Breeding crops more efficient for resource acquisition is a highly desirable target in the actual socio economical and environmental context. The ability of plants to adapt to environmental constraints is a key aspect of their efficiency. Efforts should focus on understanding the molecular bases of plant plasticity, to unravel the cellular and molecular mechanisms modulating plant development in response to environmental signals such as nutrient or water deficiency. The plant interacts with numerous and diverse microorganisms, specially in the rhizosphere. Understanding these plant-microorganism relationships in the rhizosphere is of great agronomical and ecological importance. To this end, besides developing a thorough understanding of plant emergent process involved, the main bottleneck is the development of high-throughput, non-invasive and multi-scale phenotyping systems. Several tools and methods are already available in various infrastructures and/or projects for tackling plant and soil organism interactions. These will be briefly described, with advantages and main drawbacks. The talk will then describe how we can address this challenge using the facilities of the High Throughput Plant Phenotyping Platform (PPHD) available in INRA Dijon