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

The ocean's surface is often imagined as a vast, empty blue desert, but in reality, it teems with microscopic life that forms the foundation of the marine food web. Among these tiny inhabitants are protists, a diverse group of single-celled organisms that include algae and other small drifters. In the warm, nutrient-poor waters of the subtropics, these communities are particularly difficult to study because they are sparse and change rapidly. Scientists have long known that the ocean is not static; the mix of species shifts with the seasons as water temperatures and currents change. Understanding exactly how these tiny communities grow, shrink, and swap places is crucial because they drive the global carbon cycle and support the fish that humans rely on. Without a clear picture of who is there and when, our understanding of how the ocean functions remains incomplete.

To fill this gap, researchers turned their attention to the Gulf of Aqaba, a narrow body of water in the Red Sea known for its clear, nutrient-poor conditions. For more than a year, from March 2024 to July 2025, they monitored the surface waters with a specialized instrument called an Imaging FlowCytobot. This device acts like a high-speed camera that takes pictures of individual cells as they flow past, allowing scientists to count them and identify their shapes without having to collect water samples by hand. By checking the water almost every single day, the team captured a detailed, day-by-day record of the microscopic world that had previously been missed by less frequent sampling methods.

The record revealed a distinct seasonal rhythm to life in the Gulf. During the winter months, the total number of cells in the water nearly tripled. This surge was driven primarily by a massive increase in the smallest organisms, those measuring less than 5 microns in size. Despite this explosion in numbers, the overall amount of living material, or biovolume, did not change drastically between seasons. This is because the cells present in the summer were generally larger, balancing out the sheer quantity of tiny winter cells. The most significant accumulation of living material occurred during the spring bloom, when biovolume reached its highest and most sustained levels.

While the summer months appeared quiet in terms of total numbers, the community was far from dormant. The researchers observed sudden, dramatic appearances of specific groups, including euglenophytes, flagellates, and dinoflagellates, which reached high densities in brief bursts. The seasonal progression followed a predictable path: coccolithophores and cryptophytes increased during the winter, followed by a rise in diatoms and ciliates as spring arrived. To ensure this detailed view of the Gulf's microscopic life is available to others, the team has also released a public dataset containing over 31,000 annotated images of the cells they captured, providing a visual archive of this seasonal journey.