Changes in process performance and the nitrifying bacterial community associated with an increase of thiocyanate (SCN(-)) loading were investigated in a pre-denitrification process treating industrial wastewater. The increased SCN(-) loading led to the concentration of total nitrogen (TN) in the final effluent, but increasing the internal recycling ratio as an operation parameter from 2 to 5 resulted in a 21% increase in TN removal efficiency. In the aerobic reactor, we found that the Nitrosomonas europaea lineage was the predominant ammonia oxidizing bacteria (AOB) and the percentages of the AOB population within the total bacteria increased from about 4.0% to 17% with increased SCN(-) concentration. The increase of nitrite loading seemed to change the balance between Nitrospira and Nitrobacter, resulting in the high dominance of Nitrospira over Nitrobacter. Meanwhile, a Thiobacillus thioparus was suggested to be the main microorganism responsible for the SCN(-) biodegradation observed in the system. (C) 2010 Elsevier Ltd. All rights reserved.