Agriculture is facing the challenges to improve performance and crop adaptation to climate change towards reducing negative impacts of associated abiotic stresses on crop yield and contributing to its mitigation. Climate change comprises more frequent and ample abiotic stresses that plants have to cope with, such as drought, the most important limitation to yield stability and plant harvest product quality which often lead to hydromineral nutritional stress. The capacity of plants to extract nutrients and water from a given volume of soil depends on root system architecture and on intrinsic factors such as the production of root exudates and the efficiency for resource uptake and transport. This capacity is largely influenced by complex root-soil interactions in the rhizosphere, such as relationships with beneficial microorganisms, but are still poorly understood and not taken into account in breeding. As such it is mandatory to take advantage of beneficial plant - biotic interactions to increase plant performance, lower the use of fertilizers and associated negative impacts on environment adopting an agroecology approach. Reaching the awaited promotion of bioavailability of mineral elements for plants, avoiding competition between plants and the microbiome and so promoting plant growth under low input cropping systems needs concerted approach, disciplines and methods. A selection of ongoing research projects, on various crops will illustrate how phenotyping tools and methods are being federated with a range of disciplines to identify the genetic and physiological determinants of root traits, both morphological and functional, and their plasticity to abiotic constraints, relevant to improve plant performance in low input cropping systems, via improved cultivars and the valorisation of interactions with beneficial microbes, in fine for the choice of innovative varieties by breeders.