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Cyanobacteria are favored by climate change and global warming; however, to date, most research and monitoring programs have focused on planktic cyanobacteria. Benthic cyanobacteria blooms also increase and pose a risk to animal and human health; however, there is limited knowledge of their occurrence, distribution and the toxins involved, especially in relation to their planktic conspecifics. Therefore, we analyzed the benthic and planktic life forms of cyanobacterial communities in 34 lakes in Germany, including a monitoring of cyanotoxins. Community analyses were based on microscopic examination and Illumina sequencing of the 16S rRNA gene. The analyses of cyanotoxins were carried out using LC-MS/MS and ELISA. Observed benthic mats containing cyanobacteria consisted mainly of Nostocales and Oscillatoriales, being present in 35% of the lakes. Anatoxin was the most abundant cyanotoxin in the benthic samples, reaching maximum concentrations of 45,000 µg/L, whereas microcystin was the predominate cyanotoxin in the open-water samples, reaching concentrations of up to 18,000 µg/L. Based on the results, specific lakes at risk of toxic cyanobacteria could be identified. Our findings suggest that monitoring of benthic cyanobacteria and their toxins should receive greater attention, ideally complementing existing open-water sampling programs with little additional effort. [ABSTRACT FROM AUTHOR]