Plants, like humans and other animals, host rich communities of commensal and mutualistic microorganisms. The collective genomes of this complex microbial networks encode various metabolic functions that are not found in plants, in fact constituting a functional extension for the genome of the host plant. Soil bacteria associated with plant roots (the rhizosphere) have been shown to have a profound effect on disease suppression and nutrient acquisition. Another of the most studied beneficial relationships is that established between plants and fungi for the formation of mycorrhizae, where fungi provide the plant with water and mineral nutrients with low availability in the soil, as well as a defense against pathogens. Studying the patterns of these associations and their underlying mechanisms in complementary geographic and ecological settings (tropical and montane in Mexico, sub-tropical and temperate in Japan), would greatly widen the ecological, biogeographical and evolutionary implications of these important interactions.