In recent years it has become apparent that when studying plant-herbivore interactions, it is important to also consider the multitrophic context, i.e. to what extent generalist and specialist enemies act as bodyguards for the plant. I have performed a field experiment with 25 genets, varying in plant defense levels, of meadowsweet (Filipendula ulmaria) and its herbivore, the chrysomelid beetle Galerucella tenella. Each genet was treated with four different density manipulations of G. tenella (5, 15, 30, and 60 larvae per genet). The experiment was set up on an archipelago island with natural levels of a specialist hymenopteran parasitoid Asecodes parviclava and generalist natural enemies. I set up the following hypotheses: 1) larval survival will be higher on less defended plants than on more defended plants, 2) the proportion of parasitoids will be higher on more defended plants, and 3) larval survival will increase with increasing larval densities. The most important findings of the experiment were an overall very low total survival of larvae (G. tenella pupae and A. parviclava mummies), a generally high parasitism by A. parviclava on more defended plants, and that two groups of generalist predators (hunting and web-forming spiders) were more frequent on less defended plants. My study suggests that herbivore survival may not be higher on less defended plants under situations with abundant occurrence of generalist predators, as they are able to trace high-quality foraging sites.

Certain crop plants are susceptible to pathogens or unable to develop efficient microbial symbioses. These crops adversely impact soil biological quality with consequences on plant health and productivity of cropping systems. Chickpea is a rotational pulse crop with two types: kabuli and desi, and several cultivars. Cultivation of chickpea has inconsistent effects on soil microbial communities and subsequent wheat crops. I conducted field studies and used high throughput molecular analyses to explore the variations among chickpeas to identify cultivars developing fungal communities that are conducive to plant health and productivity. I also carried out greenhouse studies and used biochemical analyses to investigate the response of chickpea cultivars to arbuscular mycorrhizal (AM) fungi and non-AM fungal endophytes and identify the influence of root and root metabolites on the endophytic and pathogenic fungi. Cultivars and types of chickpeas and environmental conditions promoted different fungal communities in the root endosphere. Funneliformis and Claroideoglomus were the dominant AM fungal genera and Fusarium and Alternaria were the dominant non-AM fungal genera in the roots of chickpea. The roots of cultivars CDC Corrine, CDC Cory and CDC Anna hosted the most diverse fungal communities in contrast to CDC Alma and CDC Xena roots which hosted the least diverse communities. Plant response to AM and non-AM fungal endophytes varied with genotype and type of chickpea. The root symbiosis effectively promoted plant growth in CDC Cory, CDC Anna and CDC Frontier and stimulated nitrogen fixation in CDC Corrine. Cultivars of chickpea responded differently to dual inoculation of the AM and non-AM fungal endophytes. Co-inoculation with AM and non-AM fungal endophytes had additive effects on CDC Corrine, CDC Anna and CDC Cory but non-AM fungal endophytes reduced the positive effect of AM fungi in Amit and CDC Vanguard. Desi chickpea appeared to form more efficient symbioses with soil fungal resources than kabuli chickpea. Protein(s) up-regulated in the mycorrhizal roots of the desi chickpea CDC Anna suppressed the growth of the fungal endophytes Trichoderma harzianum and Geomyces vinaceus and of the pathogens Fusarium oxysporum and Rhizoctonia sp. The formation of AM symbiosis decreased the production of root bioactive metabolites soluble in 25% methanol. Some of the root metabolites stimulated the growth of Trichoderma harzianum and Geomyces vinaceus, and a few inhibited Rhizoctonia sp. and Fusarium oxysporum. A few metabolites with contrasting effects on the different fungal species were detected. The non-protein phytochemicals had selective effects on the endophytes and pathogens whereas the antifungal proteins of mycorrhizal roots were non-selective. Overall the study reveals a "genotype effect" of chickpea on the soil microbiota suggesting the possibility to improve the performance of this crop through the selection of genotypes improving the communities of root associated fungi, by associating and responding to beneficial fungi and repressing the pathogens.

Les communautés microbiennes du sol peuvent améliorer la croissance de la plante en augmentant la disponibilité en nutriments du sol, favorisant ainsi leur prélèvement par la plante. Dans le contexte d’une production agricole à bas niveau d’intrants, la nutrition de la plante est susceptible de reposer de plus en plus sur les interactions plante-communautés microbiennes de la rhizosphère, qui peuvent être modulées par le génotype de la plante. Pourtant, très peu d’études se sont intéressées aux modifications des communautés microbiennes de la rhizosphère dans leur globalité et ce en relation avec à la fois le génotype et le phénotype de la plante. Ces travaux de thèse ont été consacrés à étudier l’effet du génotype de la plante sur la structure génétique des communautés microbiennes de la rhizosphère en relation avec les stratégies nutritionnelles de la plante.L’interaction plante-communautés microbiennes de la rhizosphère a été évaluée par une approche multidisciplinaire alliant écophysiologie et écologie microbienne. L’effet du génotype de la plante sur la structure génétique des communautés microbiennes de la rhizosphère qui lui sont associées a été analysé par DNA fingerprint. Les différentes stratégies nutritionnelles de la plante ont été analysées par une approche de type structure/fonction prenant en compte la mise en place des structures (feuilles, racines) et leur fonctionnement (photosynthèse, rhizodéposition, prélèvement spécifique d’azote).Dans une première expérimentation réalisée sur sept génotypes de Medicago truncatula, nous avons montré qu’à un stade précoce du développement de la plante, le génotype de Medicago truncatula affectait la structure génétique des communautés bactériennes du sol. En revanche, à ce stade précoce, peu de différences de croissance ont été observées entre les différents génotypes étudiés. Ces derniers ont par contre présenté des stratégies nutritionnelles contrastées. Les descripteurs fonctionnels sont donc plus efficaces que les descripteurs structurels pour discriminer les génotypes de plantes à un stade précoce du développement de la plante. De plus, nous avons montré un lien entre les stratégies nutritionnelles de la plante et la sélection des communautés bactériennes associées. Cette étude nous a également permis de développer un cadre d’analyse écophysiologique appliqué à l’étude des interactions plante-communautés microbiennes de la rhizosphère.Outre l’effet majeur du génotype de la plante dans les interactions plante-communautés bactériennes de la rhizosphère, nous avons également montré qu’il y avait un effet important de l’environnement, comme la disponibilité en azote minéral du sol. En effet, la disponibilité en azote minéral du sol a affecté la structure génétique des communautés bactériennes rhizosphériques via un effet indirect de la plante dépendant du génotype considéré. Les effets des différents génotypes de Medicago truncatula et de leurs stratégies de réponses à des contraintes environnementales, comme la disponibilité de l’azote du sol, se sont révélées être des composantes majeures de la sélection des communautés microbiennes. [...] / 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.