Diatoms frequently dominate seasonal phytoplankton blooms and contribute ~40% of marine primary production. Viruses drive phytoplankton mortality and bloom collapse, yet how viruses regulate diatom bloom dynamics is not well resolved. Here, using quantitative metatranscriptomics, we tracked temporal patterns of diatoms and associated viruses at near-daily resolution during the spring bloom in the Gulf of Aqaba, Red Sea. We captured distinct phases and rapid restructuring within both the diatom community and cell-associated virosphere. Diatom transcriptional profiling indicated activation of stress and death pathways prior to taxon-specific demise. RNA viruses emerged as dominant players within the bloom, with fluctuations of putative diatom-infecting RNA viruses across intracellular and extracellular fractions revealing sequential waves of active virus infection that were consistent with virus-mediated diatom mortality. Correlation and codon usage analyses further implicated specific diatom taxa as putative hosts for the identified RNA viruses. Rather than a uniform 'boom and bust', the spring diatom bloom comprised a mosaic of overlapping successional waves of diatom and viral taxa unfolding on daily timescales. These findings support RNA viruses as drivers of diatom turnover, advancing our understanding of how viruses temporally structure diverse diatom assemblages and the biogeochemical trajectory of diatom blooms in marine systems.
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