The long-and short-term effects of salt on biological nitrogen and phosphorus removal processes were studied in an aerobic granular sludge reactor. The microbial community structure was investigated by PCR-denaturing gradient gel electrophoresis (DGGE) on 16S rRNA and amoA genes. PCR products obtained from genomic DNA and from rRNA after reverse transcription were compared to determine the presence of bacteria as well as the metabolically active fraction of bacteria. Fluorescence in situ hybridization (FISH) was used to validate the PCR-based results and to quantify the dominant bacterial populations. The results demonstrated that ammonium removal efficiency was not affected by salt concentrations up to 33 g/liter NaCl. Conversely, a high accumulation of nitrite was observed above 22 g/liter NaCl, which coincided with the disappearance of Nitrospira sp. Phosphorus removal was severely affected by gradual salt increase. No P release or uptake was observed at steady-state operation at 33 g/liter NaCl, exactly when the polyphosphate-accumulating organisms (PAOs), "Candidatus Accumulibacter phosphatis" bacteria, were no longer detected by PCR-DGGE or FISH. Batch experiments confirmed that P removal still could occur at 30 g/liter NaCl, but the long exposure of the biomass to this salinity level was detrimental for PAOs, which were outcompeted by glycogen-accumulating organisms (GAOs) in the bioreactor. GAOs became the dominant microorganisms at increasing salt concentrations, especially at 33 g/liter NaCl. In the comparative analysis of the diversity (DNA-derived pattern) and the activity (cDNA-derived pattern) of the microbial population, the highly metabolically active microorganisms were observed to be those related to ammonia (Nitrosomonas sp.) and phosphate removal ("Candidatus Accumulibacter").Numerous wastewaters, like those generated in seafood canning, pickling, and cheese-processing industries, can contain significant amounts of inorganic dissolved salts (14). The use of seawater for toilet flushing in ships, offshore installations, and regions with problems related to water supply also introduces salts into freshwater. Wastewaters with a high salt content require the activity of salt-tolerant microorganisms which may not be present in high numbers in microbial inocula from sewage treatment plants. Salt ions exert high osmotic pressure on the microorganisms, and most of the freshwater-based microbial populations are unable to survive at these high osmotic pressures and either die or become dormant under these conditions (40). Besides that, inorganic salts can affect the structure and settling properties of microbial flocs as well as the maximum solubility of oxygen and its transfer to the liquid phase, which can lead to oxygen limitation. Consequently, high salt concentrations have a negative influence on existing biological wastewater treatment plants, affecting organic matter, nitrogen, and phosphorus removal (17). So far, most studies on chemical oxygen demand (COD), N, and P removal from saline wastewa...