A flow-through stream microcosm is presented which was used to investigate the impact of the mercury reducing, genetically engineered microorganism (GEM) Pseudomonas putida KT2442::mer73 on the bacterial community in Elbe River sediments and water. To simulate the discharge of an industrial bioreactor into the environment, GEMs were inoculated continuously at low density into the microcosm. Experiments were carried out in three parallel microcosms of which one remained uninoculated, one was inoculated with the GEM and one with its nonrecombinant parent strain Ps. putida KT2440. Survival of the GEM in water was low, even after cell shock with 2 x 10(6) cells ml(-1). In sediments a slight tendency towards increasing cell numbers could be observed. Community profiles based on thermogradient gel electrophoresis (TGGE) of 16S rDNA genes amplified from total community DNA showed a highly complex pattern in the sediments and a declining number of bands in the water column over the experimental period independent of the presence of GEMs. There was hardly any variation between the three treatments studied. The stream microcosm is a good laboratory representation of a river and well suitable for investigations of stream bacterial ecology. Changes in bacterial community compositon in water or sediment could not be ascribed to the GEM. (c) 2006 Elsevier Ltd. All rights reserved.