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Filamentous epipelic cyanobacteria were isolated from ponds and lakes in the Czech Republic, Austria and Italy. Morphological and genetic variation of 20 isolated strains within the genera Geitlerinema, Microcoleus and Phormidium were studied. Partial sequences of the 16S rRNA gene were used for phylogenetic analyses, and secondary structure of the 16S-23S ITS region was used to additionally define clades. Morphological and molecular were congruent, and we were able to identify the majority of strains correctly to species on the basis of morphological features. Overall diversity and morphological/genetic variation of epipelic species is not as high as described from other benthic habitats, possibly due to the relative microhabitat uniformity of lake/pond bottom sediments. The M. vaginatus clade is well defined by an 11 bp insert in 16S rRNA gene (bp 423-433) and populations from different ecological conditions differ in secondary structure in the 16S-23S ITS regions, particularly in Box-B helices. Ph. autumnale and the genus Geitlerinema appear to be polyphyletic as presently defined.

Morphological and molecular study of epipelic filamentous genera Phormidium, Microcoleus and Geitlerinema (Oscillatoriales, Cyanophyta/Cyanobacteria).