Fertilizer and fungicide use increases the abundance of less beneficial ectomycorrhizal species in a seedling nursery

► Varying chemical use altered ectomycorrhizal (ECM) associations in a tree nursery. ► Rhizopogon rubescens was most inhibited by increased fertilizer and fungicide use. ► R. rubescens abundance was positively correlated with tree seedling nutrition. ► Other ECM taxa increased in abundance but provided comparatively few benefits. ► Fertiliser and fungicide use selects for less beneficial ECM taxa in this context.