ED Sciences et environnements
Developing biocontrol for grapevine downy mildew using a synthetic microbial community (syncom) approach
by Aarti JASWA (SAVE - Santé et Agroécologie du VignoblE)
The defense will take place at 9h30 - Amphithéâtre Colette & Josy Bové - Bâtiment B2, Centre INRAE Bordeaux-Aquitaine, 71 Avenue Edouard Bourlaux, 33140 Villenave d'Ornon
in front of the jury composed of
- Thibault NIDELET - Directeur de recherche - INRAE Centre Occitanie-Montpellier - Rapporteur
- Michele PERAZZOLLI - Associate Professor - University of Trento - Rapporteur
- François DELMOTTE - Directeur de recherche - INRAE - Examinateur
- Juliana ALMARIO - Chargée de recherche - Université Claude Bernard Lyon 1 - Examinateur
- Stéphanie CLUZET - Professeure - Université de Bordeaux - Examinateur
- Corinne VACHER - Directrice de recherche - INRAE - Directeur de these
- Sophie TROUVELOT - Maîtresse de conférences - Université de Bourgogne Europe - Examinateur
- Guilherme MARTINS - Ingénieur de recherche - Bordeaux Sciences Agro - CoDirecteur de these
Downy mildew, caused by the oomycete Plasmopara viticola, is one of the most destructive diseases in viticulture. The role of grapevine-associated microbial communities in pathogen regulation has become a key focus for disease management. In the context of sustainable viticulture, the development of microbial biocontrol is a promising strategy. The main concern regarding commercially available single-strain biocontrol products is their inconsistent efficacy, particularly with variable weather conditions that can influence strain colonisation and survival. A synthetic microbial community (SynCom) approach involves designing consortia of microorganisms to test hypotheses derived from microbial ecology theories. Building SynComs by combining multiple biocontrol strains capable of associating among themselves and with the resident microbiota can mimic associations in naturally occurring communities. This increases the likelihood of colonisation and survival when SynComs are applied to plants, providing a potential solution to the efficacy problem of single-strains. Experimenting with SynComs can help us understand the microbial community properties that confer biocontrol efficacy and provide insights into plant-microbe and microbe-microbe interactions. The objective of this PhD dissertation is to use a SynCom approach to improve our understanding of the interactions between P. viticola and the leaf microbiota in order to design microbial consortia with biocontrol activity. To that end, we first built a collection of grapevine foliar microorganisms (bacteria, yeasts and filamentous fungi) using a culturomic approach with a custom grapevine leaf extract-based culture medium. We then designed a cross-kingdom SynCom of 42 strains, intended to mimic natural grapevine foliar communities. The total SynCom, alongside over a hundred subsets of it, were confronted with P. viticola on leaf discs to (i) characterize the mode of action of the total SynCom through the analysis of leaf colonization, metabolome dynamics, and plant defence gene expression; and (ii) investigate whether increasing the taxonomic and phylogenetic diversity of the SynCom subsets increases leaf colonisation and biocontrol efficacy. Single-strain and drop-one-out experiments were used to compare biocontrol efficacy of the SynCom members alone and within the consortium. Finally, the total SynCom was applied in experimental plots to test its ability to colonise leaves and control downy mildew in the field. Our results showed that the custom culture medium increased the cultivability of foliar fungal communities. The whole SynCom significantly reduced downy mildew sporulation under controlled conditions. We detected secondary metabolites produced by the colonising strains, but no strong plant immune stimulation or priming effects, suggesting that its mode of action was primarily direct. We identified a set of seven strains that acted as keystones, since their removal led to loss of SynCom biocontrol function. Among the SynCom subsets, we observed an increase in biocontrol efficacy with increasing diversity of fungi, but not bacteria. In the field trial, we observed that the fungi were able to colonise more successfully than the bacteria but the SynCom treatment was not effective against downy mildew. This might be because the physiological saline solution used to suspend the SynCom cells caused leaf burn and reduced plant vigour. This work is a first step to inform and improve the design of biocontrol SynComs against grapevine downy mildew in the short-term. The knowledge produced from using SynComs will be useful for developing commercial multi-strain biocontrol products in the long-term.