Occurrence of Microcystins and Toxin-Producing Cyanobacteria in Reservoirs of the Alqueva Water Storage System (Southern Portugal)

Cyanobacterial blooms and the associated production of cyanotoxins represent a growing concern for freshwater ecosystems, particularly in regions increasingly affected by eutrophication and climate change. In Portugal, data on the occurrence and distribution of cyanotoxins remain limited, especially in southern multipurpose reservoirs that support the water supply and irrigation in a region severely affected by water scarcity. This study investigates the presence of cyanobacteria and their major cyanotoxin groups—microcystins (MCs), cylindrospermopsin (CYN), and anatoxin-a (ANTX)—in three reservoirs of the Alqueva water storage system (EFEMA), combining chemical analyses with molecular tools to assess toxin-producing cyanobacteria. Liquid chromatography–mass spectrometry (LC–MS) detected MC-LR, MC-RR, and MC-YR exclusively in the particulate fraction of water samples, while no toxins were detected in the dissolved fraction. MC concentrations were generally low (<0.1 µg/L), with the highest levels observed during summer, particularly in July. Among the variants, MC-LR was the most common and abundant. Molecular analyses (16S rRNA) confirmed the widespread presence of cyanobacteria and identified the genus Microcystis in all reservoirs. Several genes from the microcystin biosynthesis cluster (mcyA, mcyB, mcyD, mcyE, and mcyG) were amplified, and sequencing of the mcyA gene revealed high homology with Microcystis aeruginosa. Although the detected MC concentrations remained below World Health Organization (WHO) guideline values for drinking water, their recurrent detection and the confirmed presence of toxin-producing genotypes highlight the need for continued monitoring. This study underscores the value of integrating chemical and molecular approaches for assessing cyanotoxin risks in large multipurpose reservoir systems under increasing environmental pressure.