly uses a biofilter to regulate the ammonia levels that are created as a consequence of the catabolism of fish protein. It is hypothesised that the main nitrifiers in RAS biofilters are Nitrosomonas (which oxidises ammonia), Nitrospira, and Nitrobacter (which oxidises nitrite). By describing the bacterial and archaeal communities of a commercial-scale freshwater RAS that has been in use for more than 15 years, we investigated this claim. The bacterial taxa present in the biofilter community were discovered to be diverse (>1000 genus-level taxon assignments), with Chitinophagaceae and Acidobacteria dominating (12% and 9%, respectively).A fish-raising cycle's operational adjustments and variations in biofilter depth both caused the bacterial community's composition to fluctuate significantly. The presence of AOA ammonia monooxygenase genes is assumed to indicate that the archaea are Ammonia-Oxidising Archaea (AOA), which were also prevalent. Thaumarchaeota (>95%) made up the whole low-diversity assemblage of the archaea. All depths and time intervals had nitrogen dioxide. Their abundance, however, was >3 orders of magnitude lower than that of AOA, and they displayed significant depth-time variability that was not seen for AOA. Although no Nitrobacter were discovered, phylogenetic analysis of the nitrite oxidoreductase beta subunit (nxrB) gene revealed the presence of two distinct Nitrospira populations.Complete ammonia-oxidizing (comammox) and nitrite-oxidizing Nitrospira populations co-exist in this system with comparatively equal and stable abundances, according to subsequent identification of Nitrospira ammonia monooxygenase alpha subunit genes, phylogenetic placement, and quantification of the nxrB genotypes. It seems that RAS biofilters enable a variety of ammonia oxidation lifestyles within the nitrifying consortium while housing complex microbial populations whose composition can be directly impacted by normal system operations.
