Characterization of root fungal community of European beech saplings

Nitrogen (N) is one of the most important nutrients required for plant growth. Diverse ectomycorrhizal fungi living in symbiotic association with tree roots play an important role in acquiring and delivering N to the roots, obtaining carbohydrates in return. Increased levels of ammonium and nitrate have been previously found to negatively affect ectomycorrhizal fungi diversity and abundance, but the molecular-level responses are unknown. By targeting the fungal ITS2 region, we characterized the entire root-associated fungal community from the roots of European beech saplings that were collected with the surrounding soil at a natural regeneration forest, grown for four months, and supplied with either ammonium solution, nitrate solution, or demineralized water over 2 days. We hypothesized that after just two days of exposition to treatment, the fungal community composition is similar among saplings assigned to different treatments because they have shared origin and the time length of treatment is short. We found that although some fungal OTUs were more dominant than others, no significant statistical differences were detected in the fungal OTU composition among treatment groups. Fungal genera belonging to ectomycorrhizal, saprotrophs, endophytes and pathogens comprised nearly 32 % of the overall community, whereas about 34 % had multiple lifestyles and about 35 % were unassigned. The fungal genera detected in the samples using this approach served as guide for selecting reference transcriptomes that were used for mapping RNA sequences derived from the same samples to study the transcriptional responses of the fungi to ammonium and nitrate supply.