Source-Specific Nitrogen Inputs Are Associated with Pathway Partitioning Between Denitrification and DNRA in River Water

Understanding how external nitrogen sources regulate nitrogen fate in river water is critical for improving nitrogen removal and reducing greenhouse-gas risk. Here, short-term microcosm incubations were conducted using source water as the background matrix and seven representative source inputs. By integrating hydrochemical analyses, bacterial community profiling, metagenomics, RT-qPCR, and process-rate measurements, we evaluated source-dependent shifts in nitrogen-cycling pathways. Manure-related inputs generated the highest organic and nitrogen loading, suppressed nitrification, enhanced nrfA (cytochrome c nitrite reductase) abundance and transcription, and promoted DNRA, indicating a shift toward nitrogen retention via ammonium regeneration. In contrast, sewage-related inputs maintained relatively high NO3− availability, elevated nirS (cytochrome cd1 nitrite reductase) and nosZ (nitrous oxide reductase) expression, and enhanced denitrification, but also increased N2O production. Metagenomic, transcriptional, and rate-based evidence consistently identified 12 h as a critical window for source-dependent pathway redistribution, highlighting the importance of short-term monitoring for detecting rapid nitrogen-cycle responses following pollution inputs. These findings support source-oriented nitrogen management that considers both nitrogen loading and hydrochemical controls on nitrate fate.