Long-term evolution of microphytoplankton communities remains poorly studied in anthropized coastal zones submitted to multiple stressors. Here, we investigate decadal (2005–2017) microphytoplankton community changes, focusing on abundance and biovolume of major taxa related to both local abiotic conditions (rainfall rate, temperature and salinity) and regional convection events (wintering deep mixing) in the highly urbanized and semi-enclosed Toulon Bay (NW Mediterranean Sea). Results showed that persistent variations in local rainfall regime were followed by major changes in microphytoplankton community composition. Wet period (P2) (increase of wintering precipitations observed between late 2008 and early 2015) was associated to an increase of large heterotrophic dinoflagellates and disappearance of dominant diatom taxa, while dry periods (2005–2008 (P1) and 2015–2017 (P3)) promoted diatoms, microflagellates and small mixotrophic/heterotrophic dinoflagellates including potentially toxic species. Concomitance between intense deep mixing events, reported in open Ligurian Basin (particularly during winters 2005 and 2006) and higher values in the total microphytoplankton abundance and in spring diatom abundance regardless of rainfall conditions, presents this meso-scale process as the main fertilization mechanism in Toulon Bay. Although no change was detected in the chlorophyll a concentration during the 2006–2017 period, its trend was negatively correlated to the total microphytoplankton abundance. This negative relation as well as a change of size in dinoflagellates suggested a shift in the primary producer nature, from large autotrophic cells (diatoms and microflagellates) to smaller ones, driven by a runoff intensification. Finally, different communities composition were observed during both dry periods (i.e. diatoms-dominated and autotrophic microflagellate-dominated communities during P1 and P3, respectively), suggesting another environmental driver of change for phytoplankton communities of this coastal ecosystem.
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