Two nitrifying reactors were operated under the same conditions except that one was twice inoculated with the aerobic denitrifying bacteria Microvirgula aerodenitrificans. The first bioaugmentation induced a transient nitrogen loss. Fluorescent in situ hybridization revealed that the bioaugmented bacteria had been rapidly eaten by protozoa. The second massive inoculation unbalanced the ecosystem and resulted in an overgrowth of protozoa and perturbations of nitrification, whereas both parameters remained stable in the non bioaugmented reactor. To enhance the incorporation of the added bacteria to indigenous flocs, two strategies were then tested. First, coagulating and flocculating substances were added to the reactor just after bioaugmentation and second, the bacteria were embedded in alginate beads before inoculation. The latter strategy gave the best results. After break-up of the beads, alginate fragments, containing microcolonies of M. aerodenitrificans, were found to be incorporated into the existing flocs. Alginate beads offer a temporary protection against grazing and favor the adhesion of the exogenous bacterial microcolonies to the existing flocs. These beads therefore constitute a suitable bioaugmentation vector to incorporate a bacterial strain into activated sludge flocs.