Wastewater-driven nutrient enrichment restructures viral community assembly, host interactions, and ecological function along the Nakivubo–Lake Victoria interface in Uganda

Gulf ecosystems in freshwater lakes are dynamic interfaces of microbial activity, shaped by complex interactions between natural processes and anthropogenic inputs from surrounding urban catchments. This study investigated viral community composition, functional potential, and virus-host interactions along the Nakivubo catchment-Lake Victoria interface in Murchison Bay, Uganda. Metagenomic profiling of 28 samples across four compartments: wastewater treatment plant (WWTP); a municipal channel; papyrus-dominated wetland; and Lake water, revealed spatially distinct viromes dominated by Uroviricota (45.8–94.8 %), with higher richness observed in Channel and Wetland than in WWTP and Lake samples. Community structure was strongly compartmentalized (PERMANOVA, p < 0.001), with WWTP and Channel viromes distinct from those in less impacted compartments. Human-associated viruses, including crAss-like phages (up to 29.3 %) and Picobirnaviruses (11.4 %), were enriched in WWTP samples, reflecting fecal pollution. Linear discriminant analyses and random forest modeling identified Sinsheimervirus as wetland indicator, while Fukuivirus, Bellamyvirus and Prokaryotic dsDNA virus were characteristic of lake viromes. Viral–bacterial co-occurrence networks were fragmented and less cohesive in WWTP and Channel (average path length = 3.2), but more modular and nested in Wetland (avg. path length = 1.9; modularity = 0.47), reflecting ecological structuring. Among environmental variables, ammonia-N was the strongest correlate of viral beta diversity (Mantel r = 0.67, p < 0.01). Functionally, auxiliary metabolic genes (AMGs) linked to photosynthesis, nitrogen and carbohydrate cycling were enriched in Wetland and Lake, while mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) were largely confined to WWTP, Channel, and Wetland. These patterns suggest selective viral adaptations to eutrophic, contaminated environments and their attenuation downstream. The findings demonstrate how wastewater-driven nutrient enrichment shapes viral community assembly, host associations, and ecological function along tropical freshwater continua. Viruses emerge as sensitive indicators of anthropogenic impact and offer new perspectives for water quality monitoring and ecosystem health assessment in urban-influenced lake systems.