Quantifying Viral Lysis in Microalgae Using Cell-Free rRNA

Viral lysis is a major driver of phytoplankton mortality and a key source of dissolved organic matter in the ocean, yet quantitative and taxon-resolved measurements of this process remain limited for eukaryotic plankton. Here, we demonstrate that cell-free ribosomal RNA (rRNA) dissolved in the extracellular medium serves as a quantitative proxy for viral lysis in microeukaryotes by combining laboratory infection experiments with a rate-based modeling framework. We investigated two host-virus systems: the diatom Chaetoceros tenuissimus infected by a single-stranded RNA virus (CtenRNAV) and the raphidophyte Heterosigma akashiwo infected by a large double-stranded DNA virus (HaV). By explicitly accounting for cell-free rRNA degradation, we quantified a proxy for cell lysis rate from cell-free 18S rRNA dynamics and observed up to 46- and 302-fold increases in cell-normalized lysis rates under viral infection. In C. tenuissimus, peak lysis preceded the decline in cell abundance, demonstrating that substantial viral lysis occurs while populations are still proliferating. In contrast, H. akashiwo exhibited elevated lysis in both early and late infection phases, implying that a fraction of host cells undergoes rapid, nonproductive mortality prior to viral replication, in addition to canonical lytic events. Our study provides the first experimental validation of cell-free rRNA as a quantitative marker of lytic mortality in microeukaryotes, offering a scalable approach for estimating taxon-specific mortality in natural plankton communities.