metagenomic study of fungal species by sequecing ITS1 from samples collected at varible distances of different trees

Species of the group Saccharomyces sensu stricto are commonly found inhabiting tree barks and surrounding soil, however their abundance and ecology is likely to have been underestimated due to unavoidable bias of culturing methods. Here, we sequenced the mycobiome of soils surrounding different types of trees at varying altitude. To survey for yeasts belonging to Saccharomyces sensu stricto group rather than other fungal species, we carried out an enrichment step involving the isolation of the ITS region specific to this group of yeasts. Reads mapping to Saccharomyces species were detected in all soil samples with S. kudriavzevii being the relatively most abundant species. Reads for S. eubayanus and S. mikatae were retrieved in spite of these species not being isolated in Europe yet. ITS1 alignment of S. cerevisiae, S. paradoxus and S. kudriavzevii sequences obtained in this study showed 1 to 6 bp polymorphisms with other known strains suggesting the presence of distinct geographical populations. The presence of Basidiomycetous fungi was still dominant and species of the phylum Ascomycota represented a minority; however the gel selectivity step succeeded for the first time to detect the diversity of Saccharomyces species in their natural environment.