Fungal Endophytes of<i>Populus trichocarpa</i>Alter Host Phenotype, Gene Expression, and Rhizobiome Composition

Abstract

<i>Mortierella</i> and <i>Ilyonectria</i> genera include common species of soil fungi that are frequently detected as root endophytes in many plants, including <i>Populus</i> 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 <i>P. trichocarpa</i> rhizobiome, <i>M. elongata</i> PMI93 and <i>I. europaea</i> PMI82, was studied by coupling forest soil bioassays with environmental metatranscriptomics. Using soil bioassay experiments amended with fungal inoculants, <i>M. elongata</i> was observed to promote the growth of <i>P. trichocarpa</i>. This response was cultivar independent. In contrast, <i>I. europaea</i> had no visible effect on <i>P. trichocarpa</i> growth. Metatranscriptomic studies revealed that these fungi impacted rhizophytic and endophytic activities in <i>P. trichocarpa</i> and induced shifts in soil and root microbial communities. Differential expression of core genes in <i>P. trichocarpa</i> roots was observed in response to both fungal species. Expression of <i>P. trichocarpa</i> genes for lipid signaling and nutrient uptake were upregulated, and expression of genes associated with gibberellin signaling were altered in plants inoculated with <i>M. elongata</i>, but not <i>I. europaea</i>. 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 <i>M. elongata</i> manipulates plant defenses while promoting plant growth.