Pascal Alonso defended his thesis on 12 June 2020. Carried out within the framework of the E-Space flagship project, and funded by Agropolis Fondation, his subject was on "Influence of host and phytovirus on rice microbiota assembly whithin two agrosystems"
Pascal is under the supervision of Christian Verniere and Philippe Roumagnac at Montpellier, SupAgro, in the framework of Biodiversity, Agriculture, Food, Environment, Land, Water , in partnership with BGPI - Biology and Genetics of Plant-Parasite Interactions (laboratory) and of Phytovirus Biodiversity and Plant Quarantine (research team) since 01-10-2016.
The microbial communities, or microbiota, associated with plants play an active role in plant health, i.e. they can regulate plant pathogens or promote plant growth. However, the assembly processes of the plant microbiota and the evolutionary forces that govern these processes remain far from being understood and controlled. We have chosen to tackle this problem by focusing on the rice as a plant model and addressing the following objectives: (i) determining whether the structure of the rice-associated microbial communities is shaped by the plant compartment, the plant growth stage and the plant genotype, and (ii) estimating whether the structure of the bacterial and fungal communities is significantly influenced by the presence/absence of plant viruses. To fulfil these objectives, we characterized three major components of the plant-associated microbiota, i.e. viruses, bacteria and fungi from the roots and stems of rice in two agrosystems located in Camargue (France) and in the Honghe Hani traditional rice terraces system (China). The characterization of the rice virome highlighted the presence of a plant viral outbreak in the Chinese agrosystem, though renowned for a limited impact of plant pathogens. The plant virus detected in 8.9% of the sampled plants was the Southern rice black-streaked dwarf virus (SRBSDV). A metagenomics-based approach was also carried out in France on asymptomatic plants and revealed a high prevalence (11.6%) of a persistent rice endornavirus (oryza sativa alphaendornavirus,OsEV). We show that both rice infections occurring in France and China were genotype-dependent. In addition, the characterization of bacterial and fungal communities’ at the French and Chinese study sites overall highlighted a temporal and spatial dynamic of the structure of the microbial communities. Specifically, we show that (i) the type of plant tissue, aboveground or belowground, internal or external, significantly influenced the richness and the composition of the microbial communities, (ii) the development stage of rice also influenced the composition of its microbial communities, (iii) the rice genotype had a weak effect on the microbial community structures and finally, (iv) the presence/absence of both plant viruses (SRBSDV and OsEV) did not significantly modify the rice microbial community structures. We therefore showed that the assembly of the rice microbiota is partly the result of the effect of the host by deterministic factors (selection) but that probably other ecological factors with a deterministic nature, for example through microbe-microbe interactions, and stochastic nature, contribute to the rice microbiota assembly and further to the diversity of the rice holobiont (the host and its microbiota).