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

Planktonic and benthic cyanobacteria populations can produce microcystins, potent hepatotoxins that pose risks to animal and human health. In Swiss alpine lakes, past cattle deaths have been linked to benthic cyanobacteria, yet their diversity, distribution, and ecological niches remain poorly characterized. To address this gap, we conducted a survey of 31 high-altitude lakes across Switzerland (June–October 2022), analyzing 64 planktonic and benthic biomass samples. Digital PCR targeting the mcyA gene revealed widespread occurrence of potential microcystin producers, with positive detections of the gene in 80% of planktonic and 91% of benthic samples. Benthic habitats, particularly biofilms and rock mats, exhibited the highest mcyA concentrations per unit biomass. High-throughput 16S rRNA sequencing further uncovered distinct cyanobacterial community compositions: Phormidesmis and Leptolyngbya dominated benthic assemblages, while Pseudoanabaena and Tychonema were more common in planktonic environments. Spatial autocorrelation analysis (Moran’s I) indicated significant clustering of mcyA-positive sites, with lower precipitation levels emerging as the most influential environmental driver among the tested variables. Together, these findings identify alpine lake benthic zones as critical, as described in lowland lakes, but undermonitored reservoirs of potentially toxin-producing cyanobacteria. We highlight the need for integrated surveillance of both benthic and planktonic communities to more accurately assess microcystin exposure risks in alpine ecosystems.