The increased production, consumption, and release of antibiotics account for their frequent contamination of aquatic ecosystems and detection in different biological matrices. Several antibiotics affect non-target organisms such as algae, cyanobacteria, zooplankton, and fish, making investigations on them very crucial for the health and maintenance of biodiversity. The impact of broad-spectrum antibiotics like ciprofloxacin (CPX) on toxin-producing and non-toxin-producing cyanobacteria has been poorly investigated. Therefore, the present study investigated the physiological and toxicological effects of CPX on Microcystis aeruginosa EAWAG 198, Microcystis aeruginosa LE3, and Microcystis flos-aquae UTEX-LB 2677. CPX caused a significant (p < 0.05) decrease in the cell densities and chlorophyll-a of the three strains. The antibiotic caused oxidative stress in all the strains, as demonstrated by a significant rise in the levels of intracellular hydrogen peroxide (H2O2) of the treated cultures at 96 h post-exposure. Lipid peroxidation and the activity of the antioxidant enzyme—peroxidase (POD) and glutathione-S-transferase (GST)—of the cultures were significantly (p < 0.05) altered. Exposure to CPX generally stimulated the production of biomolecules such as total proteins, lipids, and total carbohydrates as a function of increasing exposure concentration. The exception to the general trend was M. aeruginosa EAWAG 198, a non-toxin-producing strain, which suffered a significant decline in carbohydrate content during exposure to CPX. This study revealed that environmentally relevant levels of CPX could alter the population dynamics, photosynthesis, biochemical composition, and the general physiology of Microcystis species/strains in aquatic ecosystems.
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