Demonstrated transfer of cyanobacteria and cyanotoxins along a freshwater-marine continuum in France

•This study reports on the transfer of both cyanobacteria and cyanotoxins from a freshwater reservoir to the marine outlet in France.•The very high correlation between the biomass of potentially toxic species and total MC concentrations strongly suggests that the majority of the cyanobacterial present in the estuary were toxic.•Microcystis which dominated the blooms in the freshwater reservoir was the most likely genus responsible for the measured MC concentrations in the estuary, followed by P. agardhii both being relatively resistant to the salinity gradient.•The extracellular contribution to the total MCs increased from upstream to downstream in accordance with cells lysis at elevated salinity.•Both intracellular and extracellular MC variants did not show specific selection along the salinity gradient but the co-dominance of the highly toxic MC-LR and MC-YR variants is worrisome as it could impact on cyanobacterial consumers. The frequency of cyanobacterial proliferations in fresh waters is increasing worldwide and the presence of associated cyanotoxins represent a threat for ecosystems and human health. While the occurrence of microcystin (MC), the most widespread cyanotoxin, is well documented in freshwaters, only few studies have examined its occurrence in estuarine waters. In this study we evaluated the transfer of cyanobacteria and cyanotoxins along a river continuum from a freshwater reservoir through an interconnecting estuary to the coastal area in Brittany, France. We sampled regularly over 2 years at 5 stations along the river continuum and analysed for phytoplankton and cyanotoxins, together with physico-chemical parameters. Results show that cyanobacteria dominated the phytoplanktonic community with high densities (up to 2 × 106 cells mL−1) at the freshwater sites during the summer and autumn periods of both years, with a cell transfer to estuarine (up to 105 cells mL−1) and marine (2 × 103 cells mL−1) sites. While the temporal variation in cyanobacterial densities was mainly associated with temperature, spatial variation was due to salinity while nutrients were non-limiting for cyanobacterial growth. Cyanobacterial biomass was dominated by several species of Microcystis that survived intermediate salinities. Intracellular MCs were detected in all the freshwater samples with concentrations up to 60 μg L−1, and more intermittently with concentrations up to 1.15 μg L−1, at the most upstream estuarine site. Intracellular MC was only sporadicall