1. We investigated the importance of lake water chemistry and substrate properties in regulating microbial decomposer communities on macrophyte litter. Ten lakes of differing water chemistry, including such variables as nutrient concentration, pH and dissolved organic carbon, were sampled in October 2003. Water chemistry was analysed, and litter from the macrophytes Phragmites australis, Schoenoplectus lacustris and Nuphar lutea was collected from both above and below the water surface.
2. The three plant species differed widely in carbon and nitrogen content. The aerial parts of P. australis had highest C : N ratio (mean value 125), while the lowest values were found in leaves of N. lutea (19.8).
3. Fungal carbon ranged from 0.15 to 6.4 mg g−1 dry weight (DW), and was higher on aerial than on submerged plant parts. Fungal biomass was highest on S. lacustris and lowest on N. lutea. Denaturing gradient gel electrophoresis revealed no differences in the number of fungal taxa between plant species or plant parts, with the limitation that no molecular analysis was possible for N. lutea.
4. In contrast, bacteria were most abundant on N. lutea, but showed no significant difference between leaf and stem parts. The number of bacterial taxa was highest on the submerged parts of P. australis.
5. The correlations between microbial variables and the properties of lakes and litter were analysed using multivariate statistics. In a principal component analysis, litter properties explained 78% of the variation in microbial variables. In contrast, redundancy analysis revealed that the explanatory power of lake water chemistry was only 20%, indicating that the properties of the growth substratum were more important than those of the lake water for the attached microbial communities.