Analysis of seedling survival
In this study, seedling survival was monitored over three years (from March 2016 to early September 2018), which differs from most previous studies that only recorded seedling death or survival at the end of an experiment. The survival time analysis offers a more powerful test and inference on the JC effect. The Cox PH model was used to quantify hazard ratios (HRs) of seedling mortality under different treatments. In the Cox PH model, the three selected parent trees for each of the two focal tree species were treated as a “cluster” (i.e., as a random effect) in the ‘coxph’ function in the R ‘survival’ package (http://survival.r-forge.r-project.org/).

Treatment effects on relative abundances of plant-pathogenic and EcM fungi

To quantify the treatment effects on the relative abundances (frequencies) of plant-pathogenic and EcM fungi, which were presumed to be responsible for seedling mortality, negative binomial GLMMs were used to estimate the treatment effects of warming (OTC versuscontrol), pesticides (versus distilled water), and distance to selected adult trees on the relative abundances of the two fungal guilds (i.e., plant-pathogenic and EcM fungi). The total sequence counts of fungal OTUs in each soil core were included as “weights” in the negative binomial GLMMs ‘glmmTMB’ function in R package. Since our interest was to test the effects of the three treatments on the relative abundances of the two fungal guilds, variations between the two focal tree species and among the three selected adult trees of each focal tree species were treated as random effects.