Reconstructing pico- and nanophytoplankton assemblages from long-term coastal thermohaline observations

Abstract. Over the past 30 years, the Gulf of Lions in the northwestern Mediterranean Sea has undergone various environmental changes that have impacted marine ecosystems. At the beginning of the 21st century, shifts were observed in small pelagic fish and zooplankton communities. However, little is known about the impact of these changes on phytoplankton communities, especially pico- and nanophytoplankton (hereafter referred as PicoNano), which play a crucial role in the northwestern Mediterranean Sea. One major limitation is the lack of data on these size fractions during the observed shifts. In this study, we show that vertical profiles of temperature and salinity can serve to infer PicoNano assemblages from the thermohaline properties measured in a coastal area, the Bay of Marseille (BoM). We use functional data analysis and clustering methods to identify recurring vertical thermohaline structures over 20 years of temperature and salinity data (1994–2024), measured at low and high frequencies. To address the issue of truncated vertical profiles, we employ a reconstruction method based on functional principal component analysis. Using flow cytometry data collected over the past 11 years (2014–2024), we characterize PicoNano assemblages and the nutrient concentrations associated with each recurring thermohaline structure. We identify three thermohaline structures associated with the most oligotrophic conditions observed in the BoM, all involving a thermally stratified water column. The occurrence of these stratified conditions does not show any significant trend over the past 20 years. However, vertical structures indicative of Rhône River intrusions have been less frequently observed since 2004, while mixed water columns are more frequently highly homogeneous over the same period. We show that highly homogeneous water columns favour different PicoNano assemblages compared to mixed but less homogeneous water columns. Overall, these results suggest that conditions favouring larger nanoeukaryotes have become less frequent since 2004. This work highlights that easily measurable variables, such as vertical profiles of temperature and salinity, can provide valuable insights into more complex variables—such as nutrient concentrations and PicoNano assemblages—when direct observations are unavailable, a situation commonly encountered in long-term and high-frequency monitoring.