Spatial distribution and diversity of mcyA gene-carrying cyanobacteria in planktonic and benthic communities of Swiss alpine lakes

Cyanobacteria are notorious for producing harmful toxins, including microcystins, which can severely impact animal and human health. In Swiss alpine lakes, past episodes of cattle deaths have been linked to acute hepatotoxicosis caused by microcystins from benthic cyanobacteria but to date not much is known about the diversity of microcystin-producing cyanobacteria in these ecosystems, their spatial distribution or favorable ecological niches. In this study, we examined the presence and distribution of microcystin-producing cyanobacteria across 31 alpine lakes in Switzerland, conducting a comparative survey of both planktonic and benthic environments. A total of 64 biomass samples were collected from high-altitude lakes in the Alps between June and October 2022. We used digital PCR (dPCR) to quantify the mcyA gene, a marker for cyanobacteria carrying microcystin genes, and performed high throughput 16S rRNA sequencing to characterize the taxonomic diversity of cyanobacterial communities. The obtained results revealed that 80% of the planktonic samples and 91% of the benthic samples tested positive for the mcyA gene, indicating the widespread presence of potentially toxic cyanobacteria in these lakes. Benthic environments showed comparable or higher mcyA concentrations per unit biomass to planktonic samples, taken from the same locations, with biofilms and rock mats exhibiting the highest levels. Moran’s I statistic revealed significant spatial clustering of mcyA-carrying cyanobacteria, suggesting the presence of higher-risk locations in the Alps. Principal component analysis (PCA) identified lower precipitation levels as the most influential tested environmental factor driving this clustering. 16S rRNA analysis further revealed distinct cyanobacterial community compositions between planktonic and benthic environments in remote altitude lakes, with genera Phormidesmis and Leptolyngbya dominant in benthic habitats, while Pseudoanabaena and Tychonema were more prevalent in planktonic samples. Our findings suggest that water flow may play a significant role in driving the proliferation of mcyA carrying cyanobacteria in high altitdue lakes of the Swiss Alps and highlight the need for integrated monitoring of both benthic and planktonic cyanobacteria to correctly assess the risk of microcystin exposure in alpine lakes.