The effects of modified heavy metal (HM) availability on the microbial community structure and on the microbe-mediated degradation of herbicide isoproturon (IPU) were evaluated in soil with a long-term HM contamination. The fate of C-14-ring labelled IPU was investigated for over 60 days under controlled microcosm conditions. Phosphate mineral apatite and a water solution of Pb, Zn, and Cd salts were previously homogeneously mixed into the soil material to reduce and to increase the proportion of bioavailable HM, respectively. The availability of Pb, Zn, and Cd was determined by HM fractionation and plant uptake 110 days after the addition of amendments, shortly before IPU addition. Apatite treatment reduced the availability of HM, but did not affect the microbial biomass and the microbial community structure on the genotype level (total soil DNA-RAPD). However, it changed the microbial community structure on the phenotype level, based on the composition of phospholipid fatty acids (PLFA) at the end of the degradation experiment. The degradation of IPU did not change. In contrast to apatite treatment, HM supplementation increased the bioavailability of Pb, Zn and Cd, which resulted in biomass reduction and changes of microbial community structure on the genotypic (total soil DNA-RAPD) and phenotypic (PLFA) level. Increased bioavailability of HM also significantly reduced the rate of IPU degradation and mineralisation. The total mineralisation over a period of 60 days decreased from 12 to 5% of initial C-14. Increased HM bioavailability did not influence the degradation pathways and kinetics of IPU. (C) 2004 Elsevier Ltd. All rights reserved.