Process architecture governs nitrate fate by controlling dissimilatory nitrate reduction to ammonium...

Dissimilatory nitrate reduction to ammonium (DNRA) is increasingly recognized as an alternative nitrate reduction pathway, yet its quantitative importance and regulatory mechanisms in engineered wastewater treatment systems remain poorly resolved. Here, DNRA and denitrification were systematically quantified across four full-scale coking wastewater treatment plants operated under contrasting recirculation and non-recirculation modes. Long-term performance monitoring combined with ¹⁵N stable isotope tracing showed that DNRA accounted for 8.0-29.5% of total nitrate reduction, with substantially higher contributions under recirculation-based operation. Although denitrification remained the dominant pathway for nitrate removal, enhanced DNRA promoted ammonium accumulation and significantly impaired total nitrogen removal efficiency. Process configuration was associated with contrasting nitrate-reduction outcomes by reshaping local substrate stoichiometry and toxicity exposure: high COD/NO₃^- ratios and persistent nitrogenous toxicants in recirculation systems were associated with greater DNRA contribution, whereas spatially decoupled non-recirculation configurations maintained more balanced conditions that favored denitrification and supported anaerobic ammonium oxidation. Integrated analyses of microbial community assembly, ecological networks, and metagenome-resolved functions revealed that non-recirculation systems maintained higher microbial diversity, functional redundancy, and network robustness, while recirculation systems exhibited undominated assembly and enrichment of DNRA-associated taxa and genes. Collectively, these results demonstrate that nitrate reduction pathways are not solely determined by microbial functional potential, but instead emerge from the coupled interactions among process configuration, material composition, and microbial functionality. This study highlights that controlling the fate of nitrogen in engineered wastewater systems relies heavily on designing environmental conditions that selectively favor the utilization of existing metabolic potential.