Temperature and light mainly drive seasonal dynamics of microbial planktonic diversity in coastal ecosystems; however, disentangling their effects is challenging because they are always tightly coupled. Shallow coastal lagoons exhibit intense temperature changes throughout the year and high interannual temperature fluctuations, offering the opportunity to study temperature effects on microbial community diversity and succession. Weekly sampling at 16s and 18s rRNA gene OTU diversity associated with high-frequency meteorological and hydrological monitoring was conducted in the northwestern Mediterranean Thau Lagoon (South of France) from winter to spring in 2015 and 2016. While 2015 was a normal climatic year, 2016 had the warmest winter ever recorded in southern France. Water temperature was found to be the main driver of community diversity and succession from winter to spring. During the normal temperature year of 2015, bacterial communities were dominated by Proteobacteria and Bacteroidetes, archaeal community by Thaumarachaeota, and unicellular eukaryotes mainly by picochlorophytes (Bathycoccus prasinos, Micromonas bravo, and Ostreococcus spp.) in winter and diatoms (Chaetoceros spp.) in spring. The unusually warm year 2016 benefited Actinobacteria (ML602J-51), Cyanobacteria (Synechococcus), the picoeukaryote Ostreococcus spp., and several dinoflagellates. Our results suggest that in a warmer ocean, smaller organisms will dominate microbial communities in shallow coastal waters, potentially affecting ecosystem services.

Vulcanodinium rugosum is an emerging benthopelagic neuro-toxic dinoflagellate species responsible for seasonal Pinnatoxins and Portimines contaminations of shellfish and marine animals. This species is challenging to detect in the environment, as it is present in low abundance and difficult to be identified using light microscopy. In this work, we developed a method using artificial substrates coupled with qPCR (AS-qPCR) to detect V. rugosum in a marine environment. This sensitive, specific and easy-to-standardize alternative to current techniques does not require specialized expertise in taxonomy. After determining the limits and specificity of the qPCR, we searched for the presence of V. rugosum in four French Mediterranean lagoons using artificial substrates collected every two weeks for one year. The AS-qPCR method revealed its occurrences in summer 2021 in every studied lagoon and detected cells in more samples than light microscopy. As V. rugosum development induces shellfish contamination even at low microalga densities, the AS-qPCR method is accurate and relevant for monitoring V. rugosum in a marine environment.

The bloom-forming dinoflagellates and euglenophyceae were observed in the coastal waters of Hammam-Lif (Southern Mediterranean), during a green tide event on 3 June 2023. The bloom was dominated by Lepidodinium chlorophorum, identified through ribotyping with densities reaching 2.3 × 10⁷ cells·L⁻¹. Euglena spp. and Eutrepsiella spp. contributed to the discoloration, with abundances up to 2.9 × 10⁷ cells·L⁻¹. Environmental data revealed significant depletion of nitrite and nitrate, coinciding with a rapid increase in sunlight duration, likely promoting the proliferation of L. chlorophorum and euglenophyceae. By 5 June, two days after the bloom, nutrient stocks were exhausted. Diatoms appeared limited by low silicate concentrations (<0.05 µmol·L⁻¹), while dissolved inorganic phosphate and Nitrogen-ammonia were elevated during the bloom (0.88 and 4.8 µmol·L⁻¹, respectively), then decreased significantly afterward (0.23 and 1.06 µmol·L⁻¹, respectively). Low salinity (34.0) indicated substantial freshwater input from the Meliane River, likely contributing to nutrient enrichment and bloom initiation. After the event, phytoplankton abundance and chlorophyll levels declined, with a shift from dinoflagellates to diatoms. The accumulation of pigments (chlorophyll b and carotenoids) and the presence of Mycosporine-like amino acids (MAAs) during and after the bloom suggest that UV radiation and Nitrogen-ammonia were key drivers of this green tide.