Virtuellement toutes les plantes hébergent des champignons et des bactéries endosymbiontes (endophytes). Ces microorganismes façonnent le développement de leur hôte et peuvent inhiber des phytopathogènes. Au niveau moléculaire, les interactions plante-endophyte sont médiées par des molécules secrétées y compris des protéines et métabolites secondaires. Au cours des dernières années, la recherche d’endophytes a augmenté chez nombreux plantes, cependant chez les Ericaceae les endophytes ne sont pas bien connus. Alors, on s’est mis à investiguer les endophytes racinaires de la canneberge, une plante membre d’Ericaceae native de l’Amérique du Nord. On a échantillonné quatre plants provenant d’une ferme commerciale organique. Au total, 30 souches fongiques et 25 bactériens ont été isolés. Les bactéries Pseudomonas sp. EB212, Bacillus sp. EB213 et EB214; et les champignons Hyaloscypha sp. EC200, Pezicula sp. EC205 et Phialocephala sp. EC208 ont supprimé la croissance de cinq pathogènes de la canneberge, incluant Godronia cassandrae, un champignon causant la pourriture des fruits de la canneberge au Québec. EB213 a été capable de promouvoir légèrement la croissance de plantules de la canneberge. En performant des techniques microscopiques, on a constaté l’habileté de EC200, EC205 et EC208 à coloniser internement les racines des plantules de la canneberge. De plus, les génomes de ces champignons ont été séquencés, assemblés et annotés. Les analyses génomiques se sont concentrées sur les protéines secrétées et les groupes des gènes impliqués dans la biosynthèse (GGB). On a trouvé un large répertoire de gènes codant pour des enzymes qui métabolisent les carbohydrates et d’autres codant pour des protéases. Les deux groupes d’enzymes seraient utiles à dégrader de la matière organique pour libérer des nutriments. Aussi bien, ces enzymes pourraient faciliter la colonisation des racines de la plante hôte. De plus, on a prédit des nombreuses protéines effectrices qui assisteraient les endophytes à éviter l’activation du système immunitaire des plants. A noter que parmi les GGB inférés dans les génomes de EC200, EC205 et EC208, environ 90% ne sont pas caractérisés. Finalement, on a performé des analyses transcriptomiques pour élucider la réponse de EC200, EC205 et EC208 envers la présence de leur hôte, simulée par l’addition d’un extrait de canneberge au milieu de culture. Les conclusions majeures sont que les racines des plantes de la canneberge qui ont été échantillonnées sont dominées par des microorganismes avec l’habileté d’inhiber des phytopathogènes ; et que les génomes de EC200, EC205 et EC208 codent pour un grand répertoire de protéines qui pourraient être liées aux interactions plante-endophyte. / Virtually all plants host fungal and bacterial endosymbionts (endophytes). These microbes shape plant development and may inhibit phytopathogens. At the molecular level, plant-endophyte interactions are mediated by secreted compounds, including proteins and secondary metabolites. While endophytes are increasingly studied in diverse plants, little is known about their presence in Ericaceae. Therefore, we set out to investigate the root endophytes of cranberry, an ericacean member native to North America. We sampled endophytes from four plants grown on an organic farm. In total, 30 fungal and 25 bacterial strains were isolated and identified. A subset of these, notably Pseudomonas sp. EB212, Bacillus sp. EB213 and EB214; and fungi Hyaloscypha sp. EC200, Pezicula sp. EC205, and Phialocephala sp. EC208, were tested for their ability to suppress phytopathogens. Altogether, they inhibited five cranberry pathogens, including Godronia cassandrae, an important cranberry fruit-rot agent in Quebec. EB213 was the only endophyte that increased the biomass of cranberry seedlings. Using microscopy techniques, we confirmed the ability of EC200, EC205, and EC208 to colonize cranberry roots internally. The genomes of these fungi were sequenced, assembled and annotated. Genomic analyses focused on secreted proteins and biosynthetic gene clusters (BGCs). We found an extensive repertoire of carbohydrate-active enzymes and proteases that could assist in recycling organic nutrients, rendering them accessible to plants; these enzymes may also facilitate root colonization. In addition, effector proteins were predicted; these molecules may assist endophytes to escape the plant immune system and favour colonization. We inferred 139 biosynthetic gene clusters (BGCs) across the three examined fungi. Remarkably, the product of around 90% of BGCs are unknown. Finally, transcriptomic analyses were performed to determine how EC200, EC205 and EC208 respond to the presence of cranberry, simulated by the addition of cranberry extract in the culture medium. The two major conclusions of this work are that the roots of the sampled cranberry plants are dominated by endophytes with biocontrol abilities, and that EC200, EC205 and EC208 encode a broad repertoire of proteins that could be involved in plant-endophyte interactions.

<p>  </p> <p>Plant roots form an intimate relationship with a diversity of soil microorganisms. Some soil-borne microbes cause harmful diseases on crops, but others promote plant growth and enhance host resilience against stressors. Beneficial bacteria have a high potential as a strategy for sustainable agricultural management, many of which have been recognized and commercialized for improving crop growth. Unfortunately, field inoculants of beneficial bacteria often give inconsistent results due to various environmental factors hindering their beneficial properties. Improving crop production utilizing beneficial bacteria requires two approaches: 1) breeding for crops with the enhanced association for beneficial bacteria and 2) improving formulation methods for producing more potent microbial products. To contribute to these goals, we address three critical questions utilizing the tomato root microbiome as a model system. First, we asked how beneficial root-associated bacteria could be efficiently identified. We developed a strategy to select beneficial bacteria from a novel collection of 183 bacterial endophytes isolated from roots of two field-grown tomato species. The results suggest that isolates with similar traits impact plant growth at the same levels, regardless of their taxonomic classification or host origin. Next, we asked whether host genetics contribute to the root microbiome assembly and response to beneficial microbes. An assessment of the root microbiome profile and plant binary interaction experiments suggested the role of host genetics in influencing root recruitment and response to beneficial bacteria. Subsequently, we asked whether root-associated bacteria induce physiological changes in root tissues in the host. We identified two isolates from our bacterial endophyte collection that significantly promoted the growth of tomato genotype H7996 (<em>Solanum lycopersicum</em>). Plant-binary interaction experiments suggested a significant increase of cell wall lignification in the root vasculature starting 96-hour post-inoculation with beneficial bacteria. Additional studies are needed to uncover a possible correlation between the induced vasculature lignification and the growth-promoting effects of the two isolates on H7996. Altogether, our findings highlight the multi-faceted role of root-associated bacteria in promoting plant growth and support the development of crop improvement strategies in optimizing host association with soil bacteria.</p>