The "Plant Microbiome" can be described as the sum total of the genomic contribution made by the diverse microbial communities that inhabit the surface and internal tissues of the plant parts.

The rhizosphere, endosphere, phyllosphere constitute the major compartments in which the microbial communities reside in the plant. The soil microbiome is the main source from which the plant selects and builds its microbiome profile. The plant genotype (e.g., dicot bean plant and a monocot rice plant), its root exudates (indicated by blue shade for bean and green for rice), the soil types and properties, and the environmental factors influence the plant microbiome makeup (indicated by different colored microbes inhabiting the plant compartments in bean and rice plant). Mycorrhizal association in both plants is indicated by thin lines extending from the roots into the surrounding soil.