Fungal decomposers are at the center of terrestrial litter decomposition, however little is known about the successional involvement of microbial species within this process. Improved methods are needed to define exactly which microbial taxa are actively contributing to nutrient flow. In this study a characterization of the fungal community on Austrian beech litter from four different locations was conducted in a laboratory microcosm experiment, using a combined approach of RFLP typing and clone library sequencing. Richness and diversity methods as well as taxonomic analysis lead to a complete description of fungal species on Austrian beech litter based on molecular data. The highly uneven fungal community was dominated by Ascomycota. One location showed a significantly different fungal community from the other three locations, possibly because of environmental and nutrient differences. Fungal diversity and richness were shown to increase quickly during the first two weeks of incubation. In a mesocosm experiment, fungi dominated decomposition especially on high nutrient litter. From the same inoculum, very distinctive microbial communities evolved on nutritionally different beech litters within only two weeks. However eventually, the relative involvement of fungi versus bacteria during litter decomposition went down to the same ratio in all locations. The further development of the PhyloTrap method, using rRNA as a target molecule, was another task of this study. Experimental conditions were optimized with the goal to separate mixed RNAs by specific probes and increase the yield and purity of the obtained SSU RNA. The use of different probes- on various phylogenetic levels- will allow for phylogenetic separation of an environmental RNA sample in the future. Together with the use of stable isotope substrates this is a promising tool to gain insight into nutrient acquisition pathways and community shift patterns in microbial ecology.