The increasing occurrence of potentially toxic planktic cyanobacterial blooms in water bodies and the documented poisonings of animals by benthic cyanobacteria indicate a health risk due to cyanotoxins, which is not yet adequately monitored. We investigated the suitability of molecular approaches for detecting potentially toxic cyanobacteria in the environment and the possibilities for their inclusion in monitoring programmes. We evaluated existing PCR and qPCR assays for identifying potential producers of microcystins, anatoxins, cylindrospermopsins and saxitoxins, and designed two new qPCR assays for identifying potential producers of anatoxins. We applied molecular assays to plankton and benthos samples from lakes and rivers, as well as to diverse samples from less studied habitats. Potentially toxic cyanobacteria are widespread in the Alpine region; microcystin producers were prevalent in plankton, while anatoxin producers were more common in benthos. Cyanobacteria were also detected in some extreme habitats, but the presence of potentially toxic species was not confirmed. The results show that the qPCR method allows quantitative risk assessment for the presence of cyanotoxins, but the assays are currently reliable only for microcystin producers. Key obstacles in developing a molecular test for identifying potential anatoxin producers include the lack of reference nucleotide sequences and insufficient knowledge of benthic cyanobacteria. Nevertheless, molecular methods can significantly complement existing approaches for cyanobacterial research and risk assessment. We have proposed a multi-step protocol for monitoring the risks associated with cyanotoxins in recreational waters, including also molecular methods for the early detection of genetic potential for cyanotoxin production.
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