Abstract
Deep freshwater lakes exhibit distinct microbial community stratification across depth gradients, which plays important roles in biogeochemical cycling and ecosystem stability. As crucial regulators of microbiome composition and function, viruses may play key ecological roles in these stratified systems, yet their distribution patterns and ecological significance in deep‐lake surface sediments remain poorly understood. Here, we assessed viral community dynamics and functional potential across the entire water depth gradient (0–155 m) of Fuxian Lake using metagenomics from 44 surface sediment samples. A total of 11,523 viral OTUs were recovered, with only 18% annotated to the family level and approximately 93% classified as putatively lytic. Viral communities showed systematic depth‐related shifts across multiple dimensions. Specifically, alpha diversity, community turnover, and stochastic assembly processes increased significantly with water depth, accompanied by enhanced lytic virus dominance and larger genome sizes. Predicted virus‐host association networks transitioned from highly connected and generalized at shallow depths to increasingly sparse and specialized at greater depths. Virus‐encoded auxiliary metabolic genes showed significantly increasing abundance with water depth, along with functional shifts from host defense to enhanced biosynthesis and energy metabolism, especially regarding carbon fixation and organic matter degradation. Collectively, these results highlight the importance of water depth gradients in structuring viral communities within surface sediments and expand our understanding of viral ecological functions in deep lake ecosystems.