The main purpose of this thesis was to investigate the response of diatom communities to various environmental factors. Samples were taken in 12 karst ponds in alpine region during the high season of pasture (August 2016). Because agrilal was present in all karst ponds, we have decided to sample epipelon. At each location, we evaluated the hydro morphological characteristics, measured the physical and chemical characteristics with the multimeter, and took samples for further chemical analysis of water and composition preparation. We determined 105 taxa of diatoms, which belong to 32 genera. The most common species were Gomphonema parvulum, Navicula cryptocephala, Sellaphora pupula in Achnanthidium pyrenaicum, which were present in most karst ponds. Karst pond with the lowest species diversity (KRV1) is also at the highest altitude, while the karst pond with highest variability (JEL1) is at the lowest altitude. The samples of karst ponds were very heterogeneous, therefore the results did not show statistically significant correlations. We have established a positive correlation between the species variety of diatoms and the saturation of water with oxygen and a negative correlation between the species variety of diatoms and the concentration of ammonium nitrogen. The concentration of nitrates and ammonia clarifies almost 20% of the total variability of the diatoms communities. Against all expectations, the results showed a negative correlation between macroinvertebrate and diatom communities, probably because of the different response to environmental factors.
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