Fine-scale physical structures such as eddies, fronts and filaments strongly influence biogeochemical and ecological processes. The characterisation of phytoplankton communities of the Mozambique Channel and the Senegal-Gambia upwelling systems is limited to scarce in situ sampling and satellite data. Here, three mesoscale structures were targeted: an anticyclonic eddy−front−cyclonic eddy sampled during the RESILIENCE cruise in the Mozambique Channel and two filaments offshore Gambia and north of Cape Verde peninsula sampled during the SCOPES cruise. Phytoplankton functional groups (PFGs) were studied at fine-scale in surface waters by underway measurements with multispectral fluorometry and automated pulse-shape recording flow cytometry. Mesoscale structuring was evidenced in the three areas using hierarchical clustering: differences amongst PFGs in their abundance or chlorophyll biomass was observed, and common features of communities associated with mesoscale hydrodynamics across the three structures was evidenced. Finally, a partition of variation analysis conducted on cruises data pooled together showed that variability in communities composition occurred at meso- and mainly submesoscale and not amongst oceanic basins, and that large-scale variability was better characterised when accounting for fine-scale variability. Data on hydrological environment and upper trophic levels will allow investigating mechanisms behind the response of phytoplankton to meso- and submesoscale structures.
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