The aim of this study was to examine the transcription-level response of a symbiotic system comformed by the host tree Fagus sylvatica L (European beech) and the root-associated mycobiota to fluctuations in ammonium and nitrate availability in the soil. The experiment was conducted with young trees grown at a natural regeneration forest. We used ¹⁵N stable isotopes in combination with DNA-based and RNA-based molecular methods and Illumina sequencing.

We report data on the beech root-associated fungal community structure obtained by metabarcoding of the fungal ITS2 region, transcriptome data from the fungal community associated to the tree roots, and transcriptome data from Fagus sylvatica L in response to ammonium or nitrate application to the soil. We also report data from soil ammonium-N, soil-nitrate-N, tree and soil dry mass, root 15N, root N, root C, root carbohydrates, root ammonium-N, root nitrate-N, soil pH, and climate data from the experiment.

Young beech trees grown in a natural regeneration forest were excavated with the surrounding soil using cylinders. After nearly 21 weeks of adjustement period inside cosms, the tree roots were supplied with 15-N labeled ammonium, or 15N-labeled nitrate solutions, or demineralized water (control). DNA was isolated from the root tips and used for metabarcoding of the fungal ITS2 marker gene and sequenced by Illumina MiSeq. RNA was also isolated from the same root tip samples and used for transcriptome analyses of both the fungi and the host in response to nitrogen treatment relative to control conditions. Soil ammonium-N, Soil-nitrate-N, tree and soil dry mass, root 15N, root N, root C, root carbohydrates, root ammonium-N, root nitrate-N, soil pH, and climate data were measured.