• Changing precipitation regimes are a challenge for forest health under future climate scenarios. If belowground symbionts can acclimate to changing moisture regimes it may buffer forest trees from these changes.
• In this study we exposed the ectomycorrhizal fungus Suillus pungens to acute and chronic drought stress and used RNASeq of both ectomycorrhizal roots and extraradical mycelium to gauge the magnitude of stress, identify key genes involved in drought response, and gauge potential ecosystem consequences of drought.
• We found that there were major transcriptional differences for S. pungens in ectomycorrhizal roots (28% of genes) and extraradical mycelium (41% of genes) under acute drought stress, but only 0.1-2% of genes were differentially expressed in chronic drought treatments. Up to 56% of differentially expressed genes under acute drought were unique to either roots or mycelium. While a number of implicated genes, such as those encoding for trehalose, have well-known roles in osmotic stress, others, such as fungal hydrophobins and atromentin, have received less study and may also impact other ecosystem functions.
• These results suggest that functional compartmentalization is key to ectomycorrhizal fungal adaptation to stressful climatic conditions and there is high potential for fungal acclimation to ameliorate future climate stress.  

Approximately ten root tips were removed from one half of a root system (which half was determined randomly) for RNA extraction and immediately flash frozen. The other half of the root system was used for percent colonization where an average of 77 root tips were scored as non-mycorrhizal or ectomycorrhizal (min = 27, median = 75, max = 125). To assess treatment effects on plant biomass and total moisture content, the remaining plant tissue was separated into roots and shoots, weighed fresh to assess initial moisture content, dried for 48 hours at 80 °C, and weighed again. To determine gravimetric percent soil moisture, 10 g ± 2 g soil was weighed out, oven-dried for at least 72 hours at 80 °C, then weighed again to determine water mass loss.