Fluorescence imaging is an efficient and powerful technique, which has been often utilized for tracking compounds in animals, however its application on plants or other organisms is not very common. In this work, the fluorescence imaging was used to investigate the effect of selected nanoparticles - NPs (ZnO, CdTe, etc.) on microalgae (Scenedesmus quadricauda and Chlorella vulgaris) growth. The growth and metabolic activity of microalgae was influenced by application of nanoparticles into the growing medium (liquid and solid) and therefore the intrinsic fluorescence was affected. Microalgae pigments (chlorophylls, carotenoids) are responsible for the autofluorescence of the species and therefore, the fluorescence can be used as a tool for quick and easy evaluation of expression these compounds. These pigments have main role in light harvesting and minimize photo-oxidative damage of the cells. Such protection mechanism can be disturbed by another stress related compounds like NPs that presumably damage this protection mechanism i) indirectly (reactive oxygen species) and ii) directly (disruption of biomembranes). Owing to broad fluorescence imaging and correlation with total amount of chlorophylls and carotenoids it was possible to evaluate the influence of NPs on individual microalgae just only by in vivo imaging.Keywords: nanoparticles, Scenedesmus quadricauda, Chlorella vulgaris, fluorescence, abiotic stress, metabolic,
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