Spatial Organization of Microbiome Stability and Nitrogen Removal Resilience in a Full-Scale Plug-Flow PN/A System

Partial nitritation/anammox (PN/A) enables energy-efficient nitrogen removal, yet the ecological drivers of stability and resilience in full-scale systems remain insufficiently characterized. Here, this study integrated 13-month performance monitoring with multiomics analyses to characterize spatial heterogeneity and recovery patterns following a dissolved oxygen (DO) shock in a full-scale plug-flow PN/A system. During stable operation, the system achieved a total nitrogen removal efficiency of 84.5 ± 4.8%, with the upstream zone accounting for 61.3 ± 10.1% of total removal. Along the decreasing nutrient gradient, community composition shifted markedly, and metatranscriptomes indicated spatially differentiated nitrogen-cycling transcription, with anammox-related transcripts enriched upstream. A 3-day DO shock (>0.5 mg/L) reduced the nitrogen removal rate (NRR) from 0.16 ± 0.03 to 0.07 ± 0.04 kg N/(m 3 ·d). Although NRR recovered to baseline within three months, community structure and total bacterial 16S rRNA gene copies did not return to preshock levels, indicating a decoupling between microbiome and functional recovery. Across zones, higher bacterial diversity and nitrogen cycling functional redundancy were positively associated with faster recovery trends, and upstream microbiome stability was most representable of whole-system resilience. These findings provide measurable ecological indicators and an upstream-focused control target to strengthen full-scale PN/A operation under dynamic aeration disturbances.