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RESEARCH PRODUCT

Etude de l’interaction plante-communautés microbiennes de la rhizosphère chez l’espèce modèle Medicago truncatula par une approche multidisciplinaire : contribution à la réflexion sur le pilotage des interactions par la plante

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The soil microbial communities can improve plant growth by increasing soil nutrient availability, thereby promoting their uptake by the plant. In an overall context of input reduction, the plant nutrition should be increasingly based on plant- rhizosphere microbial communities’ interactions. Yet, very few studies have examined the entire rhizosphere microbial communities in relationship with both plant genotype and phenotype. The aim of this thesis was to study the plant genotype effect on the rhizosphere microbial communities in relationship with the plant nutritional strategies. To do so, the plant-rhizosphere microbial communities’ interaction was assessed by a multidisciplinary approach combining ecophysiology and microbial ecology. The plant genotype effect on the genetic structure of the associated rhizosphere microbial communities was analyzed by DNA fingerprinting. The different plant nutritional strategies were analyzed by a structural/functional approach taking into account both structure establishment e.g. leaves and functions e.g. photosynthesis. In a first experiment carried out on seven genotypes of Medicago truncatula, we showed that the Medicago truncatula genotype affected the genetic structure of the rhizosphere bacterial communities very early relatively to the plant development stages. However, at this early stage, few growth differences could be observed among the different genotypes. Yet, those genotypes presented contrasted nutritional strategies. Therefore, the functional descriptors were more efficient than the structural ones to discriminate plant genotypes at an early developmental stage. In addition, we showed that a link existed between the plant nutritional strategies and the rhizosphere bacterial communities selection. Finally, this study enabled to develop a multidisciplinary framework applied to the study of the plant- rhizosphere microbial communities’ interactions. In addition to the plant genotype effect, we showed that there is an environmental effect e.g. soil mineral nitrogen availability on the rhizosphere bacterial communities. Indeed, the soil mineral nitrogen availability affected the genetic structure of the rhizosphere bacterial communities via an indirect effect of the plant depending on its genotype. The effects of the different Medicago truncatula genotypes and their response strategies to environmental constraints (soil mineral nitrogen availability), proved to be a major component of the selection of the rhizosphere microbial communities. In order to identify the genetic determinisms of the interaction between the plant and the rhizosphere microbial communities, a second experiment was conducted on a core collection of 184 genotypes of Medicago truncatula. Initial results enabled to identify and characterize four groups of genotypes with contrasted phenotypes for their growth and their specific nitrogen uptake. Thanks to high-throughput sequencing, we will analyze the rhizosphere microbial communities’ diversity associated with the different Medicago truncatula genotypes. These results should determine if the plant genotype influences the selection of beneficial rhizosphere microbial communities. Moreover, when the whole genome sequencing data would be available for the 184 genotypes of the Medicago truncatula core collection, a genome-wide association study will be proceed. The creation of plant ideotypes, which will promote beneficial interactions with rhizosphere microbial communities, will be possible. Plant growth and yield will be improved without the concomitant increase of agricultural inputs.