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, sloppy feeding, and other mechanical stresses as the dissolved organic matter released contributes to rapid nutrient recycling and long-term carbon sequestration following microbial transformation. To examine the lytic cell death of marine microeukaryotes, we applied a quantitative and comprehensive analysis of the dissolved constituents of seawater using the Mortality by Ribosomal Sequencing (MoRS) method. Our experimental pipeline successfully recovered 83% of cell-free rRNA. A higher number of protist phylotypes was significantly lysed in the mesopelagic zone than in the surface ecosystems, indicating that the mesopelagic zone is a potential hotspot for eukaryotic cell lysis. Many protist lineages, including phytoplankton such as haptophytes, were less susceptible to cell lysis in the epipelagic layer yet were actively lysed in the mesopelagic zone. Notably, over 86% of the significantly lysed species in the mesopelagic layer had a habitat preference for the epipelagic layer. These findings suggest that sinking from the surface and lysis in the mesopelagic may represent prevalent dynamics for various eukaryotes.