Mineral nitrogen nutrition of Fagus sylvatica L roots colonized by ectomycorrhizal fungi in native forest soil

Transcriptional Landscape of Ectomycorrhizal Fungi and Their Host Provides Insight into N Uptake from Forest Soil

“…The global fungal community associated with beech roots in this experiment was dominated by six genera containing ectomycorrhizal fungi ( Amanita [7.18%], Cenococcum [9.05%], Scleroderma [4.83%], and Xerocomus [29.17%]), ericoid fungi ( Oidiodendron [1.09%]), and saprotrophic fungi ( Mycena [3.75%]) ( Fig. 1A ; see also Data Set S1 at Dryad [ 132 ]). The remaining taxa were rare (<1% per genus) and belonged to the phyla Ascomycota (2.31%), Basidiomycota (2.51%), Mucoromycota (0.11%), and Mortierellomycota (0.02%), and the rest were fungi of unknown phylogenetic lineages (39.98%) ( Fig.…”

“…The remaining taxa were rare (<1% per genus) and belonged to the phyla Ascomycota (2.31%), Basidiomycota (2.51%), Mucoromycota (0.11%), and Mortierellomycota (0.02%), and the rest were fungi of unknown phylogenetic lineages (39.98%) ( Fig. 1A ; see also Data Set S1 at Dryad [ 132 ]). We did not detect any significant effects of short-term ammonium or nitrate treatment on fungal operational taxonomic unit (OTU) richness ( F 2,9 = 0.288; P = 0.756), Shannon diversity ( F 2,9 = 0.437; P = 0.659) (see Table S1 in the supplemental material), or the composition of the fungal OTU assemblages ( R 2 = 0.146; pseudo- F 2,9 = 0.767; P = 0.861; 9,999 permutations [adonis]) ( Fig.…”

“…The RNA data containing ectomycorrhizal, ericoid mycorrhiza, endophytic, and saprotrophic fungi comprised a total of 175,531 transcript identifiers or gene models, covering 3,759 unique Eukaryotic Orthologous Groups of protein identifiers (KOGs). From these, 122,437 transcript identifiers (covering 3,708 unique KOGs) belong purely to the EMF (see Data Set S2 at Dryad [ 132 ]). Given the patchy occurrence of fungi within replicates ( Fig.…”

“…Given the patchy occurrence of fungi within replicates ( Fig. S2 ), the fungi were aggregated according to KOGs into a metatranscriptome, and after normalization in DESeq2, the full-list fungal metatranscriptome (17 fungi) ( Table 1 ) resulted in 3,619 unique KOGs, whereas the EMF-specific metatranscriptome (13 EMF species) ( Table 1 ) comprised 3,593 KOGs (see Data Set S3 at Dryad [ 132 ]). We evaluated the molecular functions of the EMF metatranscriptome according to KOG functional classifications.…”

“…We further tested with DESeq2 whether the KOGs belonging to the full fungal metatranscriptome list or only to the EMF metatranscriptome were significantly differentially expressed in response to ammonium or nitrate treatment relative to the control. In response to ammonium, not a single KOG was significantly affected (see Data Set S3 at Dryad [ 132 ]). In response to nitrate, one differentially expressed KOG (KOG4381) was detected in the full fungal metatranscriptome list, and two KOGs (KOG4381 and KOG4431) were detected in the EMF metatranscriptome (see Data Set S3 at Dryad [ 132 ]).…”