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Epipelic assemblages have not been studied in the Czech Republic yet. The sampling method following Round (1953) was used for the fist time in the Czech Republic. The epipelic assemblages were dominated by diatoms, particularly in mesotrophic and meso-eutrophic fishponds, eutrophic fishponds were dominated by green algae and cyanobacteria. A total of 130 diatom species were found in 16 fishponds, their list with trophic preferences is presented. Seven morphospecies were distinquished within Sellaphora pupula species complex, their clonal cultures will be studied later by molecular methods.

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