The microbial communities in the soil are responsible for material cycling and thus also for maintaining the fertility of agricultural soils. In order to assess pesticide side effects on the soil processes, detailed knowledge is required about the structure and function of the soil microflora. Therefore, the degradation and humification of 14C-labeled maize straw was studied in process-oriented microcosms. Apart from a native orthic luvisol, a heat-treated soil was used that has been freed from organic carbon by incineration at 600 degrees C. Microbial communities involved in the turnover of the crop residues were investigated using denaturing gradient gel electrophoresis (DGGE) of 16S rDNA sequences. Both 13C-nuclear magnetic resonance (NMR) spectroscopy and gel permeation chromatography were used to analyze humic acids produced in the microcosms. To evaluate the sensitivity of the microcosms, the influence of the fungicide dithianon was used in a case study at a concentration of 50 mg/kg. Microbial activity was reduced because of the application of the pesticide, especially in the native soils, while mineralization of 14C-labeled maize straw was only slightly affected. The buildup of fungal biomass was inhibited for at least three weeks. Despite these effects on the microbial communities, no significant differences in the humification products after 26 weeks of incubation were observed.