and genera include common species of soil fungi that are frequently detected as root endophytes in many plants, including spp. However, the ecological roles of these and other endophytic fungi with respect to plant growth and function are still not well understood. The functional ecology of two key taxa from the rhizobiome, PMI93 and PMI82, was studied by coupling forest soil bioassays with environmental metatranscriptomics. Using soil bioassay experiments amended with fungal inoculants, was observed to promote the growth of . This response was cultivar independent. In contrast, had no visible effect on growth. Metatranscriptomic studies revealed that these fungi impacted rhizophytic and endophytic activities in and induced shifts in soil and root microbial communities. Differential expression of core genes in roots was observed in response to both fungal species. Expression of genes for lipid signaling and nutrient uptake were upregulated, and expression of genes associated with gibberellin signaling were altered in plants inoculated with , but not . Upregulation of genes for growth promotion, downregulation of genes for several leucine-rich repeat receptor kinases, and alteration of expression of genes associated with plant defense responses (e.g., jasmonic acid, salicylic acid, and ethylene signal pathways) also suggest that manipulates plant defenses while promoting plant growth.