Network of Nitrifying Bacteria in Aquarium Biofilters: An Unfaltering Cooperation Between Comammox Nitrospira and Ammonia-Oxidizing Archaea

Nitrification plays a crucial role in aquatic ecosystems and in the biofilters used in fish farms. Despite their importance, the role of canonical nitrifiers, comammox bacteria, and archaea has not yet been sufficiently investigated. The aim of this study was to characterize the microbiome of the external canister biofilter in a freshwater fish aquarium, with particular focus on the role of comammox Nitrospira and their competition with other nitrifiers. To achieve this, a comprehensive approach combining metagenome sequencing and co-occurrence network analysis was used to study the interactions between microorganisms in portable biofilter. The fish were subjected to a changing feeding regime that affected the ecological relationships and abundance of different microbial taxa. The results showed the presence of two types of nitrifiers in the biofilter: comammox Nitrospira and ammonia-oxidizing archaea (AOA). Five comammox Nitrospira genomes were reconstructed, with comammox clade B being the most abundant with an average abundance of 7.8 ± 0.4%. In addition, two families of archaea were identified: Nitrosopumilaceae and Nitrososphaeraceae, with an average abundance of 4.3 ± 0.4%. Heterotrophs were also abundant in the bacterial community, particularly in the genera Actinomycetota, Planctomycetota, and Pseudomonadota. Network analysis indicated competitive interactions between comammox and heterotrophs, whereas no competition was observed between comammox and AOA. The predominance of comammox Nitrospira, and AOA over canonical nitrifiers emphasizes their better adaptation to oligotrophic environments. This study highlights the importance of competition within the biofilter microbiome and the role of ecological interaction networks, which can contribute to the optimization of water purification systems in RASs.