Microbiomes across root compartments are shaped by inoculation with a fungal biological control agent

Abstract While the endosphere is a hotspot for close interactions between plants and microbes, the influence of different components of the root endosphere on microbiome composition are seldom explored. This study used the fleshy taprooted plant, American Ginseng (Panax quinquefolius) and the recently discovered beneficial microbe, Trichoderma atroviride strain HB20111, to provide insights into microbiome shifts across plant-soil compartment niches including the bulk soil, rhizosphere, epidermis, cortex and vascular tissue. Trichoderma impacted both plant growth and microbiome composition. The survival rate of ginseng plants significantly increased from 70.8% to 85.4%, following Trichoderma treatment while root biomass production increased by 1.2 to 1.5 times compared with the uninoculated control. Microbiome diversity gradually decreased in niches from the bulk soil outside the root toward the vascular tissue, indicating increased selection and suggesting the possibility of a Trichoderma-driven induced systemic or localized resistance. The significant reduction (P