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The soil fungal diversity and community partitioning between the bulk soil and stone compartments was investigated using PCR based approaches targeting the barcoding internal transcribed spacer (ITS) of rDNA and the laccase encoding functional gene as genetic markers. Soil samples were collected from the B-horizon of spruce and beech forests at the Hainich Biodiversity Exploratory, central Germany. The targeted markers were amplified from the respective DNA extracts using general fungal primers and basidiomycete laccase gene specific primers, cloned and sequenced. Differences in the fungal community composition between the two forest types and the soil compartments were indicated by both markers. When the effects of ecological factors were considered, the two markers produced different patterns of results. The ITS rDNA marker revealed communities principally influenced by forest type, while those detected with the functional marker were mainly affected by soil pH. The fungal communities detected by the functional marker in particular, differed significantly between soils and stones, indicating that laccase-producing fungi are specifically adapted to degrade organic matter in soils rather than weathering of stones. The study underlines the fact that coherent and complementary results may be obtained with both genetic markers used.

Fungi are important members of soil microbial communities with a crucial role in biogeochemical processes. Although soil fungi are known to be highly diverse, little is known about factors influencing variations in their diversity and community structure among forests dominated by the same tree species but spread over different regions and under different managements. We analyzed the soil fungal diversity and community composition of managed and unmanaged European beech dominated forests located in three German regions, the Schwa "bische Alb in Southwestern, the Hainich-Dun in Central and the Schorfheide Chorin in the Northeastern Germany, using internal transcribed spacer (ITS) rDNA pyrotag sequencing. Multiple sequence quality filtering followed by sequence data normalization revealed 1655 fungal operational taxonomic units. Further analysis based on 722 abundant fungal OTUs revealed the phylum Basidiomycota to be dominant (54%) and its community to comprise 71.4% of ectomycorrhizal taxa. Fungal community structure differed significantly (p