Viruses are integral yet underexplored components of coral holobionts, with their roles in shaping microbial diversity, modulating symbioses, and contributing to Darwin's paradox remaining largely unresolved. Here, we present the Global Coral Holobiont Virome Database (GCHVD), encompassing 76,755 viral contigs and 36,860 unique viral operational taxonomic units (vOTUs) identified from 36 coral species across 18 regions worldwide. The virome is dominated by Uroviricota, Nucleocytoviricota, Preplasmiviricota, and Artverviricota, with lytic lifestyles prevailing. Host identity emerged as the primary determinant of viral community structure, exerting a stronger influence than geographic factors. Extensive virus-microbe interaction networks revealed that viruses enhance biogeochemical cycling by augmenting host metabolic processes. Functional profiling uncovered a diverse repertoire of auxiliary metabolic genes (AMGs) associated with P, Fe, S, N, and CH₄ metabolism. Moreover, controlled microcosm experiments demonstrated that viral addition reshapes microbial community composition, enhances diversity, and drives elemental cycling within the holobiont. Together, these findings establish viruses as previously overlooked regulators of coral symbioses, orchestrating microbial dynamics, fueling nutrient fluxes, and sustaining reef productivity. Our work provides new insights into resolving Darwin's paradox from a viral ecological perspective.
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