Determining species diversity of microfungal communities in forest tree roots by pure-culture isolation and DNA sequencing

Pure-culture isolation from roots was compared with transformation of total DNA from roots followed by sequence analysis of ITS 1/2 rDNA of representative clones as methods for determining the abundance and composition of microbiota in roots of Betula pendula, Fagus sylvatica, Larix decidua, Prunus serotina and Quercus petraea. The results from the two methods differed greatly, with no overlap between the taxa identified. Pure-culture isolation revealed greater species diversity (47 taxa), the most frequent fungi being Ascomycota, including Penicillium spp., Phialocephala fortinii, Pochonia bulbillosa, Sesquicillium candelabrum and Trichoderma spp. Transformation of total DNA and sequencing revealed less diversity (22 taxa), the most frequent taxa being Basidiomycota, including Coprinus fissolanatus and Mycena spp., and Ascomycota, including Podospora–Schizothecium spp., Helgardia anguioides and Microdochium sp. Communities characterized by either method showed slightly greater fungal diversity and less species dominance on F. sylvatica than on roots of other trees, whilst DNA sequencing showed least diversity and greatest species dominance on Q. petraea.