Exploring the regional diversity of eukaryote phytoplankton by combining high throughput approaches

Monitoring marine microorganisms, particularly phytoplankton, is essential for understanding the functioning of marine ecosystems, especially in productive regions like the English Channel. In this study, high-throughput sequencing (HTS) and automated pulse-shape recording flow cytometry (PSR FCM) were applied to investigate the spatial and seasonal variability of phytoplankton diversity in French waters of the English Channel during the ECOPEL cruises in spring (April) and summer (July) 2018). Our findings revealed significant seasonal shifts in phytoplankton size structure, total red fluorescence and community composition. PSR FCM provided high-resolution discrimination between size classes, revealing an increase in picoeukaryote abundance and lower total fluorescence (FLR) in summer compared to spring. HTS enable detailed taxonomic insights, showing that in spring, picoeukaryotes (e.g. Ostreococcus) dominated in the Western English Channel, except in Finistere/Celtic Seas waters, where microphytoplankton dominated. Nanoeukaryotes (Phaeocystis) were dominant in the Eastern English Channel. In summer, diversity increased, with co-dominance of picoeukaryotes (Micromonas, Bathycoccus, Ostreococcus), microphytoplankton (Chaetoceros, Leptocylindrus, Guinardia) and nanoeucaryotes (Teleaulax, Gephyrocapsa) in central English Channel waters (Bay of Seine). HTS also highlighted rarer groups, including pigmented dinoflagellates, which occasionally dominated the microphytoplankton compartment, notably off Finistere in spring. Beyond a pronounced west-east spatial disparity, the Bay of Seine exhibited remarkable taxonomic and functional diversity, as reflected by higher local contribution to beta diversity (LCBD) values in both seasons. Diversity patterns were strongly influenced by temperature and nutrient concentrations (phosphate, nitrogen), with secondary influences from salinity and turbidity. PSR FCM further revealed sub-mesoscale variability in abundance and size structure, complementing the mesoscale patterns observed through HTS. This study highlights the importance of integrating both methods to capture fine-scale phytoplankton dynamics and improve ecosystem management in nutrient-sensitive, highly productive marine regions.