Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems

•Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, andmycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has comparedthe actual gene expression of these guilds in different forest soils.
•We used metatranscriptomics to study the competition for organic resources by these fun-gal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNAannotation pipeline combined with the JGI MycoCosm database, we compared the transcriptsof these three fungal guilds, targeting enzymes involved in C- and N mobilization from plantand microbial cell walls.
•Genes encoding enzymes involved in the degradation of plant cell walls were expressed at ahigher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However,ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genesencoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transpor-ters were more highly expressed in ectomycorrhizal fungi than in other groups. We showedthat ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggestingthat their interactions could decelerate C cycling.
•Metatranscriptomics provides a unique tool to test controversial ecological hypotheses andto better understand the underlying ecological processes involved in soil functioning and car-bon stabilization.