Microbial Community Responses and Nitrogen Cycling in the Nitrogen-Polluted Urban Shi River Revealed by Metagenomics

Nitrogen pollution in urban rivers, exacerbated by rapid urbanization, poses a growing threat to water quality. Microbial communities are essential in mediating nitrogen cycling and mitigating pollution in these ecosystems. This study integrated three-year (2021–2023) water quality monitoring with metagenomic sequencing to investigate microbial community dynamics, nitrogen cycling processes, and their responses to nitrogen pollution in the Shi River, Qinhuangdao, China. Nitrogen pollution was predominantly derived from industrial discharges from enterprises in the Shi River Reservoir upstream (e.g., coolant and chemical effluents), agricultural runoff, untreated domestic sewage (particularly from catering and waste in Pantao Valley), and livestock farming effluents. Total nitrogen (TN) concentrations ranged from 2.22 to 6.44 mg/L, exceeding China’s Class V water standard (2.0 mg/L, GB 3838-2002), with the highest level at the urbanized W4 site (6.44 mg/L). Nitrate nitrogen (NO3-N) accounted for 60–80% of TN. Metagenomic analysis revealed Fragilaria, Microcystis, and Flavobacterium thriving (up to 15% relative abundance) under nitrogen stress, with nitrogen metabolism genes (narG, nifH, nirK) enriched at polluted sites (W2, W4), narG reaching 26% at W1. Dissolved oxygen positively correlated with nitrate reductase gene abundance, while ammonia nitrogen inhibited it. Burkholderiales and Limnohabitans dominated denitrification, offering insights into sustainable urban river management.