Seasonality of protists in the oligotrophic Gulf of Aqaba revealed by imaging flow cytometry

Oligotrophic subtropical waters are some of the ocean's largest continuous ecosystems, yet their protist diversity and community succession remain poorly understood. We examined the protist community in the surface waters of the Gulf of Aqaba at near-daily resolution from March 2024 to July 2025 using an Imaging FlowCytobot. The record revealed a clear seasonal succession. Total cell density increased nearly threefold during winter mixing, driven mainly by an increase in cells smaller than 5 microns. Cells were generally larger during summer, making total biovolume similar in summer and winter. Biovolume reached its highest sustained values during the spring bloom. Despite its low cell density, the summer community was dynamic, with sudden appearances of euglenophytes, flagellates and dinoflagellates at high densities. Coccolithophores and cryptophytes increased during winter, followed by diatoms and ciliates in spring. We also provide a dataset of 31,700 annotated IFCB images.