Caractérisation de la composition et de la dynamique du microbiote du riz et impact sur la santé des plantes

par Pascal Alonso

Projet de thèse en Mécanismes des Interactions parasitaires pathogènes et symbiotiques

Sous la direction de Christian Verniere et de Philippe Roumagnac.

Thèses en préparation à Montpellier, SupAgro , dans le cadre de GAIA - Biodiversité, Agriculture, Alimentation, Environnement, Terre, Eau , en partenariat avec BGPI - Biologie et Génétique des Interactions Plante-Parasite (laboratoire) et de Biodiversité des phytovirus et quarantaine des plantes (equipe de recherche) depuis le 01-10-2016 .


  • Résumé

    L'hypothèse centrale de la thèse est que les pratiques culturales (intensives vs traditionnelles) de la culture du riz dans la province chinoise du Yunnan modifient les communautés du phytobiome, entrainant une plus forte pression sanitaire et plus de maladie chez les cultures intensives. Nous décrirons les biodiversités des phytovirus, des bactéries (et peut être des champignons présents au sein de l'appareil aérien de plants de riz (i.e. endosphère + phyllosphère) collectés au niveau de systèmes rizicoles traditionnels et intensifs. L'ubiquité et la persistance des communautés virales et microbiennes seront analysées à différentes échelles et à différentes périodes afin de définir le microbiote cœur. Ce microbiote cœur peut-il être un proxy de « l ‘état de santé » du système rizicole étudié ? Plus de détails sur le contexte et les méthodes sont fournis dans les parties ci dessous.

  • Titre traduit

    Structure, variation and dynamics of the microbiota of rice: impact on the host health


  • Résumé

    While the environmental and evolutionary forces driving emergence have legitimately received much attention, it still remains difficult to understand the factors preventing diseases to emerge in some agro-ecosystems. Recent methodological advances in sequencing technologies reveal the tremendous microbial diversity sharing the same host individual and we formulate the hypothesis that the phytobiome, i.e. the entire community of living organisms in, on and adjacent to plant, may play a key role in driving disease dynamics, and explaining pathogen emergence or non-emergence. Indeed, any pathogen species infecting a plant will not only face its host plant response, but also microbial community of the phytobiome. Such microbes (pathogenic or not) sharing a plant may drastically affect disease expression, either directly with competition for the plant resources, or indirectly through host immune system mediated interactions. Pathogen fitness is then determined not only by the host plant per se but also by the microbial community of the phytobiome as emphasized with the recent introduction of the “pathobiome” concept, which represents the pathogenic agent integrated within its biotic environment. Recent studies in human and wild animals highlight the importance of integrating the biotic environment to understand disease dynamics, with for example the acquisition of virulence by commensal bacteria of the intestinal flora under the influence of diverse factors, the unexpected effect a treatment against one pathogen may have on others, or the modulation of infection risk. In addition, the promiscuity existing within ecological niches favours gene exchange and horizontal gene transfer, which contributes to shuffle the genetic diversity on which the natural selection will be exerted. Unfortunately, plant pathology studies focusing on pathogens integrated within their biotic environments remain scarce. Fundamental information remains scarce about plant-associated microbial dynamics in managed ecosystems (agroecosystems), unmanaged ecosystems and interfaces between ”wild” and cultivated areas. This situation hinders our understanding of evolutionary and ecological processes underlying the emergence of agricultural plant pathogens. In addition, ecological processes that lead to the non-emergence of pathogens (e.g. the non-emergence of the blast fungus Magnaporthe oryzae (Mo) in traditional Chinese rice paddies) have been overlooked. This proposal aims at focusing on the analysis of phytobiome dynamics of Yunnan rice pilot agroecosystems in order to better understand the impact of biotic (both plant and microbial) diversity on the occurrence, persistence, transmission and evolution of rice pathogens.