Explosives used in mining, such as ammonium nitrate fuel oil (ANFO), can cause eutrophication of the surrounding environment by leakage of ammonium and nitrate from undetonated material that is not properly treated. Cold temperatures in mines affect nitrogen removal from water when such nutrients are treated with bioreactors in situ. In this study we identified bacteria in the bioreactors and studied the effect of temperature on the bacterial community. The bioreactors consisted of sequential nitrification and denitrification units running at either 5 or 10 degrees C. One nitrification bioreactor running at 5 degrees C was fed with salt spiked water. From the nitrification bioreactors, sequences from both ammonia- and nitrite-oxidizing bacteria were identified, but the species were distinct at different temperatures. The main nitrifiers in the lower temperature were closely related to the genera Nitrosospira and Candidatus Nitrotoga. 16S rRNA gene sequences closely related to halotolerant Nitrosomonas eutropha were found only from the salt spiked nitrification bioreactor. At 10 degrees C the genera Nitrosomonas and Nitrospira were the abundant nitrifiers. The results showed that bacterial species richness estimates were low, <150 operational taxonomic units (OTUs), in all bioreactor clone libraries, when sequences were assigned to operational taxonomic units at an evolutionary distance of 0.03. The only exception was the nitrification bioreactor running at 10 degrees C where species richness was higher, >300 OTUs. Species richness was lower in bioreactors running at 5 degrees C compared to those operating at 10 degrees C. Biotechnol. Bioeng. 2011; 108: 2876-2883. (C) 2011 Wiley Periodicals, Inc.