Urban sewer sediments are critical hotspots for microbial processes that drive sulfide-induced concrete corrosion, greenhouse gas emissions, and the dissemination of antibiotic resistance genes (ARGs), posing substantial economic losses and public health threats. However, the regulatory roles of viruses and the influence of urban functional zoning on these risks remain largely unexplored. Integrating metagenomics, viromics, and global 16S rRNA amplicon datasets from 76 cities across six countries, this study systematically investigated microbial sulfur/methane cycling, ARG mobility, and virus-host interactions in sewer sediments from three distinct functional areas (commercial, multifunctional, and residential) in Ningbo, China.
Our results demonstrate that multifunctional areas, characterized by higher nutrient contents (TOC, TN, AS) and lower pH, exhibit the highest public risk potential, with significantly enriched methane/sulfur metabolic pathways, elevated abundances of mobile genetic elements (MGEs) and high-risk ARGs, and more complex co-occurrence networks among ARGs, MGEs, and opportunistic pathogens. Notably, the sulfur-oxidizing genus Thiobacillus was identified as a key host of high-risk ARGs, widely distributed in global sewer systems, with total organic carbon (TOC) emerging as the primary environmental driver of sediment public risk.
Concurrently, viruses act as metabolic "tuners" of sulfur dynamics, displaying a functional area-dependent lysis-lysogeny switch. Nutrient-induced acidification in multifunctional areas promotes lysogenic infection, enhancing the insertion of sulfate reduction-related auxiliary metabolic genes (AMGs, e.g., cysH) into host genomes and increasing sulfide formation. Conversely, single-function areas favor lytic infection that suppresses sulfate-reducing microorganisms. Phage transplantation experiments validated the efficacy of lytic viruses in mitigating H₂S generation, while global network analyses confirmed the universality of key viral hosts.
Collectively, these findings reveal the dual role of viruses as both risk amplifiers and mitigators in sewer ecosystems, and highlight TOC and viral lysis as promising targets for sustainable sewer management. This study provides a novel framework for integrating viral biocontrol and nutrient regulation into urban infrastructure resilience strategies.

Sewer system,Metagenome,Virome,Methane cycle,Sulfur cycle