BACKGROUND: The impact of mixtures of chloro-triazinic herbicides, such as atrazine and simazine, on aquatic ecosystems is of environmental concern. To study their biodegradation under various operational conditions, a binary community comprising Stenotrophomonas maltophilia and Arthrobacter sp. attached to the porous support of a packed bed reactor, was evaluated. RESULTS: The genetic analysis of the two atrazine-degrading strains revealed that genes atzA, atzB, atzC are present in both bacteria, but only S. maltophilia possess atzD. Thus, by cultivating Arthrobacter sp. on these herbicides, cyanuric acid accumulation was observed. When the binary community was cultivated in the biofilm reactor, at all the loading rates probed, both herbicides were entirely removed. However, complete biodegradation of cyanuric acid was not achieved. CONCLUSIONS: Even with a two-stage reactor, cyanuric acid was only partially removed. This fact could be attributed to the absence, in the second stage, of an easily degradable energy source, required by S. maltophilia for the uptake and cometabolic degradation of the recalcitrant heterocyclic ring. Responding to differences in nutritional conditions prevailing at each reactor stage, local differences in species' predominance were clearly detected by microbiological and molecular biology methods. (C) 2010 Society of Chemical Industry