The Hologenome Hypothesis and Its Application to Plant-Microbe Interactions on an Evolutionary Scale

When roots are pulled from the ground, one cannot ignore the soil particles with their rhizosphere microbes still attached to the root surface and root hairs. The rhizosphere is home to a vast variety of microorganisms that associate with plants and either positively or negatively influences plant growth, while the rhizosheath is defined as the weight of soil strongly attached to the plant root surfaces. Root hairs, epidermal extensions that increase surface area, are a critical component of rhizosheaths. Within the root and in continuation with the aerial portion of the plant is the endosphere, providing both intra- and extracellular locations for microbial habitation. Endophytic microbes often enter plant roots through cracks in the epidermis or in areas where lateral roots emerge, or through stomata, openings for gas exchange, in the aerial parts of the plant. Microbial pathogens as well as symbionts and commensals enter into roots, stems, or leaves employing these “doorways” to enter plant tissues—sources of nutrients and carbon for microbes.