A new conceptual framework shows that plant genotype and soil nitrogen availability modify both plant nutritional strategies and diversity of their associated rhizosphere microbiome

In the context of sustainable agriculture, it is desirable to lower the input of mineral fertilizers. Therefore, we need to select ‘new’ genotypes that are both adapted to ‘low fertilizer inputs’ and more efficient in nutrient use. A better understanding of plant-microbe interactions under low input of fertilizers is now needed. Nevertheless, in microbial ecology, conceptual frameworks or models are used to analyse plant-microbe interactions but plant phenotype is currently viewed as a “black box”. We developed a new conceptual framework to study plant-microbe interactions using a multidisciplinary approach combining Microbial Ecology and Plant Ecophysiology.The links among plant genotype, soil nitrogen availability and the plant associated rhizosphere microbiome were assessed at both structural and functional level. On the one hand, the influence of both Medicago truncatula genotype and soil nitrogen availability on the genetic structure of the soil microbiome was determined by DNA fingerprint and 454 pyrosequencing. On the other hand, the different nutritional strategies of the plant-microbe interactions were evaluated using an ecophysiological framework.We observed that nitrogen availability affected rhizosphere bacterial communities only in presence of the plant. Furthermore, we demonstrated the existence of a strong Medicago truncatula genotype x nitrogen availability effect on the rhizosphere bacterial communities. Finally, the nutritional strategies of the plant varied greatly in response to a modification of nitrogen availability. Three contrasted structural and functional adaptive responses of plant-microbe interactions to nitrogen availability were thus identified.With recent developments in statistics and high throughput genotyping, this new conceptual framework is now used in a genome-wide association studies (GWAS) to identify plant genetic determinants that may be linked to the selection of more beneficial microbiome for plant under low input of fertilizers.