Extracellular rRNA profiling reveals the sinking and cell lysis dynamics of marine microeukaryotes

Marine plankton communities consist of numerous species, and their composition and physiological states are closely linked to ecosystem functions. Understanding biogeochemical cycles requires measuring taxon-specific mortality due to viral lysis or sloppy feeding, as the dissolved organic matter released contributes to rapid nutrient recycling and long-term carbon sequestration following microbial transformation. This study introduces a quantitative and comprehensive analysis of microeukaryotes in the dissolved constituents of seawater by using Mortality by Ribosomal Sequencing (MoRS) method. Our experimental pipeline successfully recovered 83% of cell-free rRNA. The ratio of cell-free rRNA to cell-associated rRNA was more than 10-fold higher in the mesopelagic layer than in the upper epipelagic layer, suggesting the mesopelagic zone as a hotspot for eukaryotic cell lysis. Many protist lineages, including phytoplankton such as haptophytes, are less susceptible to cell lysis in the epipelagic layer yet are actively lysed in the mesopelagic zone. Notably, over 86% of the significantly lysed species in the mesopelagic layer showed a habitat preference for the epipelagic layer. These findings indicate that sinking from the surface and lysis in the mesopelagic are prevalent dynamics for various eukaryotes.