Unraveling biomolecular and ecological mechanisms underlying the response of anammox consortia under xenobiotic stress by multi-omics strategy

Anaerobic ammonium oxidation (anammox) emerges as a sustainable solution for nitrogen removal in sewage, but it is susceptible to stress induced by xenobiotics that are ubiquitous in sewage. Despite wide recognition of this critical issue, a comprehensive understanding of the molecular and ecological mechanisms underlying the response of anammox consortia to xenobiotic stress remain elusive. Here, we integrated multi-omics approaches with biofilm reactor operation to unravel how bisphenol A (BPA, a representative xenobiotic) perturbs anammox consortia across environmentally relevant concentrations. We show that anammox consortia tolerated low BPA levels (0.2–2 mg/L), where nitrogen removal efficiency transiently declined and subsequently recovered, aided by a 30.9% increase in quorum-sensing (QS) signal C6-HSL. By contrast, exposure to ≥10 mg/L BPA caused severe and irreversible inhibition, with total inorganic nitrogen removal dropping to 17.8%. High BPA concentrations suppressed QS signaling, intensified oxidative stress, and compromised membrane integrity, leading to enzymatic inhibition and transcriptional repression of anammox functional genes. Multi-omics evidence revealed that BPA stress also promoted horizontal transfer of the BPA-degrading gene bisdA via extracellular DNA, suggesting a new community-level adaptive mechanism. Metagenomic and metabolomic analyses further indicated BPA-driven restructuring of microbial networks, namely high BPA levels favored denitrifiers and BPA degraders while suppressing anammox bacteria, and triggered metabolic reprogramming toward xenobiotic degradation at the expense of nucleotide and amino acid biosynthesis. Together, these findings reveal a multifaceted collapse mechanism of anammox under BPA stress, providing a mechanistic basis for designing strategies to safeguard microbial nitrogen removal in xenobiotic-laden wastewaters.