The treatment of reconstituted whey wastewater was performed in a 400 L digester at 20 degrees C, with an anaerobic digestion step, followed by a step of aerobic treatment at low oxygen concentration in the same digester. In a first set of 48 cycles, total cycle time (T(C)) of 2, 3 and 4 days were tested at varying organic loading rates (OLR). The COD removal reached 89 +/- 4, 97 +/- 3 and 98 +/- 2% at T(C) of 2, 3 and 4 days and OLR of 0.56. 1.04 and 0.78 gCOD L(-1) d(-1), respectively. The activity of the biomass decreased for the methanogenic population, while increasing by 400% for the acidogens, demonstrating a displacement in the predominant trophic group in the biomass bed. A second set of 16 cycles was performed with higher soluble oxygen concentration in the bulk liquid (0.5 mg L(-1)) during the aerobic treatment at a T(C) of 2 days and an OLR of 1.55 gCOD L(-1) d(-1), with a soluble COD removal of 88 +/- 3%. The biomass specific activities showed a compartmentalization of the trophic group with methanogenic activity maintained in the biomass bed and a high acidogenic activity in the suspended flocs. Crown Copyright (C) 2009 Published by Elsevier Ltd. All rights reserved.