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Two bubble column sequencing batch reactors fed with an artificial wastewater were operated at 20, 30 and 35°C. In a first stage, stable granules were obtained at 20°C whereas fluffy structures were observed at 30°C. Molecular analysis revealed high abundance of the operational taxonomic unit 208 (OTU 208) affiliating with filamentous bacteria Leptothrix spp. at 30°C, an OTU much less adundant at 20°C. The granular sludge obtained at 20°C was used for the second stage during which one reactor was maintained at 20°C and the second operated at 30 and 35°C after prior gradual increase of temperature. Aerobic granular sludge with similar physical properties developed in both reactors but it had different nutrient elimination performances and microbial communities. At 20°C, acetate was consumed during anaerobic feeding and biological phosphorous removal was observed when Rhodocyclaceae-affiliating OTU 214 was present. At 30°C and 35°C, acetate was mainly consumed during aeration and phosphorous removal was insignificant. OTU 214 was almost absent but the Gammaproteobacteria-affiliating OTU 239 was more abundant than at 20°C. Aerobic granular sludge at all temperatures contained abundantly the OTUs 224 and 289 affiliating with Sphingomonadaceae indicating that this bacterial family played an important role in maintaining stable granular structures.