Recent evaluations of ecosystem services highlight the need to fill the major knowledge gap concerning the role of belowground biodiversity on services linked to soil. Key processes in carbon and nitrogen cycling occurred in the rhizosphere but most studies are based on shallow soil layers although many plants develop deep roots that can play a significant role on soil biochemical properties in interaction with microbial activity. We investigate soil erodibility and carbon and nitrogen cycling under different root profiles and soil microbial functioning in sites with different land covers in temperate and tropical climates. Roots and soils are sampling in several agroforests in France and in the North Vietnam. The soil profile is studied from the soil surface to 2 m. We use a standard method for coring to quantify root distribution along the profile. We use the MicroRespTM method as a viable indicator for microbial activity and microbial community level physiological profile. Organic carbon content and higher soil aggregate stability in the surface zone is associated with higher root biomass and specific morphological characteristics. Fine roots are found down to the bedrock and to 2 m deep. Future results may show that land use change be a driver of microbial functioning linked to land cover and specificity of root systems. The presence of roots deep in the soil profile, in agroforest systems and natural vegetation, should be taken into account as a significant contributor to belowground ecosystem services and long-term carbon storage.