Recombination maintains metastable viral populations across global hypersaline ecosystems

Viral populations in natural environments display extensive microdiversity, yet how they maintain genomic cohesion across space and time remains unresolved. Hypersaline crystallizer ponds, characterized by low host diversity and extremely high viral abundance, provide a simplified system to investigate viral population structure under strong environmental selection. Here, we applied long-read metagenomics to the cellular fraction (0.22–5 μm) to characterize viruses associated with Haloquadratum walsbyi , enabling direct investigation of actively infecting viral populations and their fine-scale population structure. Long-read sequencing revealed extensive viral genomic diversity that was largely missed by assembly-based approaches, substantially expanding the diversity of H. walsbyi -associated viruses. Despite this diversity, viral populations from geographically distant hypersaline systems displayed near-identical population-level nucleotide identity and largely conserved gene content, indicating a globally preserved genomic backbone. In contrast, fine-scale analyses revealed extensive local microdiversity, with limited overlap of single-nucleotide polymorphisms among sites and variability concentrated in genes involved in host interaction and attachment. Consistently low pN/pS ratios indicated pervasive purifying selection, while elevated recombination signals were consistent with frequent genetic exchange among co-occurring viral lineages. Metatranscriptomic analyses further showed that these viral populations remain transcriptionally active throughout the year, with higher activity in winter, and environmental comparisons indicated that salinity acts as a selective pressure shaping viral microdiversity. We propose a “metastable cohesive viral cloud” model in which viral populations maintain global genomic coherence while continuously reshaping local genetic variation. In this framework, recombination and purifying selection contribute to preserving a conserved genomic backbone, whereas environmental filtering drives fine-scale diversification. This regime reconciles global connectivity with local microdiversity and may represent a strategy for persistence among dominant H. walsbyi -associated dsDNA viral populations inhabiting high-density microbial ecosystems. Video Abstract