Temperature limitations pose a critical challenge to anammox in mainstream applications, yet the underlying mechanisms of microbial cold adaptation remain elusive. Here, we reveal that the biofilm extracellular matrix plays a central regulatory role in synchronizing quorum sensing and nitrogen metabolism under thermal constraint. Through integrated structural, biochemical, and genomic analyses of engineered systems, we demonstrate that biofilms form hydrophobic, α-helix–rich protein scaffolds that stabilize enzyme conformation and signal retention at low temperature. This matrix architecture enables selective accumulation of signaling molecules and promotes coordinated metabolic responses via centralized quorum regulation. Functional gene enrichment and phylogenetic convergence within biofilms point to an evolutionarily compressed community structure, where metabolic redundancy and signal alignment minimize noise while maximizing stability. In contrast, granular sludge systems exhibit decentralized, composition-driven adaptations with reduced cold resilience. Network and multivariate analyses highlight matrix-governed signal structuring as the key driver of functional coherence. These findings propose a paradigm in which microbial cold tolerance is not solely dictated by species composition or enzyme activity but is emergent from matrix-mediated communication frameworks offering a new blueprint for the design of resilient bioprocesses in fluctuating environments.
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