Portable canister filters are often used in aquaria or smaller recirculating aquaculture systems (RAS) systems. However, the microbiome of these canister filters, especially the presence of comammox bacteria, has not been extensively studied. The aim of this study was to explain the mechanisms of nitrogen transformation, with a focus on the comammox process, in a portable filter under varying organic compound availability. Biomass samples were collected before and after feeding, and the microbial community was profiled using metagenomics and metatranscriptomics, with ecological relationships analyzed through network analysis. The results showed that comammox Nitrospira was the dominant nitrifier in the biofilter, with an average abundance of 4.2%, while other nitrifiers, such as Nitrosomonas, were present at significantly lower levels (e.g., 0.1% average abundance). High transcription levels of the amo, hao and nxr genes of comammox Nitrospira further indicated their critical role in nitrification within the filter. Aerobic denitrifiers, e.g. Pseudomonas, Flavobacterium and Aeromonas, were also abundant in the biofilter (8.3%, 4.2% and 1.6% average abundance respectively) . Nitrogen transformations varied across filter layers, with more intensive nitrification occurring in the lower layers and increased denitrification in the upper layers. After feeding, the increase in organic compounds favored the proliferation of heterotrophs, which competed with comammox Nitrospira and inhibited their activity. These findings provide insights into nitrogen conversion in canister filters at the molecular level and offer practical recommendations for engineers when designing this type of filter.
