The new strategy of the EU addressing healthy soils is crucial due to the extremely important ecosystem services a soil provides directly linked with human and animal health. Soil is a very complex medium and dynamic both in space and in time; thus, studies focusing on the interactions between plant roots, soil and microorganisms (i.e. occurring in the rhizosphere) are crucial in unraveling soil dynamics. The linkage between rhizosphere dynamics at mm-scale and the m/km-scale ecosystem is fundamental. In particular, the soil can be considered a non-renewable resource reservoir of biodiversity useful not only for plant health but also for animal and for human health. In fact, there are pieces of evidence regarding the linkage between the animal and human gut microbiome and the soil biodiversity and composition.