Functional genes with their expression and horizontal gene transfer drive microbial interactions in anammox systems: Critical review and potential applications.

The anaerobic ammonium oxidation (anammox) process, a low-carbon and energy-efficient biological nitrogen removal technology, is crucial for sustainable wastewater treatment and energy self-sufficiency. However, its performance stability is influenced by complex microbial interactions, and the gene-level mechanisms, particularly horizontal gene transfer (HGT), remain underexplored. This review comprehensively examines the interactions between anammox bacteria and their syntrophic partners, focusing on the functional genes involved in substrate degradation, electron transfer, cofactor biosynthesis, and quorum sensing (QS). These interactions form a network that supports wastewater treatment and system stability under external disturbances. Additionally, HGT mediated by bacteriophages, plasmids, transposons, and integrons reshapes anammox bacterial genomes, enhancing environmental adaptability, and promoting dynamic coexistence through competition and cross-feeding. This results in improved and stabilized nitrogen removal efficiency at the system level. A new paradigm is proposed, integrating multi-omics analysis with global bioinformatics and generative artificial intelligence to uncover the links between genetic activities and process performance. The review, by summarizing microbial interactions, functional genes, and HGT mechanisms in the anammox process under multi-omics analysis, is significance for improving system's nitrogen removal efficiency and system stability, and provides a theoretical basis for optimizing and regulating the process.