<p> As the root microbiome’s role in plant defenses against herbivory becomes clearer, scientific focus has lingered on a single side of plant defenses: resistance. Its counterpart, tolerance, is comparatively overlooked despite its power as an evolutionarily sustainable mitigator of herbivore damage. This thesis seeks to supplement our limited understanding of the extent to which tolerance to herbivory may be influenced by rhizosphere microbial communities. First, in an agricultural field setting, I (1) quantified domesticated tomato cultivar and wild ancestor tolerance to herbivory form the specialist tobacco hornworm (<em>Manduca sexta</em>) and (2) characterized the bacterial and fungal rhizosphere communities associating with high and low tolerance plants. In a subsequent greenhouse experiment, I grew these same tomato lines in either sterilized or unsterilized soil and re-challenged plants with tobacco hornworms to tease apart the contributions from host plant and rhizosphere microbiome in expressing tolerance to herbivory. In the field, wild tomato lines excelled at tolerating hornworm herbivory, while their domesticated counterparts suffered 26% yield losses under herbivory. Rhizosphere community characteristics were most reliably shaped by timepoint of rhizosphere sampling, and more subtly by tomato line and herbivory treatments. Fungal and bacterial community traits that associated with high tolerance lines include (1) high diversity, (2) resistance to community shifts under herbivory, and (3) the abundance of ASVs belonging to <em>Strenotrophomonas</em>, <em>Sphingobacterium</em>, and <em>Sphingomonas</em>. When re-challenging these lines with hornworm herbivory in the greenhouse, expressed tolerance to tobacco hornworm damage was inverted from field trends. Though wild lines suffered yield losses when grown in +microbiome treatments, we found no consistent interactions between herbivory and microbiome treatments that might indicate that +microbiome treatments either helped or hampered plant expression of tolerance to herbivory under greenhouse conditions. These experiments shed light on what role, if any, the rhizosphere microbiome plays in plant tolerance to herbivory. Ultimately, understanding the qualities of tolerance-conferring microbiomes can (1) open avenues through which plant defenses may be amended in pest management, either through microbial inoculants or plant breeding efforts aimed at enhancing crop recruitment of beneficial microbiomes; and (2) ameliorate our understanding of the tripartite interactions between host plants, their rhizospheres, and their specialist herbivores. </p>

Le bleuet sauvage (Vaccinium angustifolium Ait. et V. myrtilloides Michaux) représente un marché en plein essor au Canada, premier pays producteur et exportateur mondial de ce fruit. Pour faire face à la demande, les producteurs cherchent continuellement à adapter leurs pratiques de production dans le but d’améliorer leur rendement et l'état de santé de leurs bleuetiers. Or, les micro-organismes présents dans les racines et dans le sol jouent un rôle non négligeable en lien avec la santé des plantes. Ce microbiote est donc d’intérêt d’un point de vue agronomique, pourtant, contrairement à d’autres cultures, très peu d’études se sont penchées spécifiquement sur le microbiote du milieu racinaire du bleuetier sauvage. Ce doctorat s’inscrit donc dans l’optique d’accroître les connaissances sur les communautés bactériennes et fongiques présentes dans les bleuetières au Québec. Les objectifs de ce projet sont de détecter les taxons qui pourraient avoir un impact sur les variables agronomiques des bleuetiers telles que le rendement; d’identifier les variables physico-chimiques du sol influençant ces communautés; et d’étudier les impacts que peuvent avoir les différentes pratiques agricoles, telles que la fertilisation et la fauche thermique, sur ces micro-organismes. Nous nous sommes appuyés sur le séquençage de nouvelle génération et le métacodage à barres de l’ADN environnemental de nos échantillons de racines et de sol afin d’obtenir une analyse des communautés bactériennes et fongiques de la rhizosphère et des racines des bleuetiers. Les analyses multivariées effectuées par la suite permettent de comparer ces communautés et de voir si certaines espèces sont spécifiques à une condition particulière. Dans l’ensemble, cette thèse a donc permis de caractériser les communautés fongiques et bactériennes du milieu racinaire du bleuetier sauvage in situ dans plusieurs bleuetières du Québec. De nombreuses espèces de champignons mycorhiziens éricoïdes ont été systématiquement identifiées dans les trois études et leur prédominance suggère leur importance pour le bleuetier sauvage. Nous avons également trouvé que l’ordre bactérien des Rhizobiales, connu pour sa capacité à fixer l’azote atmosphérique, occupait une part importante de la communauté bactérienne. Les études sur la fertilisation et la fauche thermique ont démontré que ces deux pratiques agricoles avaient peu d’impact significatif sur les communautés microbiennes étudiées. Enfin, cette thèse donne des pistes de réflexion sur la fixation d’azote par les communautés bactériennes et pose les premières bases pour des essais de bio-inoculation avec les espèces fongiques et bactériennes détectées ayant un potentiel impact bénéfique sur la culture des bleuets sauvages. / The wild blueberry (Vaccinium angustifolium Ait. and V. myrtilloides Michaux) market is booming in Canada, the world's leading producer and exporter of this fruit. In order to meet the demand, growers are constantly trying to adapt their production practices to improve their yields and the health of their blueberry fields. Micro-organisms present in the roots and in the soil play a significant role in the health of the plants. This microbiota is therefore of interest from an agronomic point of view, yet, contrary to other crops, very few studies have been conducted specifically on the microbiota of the root environment of wild blueberries. This doctoral project therefore aims at increasing our knowledge of the bacterial and fungal communities present in wild blueberry fields in Quebec. The objectives of this project are to detect taxa that could have an impact on agronomic variables of wild blueberry fields such as fruit yield; to identify soil physico-chemical variables influencing these communities; and to study the impacts that different agricultural practices, such as fertilization or thermal pruning, may have on these micro-organisms. We relied on next generation sequencing and metabarcoding of environmental DNA from our root and soil samples to obtain an analysis of the bacterial and fungal communities in the rhizosphere and roots of blueberry shrubs. Subsequent multivariate analyses allow us to compare these communities and see if certain species are specific to a particular condition. Overall, this thesis has characterized the fungal and bacterial communities in the root environment of wild blueberry in situ in several Quebec wild blueberry fields. Numerous species of ericoid mycorrhizal fungi were systematically identified in all three studies, and their predominance suggests their importance to wild blueberries. We also found that the bacterial order Rhizobiales, known for its ability to fix atmospheric nitrogen, occupied an important part of the bacterial community. Studies on fertilization and thermal mowing showed that these two agricultural practices have limited significant impacts on the microbial communities studied. Finally, this thesis provides insights into nitrogen fixation by bacterial communities and lays the groundwork for bio-inoculation trials with the fungal and bacterial species detected to have a potential beneficial impact on wild blueberry cultivation.