As a major contributor to the reduced nitrogen pool in the biosphere, symbiotic nitrogen fixation by legumes plays a critical role in a sustainable production system. However this legume contribution varies with the physico-chemical and biological conditions of the nodulated-root rhizosphere. In order to assess the abiotic and biotic constrains that might limit this symbiosis at the agro-ecosystem level, a nodular diagnosis is proposed with common bean as a model grain-legume, and a major source of plant proteins for world human nutrition. The engineering of the legume symbiosis is addressed by participatory assessment of bean recombinant inbred lines contrasting for their efficiency in use of phosphorous for symbiotic nitrogen fixation. With this methodology, in field-sites chosen with farmers of an area of cereal-cropping in the Mediterranean basin, a large spatial and temporal variation in the legume nodulation was found. Soil P availability was a major limiting factor of the rhizobial symbiosis. In order to relate the field measurements with progress in functional genomics of the symbiosis, in situ RT-PCR on nodule sections has been implemented showing that the phytase gene is expressed in the cortex with significantly higher number of transcripts in P-efficient RILs. It is concluded that various tools and indicators are available for developing the ecological engineering of the rhizobial symbiosis, in particular for its beneficial contribution to the bio-geochemical cycle of N, and also P and C.