Genetic diversity of fungi closely associated with common reed.

•   Variation in endophytic fungal diversity closely associated with roots, stems and leaves of common reed (Phragmites australis) is reported here at sites with different oxygen conditions. •   Fungi isolated from surface-sterilized reed tissue were identified and characterized by morphological and molecular methods including internal transcribed spacer (ITS) sequence analysis from two dry and two flooded sites at Lake Constance (Germany). •   Most isolates were ascomycetes, some basidiomycetes. There were differences in distribution between dry and flooded sites. Trichoderma sp. and Cylindrocarpon sp. were almost exclusively recovered from roots of reed growing at dry sites, whereas Microdochium sp. and Cladosporum sp. were more frequently found at flooded sites. The preference of Trichoderma sp. for drier sites was confirmed by a nested PCR assay targeting the variable ITS region. •   A diverse assemblage of endophytic fungi that differ in distribution between aerated and nonaerated soils is found in reed habitats. The rich mycoflora associated with roots in completely anaerobic soils might depend on downward oxygen transport via an aerenchyma-based ventilation system.