Contrasting changes in phytoplankton assemblage and size to environmental shifts in the Mediterranean Sea using novel deep-learning protocols

Understanding the spatial and temporal changes in phytoplankton assemblages is essential in the context of climate change, due to their impact on carbon burial and the marine food web. Here we investigate the effects of environmental shifts in the Mediterranean Sea on phytoplankton taxonomy and size structure using an AI-based approach. We analyzed two sediment trap series from the northwestern Mediterranean Sea between 2010 and 2018: one in the oligotrophic Ligurian Sea and the other in the Gulf of Lion, a region where deep convection occurs regularly in the winter. We used novel deep-learning protocols for image analysis to generate data for phytoplankton particle fluxes, size distributions, and relative assemblages, with a focus on coccolithophores and diatoms. This automated approach enabled the rapid, high-throughput processing of microscope images, producing a standardized dataset across both time series. Our results show a general decline of phytoplankton fluxes towards the seafloor, mirroring the decrease in vertical mixing that affects the water column. Both sites show a shift towards phytoplankton species associated with stratified and nutrient-depleted conditions, but with contrasting patterns despite their proximity: In the Ligurian Sea, deep-dwelling coccolithophore species become increasingly dominant, while in the Gulf of Lion, summer-associated siliceous species, including large diatoms and silicoflagellates, show an increase. These contrasting trends likely result from differences in nutrient inputs and surface pH changes between the sites. We find that the increasing dominance of smaller phytoplankton in the Ligurian Sea leads to a reduction in carbon burial efficiency, while in the Gulf of Lion, the enhanced contribution of larger diatoms may sustain relatively higher export and burial rates in the future. These findings highlight the heterogeneous responses of phytoplankton communities to the increasing surface temperatures and stratification in the Mediterranean Sea, and their contrasting impact on carbon burial.