Thèse Décrypter les Interactions Entre l'Hôte et le Microbiote chez des Organismes Photosynthétiques Éloignés sur le Plan Évolutif H/F

Doctorat.Gouv.Fr

Établissement : Université de Toulouse École doctorale : SEVAB - Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingenieries Laboratoire de recherche : LIPME - Laboratoire des Interactions Plantes-Microbes-Environnement Direction de la thèse : Fabienne VAILLEAU ORCID 0000000268792695 Début de la thèse : 2026-10-01 Date limite de candidature : 2026-06-01T23:59:59 Les communautés microbiennes associées aux organismes photosynthétiques - en particulier dans la rhizosphère et la phycosphère - sont essentielles à la santé et à la résilience de l'hôte. Au sein de la lignée verte, un core microbiote conservé a été identifié au niveau de l'ordre, mais les mécanismes sous-jacents à son assemblage et à sa conservation restent mal compris. En particulier, on ignore si les signaux provenant de l'hôte qui régissent ce microbiote central sont conservés sur le plan évolutif chez les plantes et les algues.
Ce projet vise à tester deux hypothèses complémentaires : (i) que des voies génétiques conservées de l'hôte, y compris des composants liés aux réponses immunitaires, régulent l'assemblage du core microbiote; et (ii) que des productions métaboliques conservées, telles que les exsudats dérivés de la photosynthèse, contribuent à façonner ces communautés microbiennes. Pour répondre à ces questions, le projet combinera des analyses comparatives de mutants chez la plante modèle Arabidopsis thaliana et l'algue modèle Chlamydomonas reinhardtii, le séquençage d'amplicons à haut débit et des approches d'écologie microbienne afin de caractériser la structure et la dynamique des communautés.
En utilisant à la fois des communautés microbiennes naturelles et synthétiques, le projet analysera la contribution de la génétique de l'hôte à l'assemblage du microbiote et évaluera dans quelle mesure ces effets sont conservés chez des hôtes éloignés sur le plan évolutif. Enfin, la génomique comparative au sein de la lignée verte sera utilisée pour évaluer la conservation et les trajectoires évolutives des gènes candidats impliqués dans la structuration du microbiote.
Dans l'ensemble, ces travaux apporteront des connaissances fondamentales sur les bases évolutives et mécanistiques des interactions entre l'hôte et le core microbiote, et permettront d'identifier les déterminants conservés de l'assemblage du core microbiote chez les organismes photosynthétiques.
Microbial communities in the rhizosphere and phycosphere are key to the health and resilience of photosynthetic organisms (Trivedi et al., 2020; Seymour et al., 2017; Durán et al., 2022). Within these complex communities, 'core microbiota' are recurrent taxa found across hosts and environments. Specifically, this core microbiota has been described to be formed by 7 bacterial orders and 5 fungal orders, across the green lineage, from flowering plants to terrestrial algae (Durán et al., 2024; Garrigues et al., in preparation). Interestingly, recent studies by the team indicate taxonomic stability at higher levels, but that there is species-level variability shaped by environmental factors and microbe-microbe interactions (Garrigues et al., in preparation). Whether host signals are required to assemble such conserved core microbiota remains unresolved. Importantly, it is unknown whether these host-derived signals are conserved across photosynthetic hosts.
From the literature, two main hypotheses arise to explain the factors shaping these core communities. First, the immune system of land plants has been proposed to be a regulator of commensal microbiota (Hacquard et al., 2017; Thoms et al., 2023). While land plant immune pathways have not been yet described in terrestrial algae, it has been demonstrated that Chlamydomonas reinhardtii (model algae) responds to biotic stresses, such as Pseudomonas protegens (Aiyar et al., 2017). A preliminary orthologous gene prediction analysis performed in the team between the genomes of A. thaliana and C. reinhardtii identified several homologous genes in C. reinhardtii for different immune pathways in A. thaliana. Therefore, the first hypothesis to be tested in this PhD project will be that host genes conserved in both plants and algae drive the assemblage of the core microbiota, some of which may be related to immune pathways.
Secondly, one of the major drivers of the plant and algal microbiota is secretion of photosynthetic products (Loo et al., 2024; Schultes et al., 2025; Shibl et al., 2020). Indeed, it has been demonstrated that different microbial communities converge at the same high taxonomic level community structure when fed with the same carbon source, but variable at the strain-level composition (Goldford et al., 2018). This trait is very reminiscent of core microbiotas in the field and therefore the second hypothesis to be tested in this PhD project is that, in addition to a more controlled host genetic regulation, a set of conserved host secretions drives the structure of a core microbiota, which may then differentiate depending on the host and environment.
The ECOGEN team has strong skills in both plant genetics and microbial ecology, and therefore the PhD student will address the two hypotheses by coupling host mutant screens, amplicon sequencing and comparative genomics. By combining plant and algae biology, microbial ecology, and bioinformatics, the PhD project aims to understand the host genetic basis of structure of the core microbiota, across photosynthetic organisms.
Two explore these two hypothesis, the PhD project will be divided in three work packages (WP):

WP1: Comparative reverse mutant screen in both immune and metabolic pathways
An orthologous-gene prediction analysis has been performed in the team based on genes involved in complex immune pathways in A. thaliana, such as QDR (Quantitative Disease response), ETI (Effector-Triggered Immunity) and PTI (Pattern-Triggered Immunity) (Delplace et al., 2020 and Huard-Chauveau et al., unpublished for QDR; Dong et al., 2015 and Hatsugai et al., 2017 for ETI/PTI) to predict C. reinhardtii genes which may be involved in similar pathways. We identified 5 common and several specific orthologous genes to each of the three immune pathways. In this WP, the student will perform an additional analysis, including a set of general non-self response genes (a core set of 24 genes identified in Maier et al., 2021 and validated in natural populations by the team in Leite-Montalvão et al., 2026), as well as primary metabolites biosynthetic genes. Combining the two analyses, a maximum of 30 genes will be selected, both for A. thaliana and C. reinhardtii, and plant and algae mutants will either be selected from the available A. thaliana collection in the team or ordered from the Chlamydomonas mutant library (Lunardon et al., 2024). Mutants will be grown in natural soil previously characterized in the team, and from which microbial culture collections have been isolated (important for WP2) to explore the effect of host genes on the microbial community and, specifically, on the core microbiota, by using amplicon sequencing technologies. Microbial ecology bioinformatics methods will be used to explore whether microbial interaction networks are affected by host genetics and whether each core member is affected differently by host genotype. From this WP, the main questions to be addressed will be: 1) Which immune and/or metabolic pathways predominantly drive the assembly of a core microbiota? Furthermore, can a hierarchy of genes be established to highlight the key determinants of this process? 2) Are the effects conserved across evolutionarily distant photosynthetic hosts? 3) Do all core members equally respond to host signals?
The methods used in this WP will include comparative genomic analysis, greenhouse experiments, plant and algal mutant handling, molecular biology, amplicon sequencing data analysis, microbial ecology analysis.

WP2: Validation of host genetics-driven effects using synthetic communities
The ECOGEN team has generated culture collections derived from the rhizosphere of four A. thaliana accessions, as well as from the phycosphere from four Chlamydomonas accessions. Among this culture collection, representatives of core groups are found. To validate the key immune and metabolic genes highlighted in WP1, we will take advantage of these diverse collections to reconstitute a synthetic core microbiota (SynCore). This SynCore, as well as its individual core members, will be inoculated onto both A. thaliana and C. reinhardtii wild-type and the corresponding mutants for the WP1 candidate genes identified to impact the core microbiota. This approach will allow the PhD student to ask the following questions: 1) Is the effect observed in natural communities retained in a SynCore (i.e. is the effect directly observed in core groups or indirectly through the rest of the microbial community)? 2) How are each member of the core microbiota affected by host genetics? 3) Do A. thaliana and C. reinhardtii impact similarly core members?
The methods used in this WP will include growth chamber experiments, plant and algal mutant handling, microbiology, molecular biology, amplicon sequencing data analysis, microbial ecology analysis.

WP3: Comparative host genomics analysis
The results in WP1 and WP2 will produce a list of candidate genes involved in shaping the core microbiota, either key genes that influence community structure or a single core strain. While using A. thaliana and C. reinhardtii will allow the PhD student to identify genes relevant across evolutionarily distant hosts, whether these genes are generally conserved across photosynthetic organisms will remain unknown. Therefore, in WP3, the PhD student will perform a comparative genome analysis across the green lineage. For that, the student will download already-published genomes from terrestrial photosynthetic species. This WP will run in parallel to the other two, so that on one hand, the student will screen the presence/absence of the candidate genes from WP1; at the same time, the student will be able to identify new candidate genes which could be tested in WP1 and WP2. This approach will allow assessing the conservation of candidate genes, their divergence, and their potential functional relevance.This work will be performed in collaboration with Dr. Jean Keller, CR CNRS at the LRSV, expert in phylogenomics analysis.
The methods used in this WP will include comparative and evolutionary genomics, ortholog detection, sequence alignment, phylogenetic analysis, and gene family characterization across plant genomes.