Détail du poste
Établissement : Université de Rennes École doctorale : École doctorale Écologie, Géosciences, Agronomie et Alimentation Laboratoire de recherche : ECOSYSTEMES, BIODIVERSITE, EVOLUTION Direction de la thèse : Philippe VANDENKOORNHUYSE Date limite de candidature : 2026-05-28T00:00:00 Climate change-induced heat and drought act as strong filters on soil microbiomes, selecting for stress-tolerant taxa and reshaping functions like those involved in carbon and nitrogen cycling. Plant microbiota is largely recruited from soil and play a major role in plant nutrition, stress tolerance, and productivity. Consequently, any changes in soil microbial communities may affect plant microbiota and have important consequences on agroecosystems Effects of drought and heat on soil microbial communities is well-documented. However, the population selection processes are still unknown. In this PhD project, we aim to address this gap by testing the following 3 hypotheses: 1) Exposure to heat and drought is expected to reduce soil and plant microbial richness and diversity while increasing the relative abundance of generalist microorganisms 2) Microbial responses to stress are hypothesized to be highly heterogeneous, even among genetically identical cells. This heterogeneity would be driven by differences in gene expression, growth rate, metabolic state, and local interactions. 3) Selective advantage for this heterogeneity would rely on division of labor, subpopulations with slower growth or altered gene expression and microbe-microbe interactions as well as cross-feeding. To test these hypotheses, the project will combine sampling (soil and plant) from a long-term field experiment to single-cell DNA and RNA sequencing approaches. These high-resolution approaches will be used to resolve cellular heterogeneity, rare taxa, and functional dynamics. By removing the locks from bulk methods, single-cell sequencing represents a promising new challenge to explore eco-evolutionary processes in microbial communities. Collaborations internationales pour le travail envisagé : The work is embedded within an EU funded project (Microbe4Climate) The international dimension of the PhD project is strong with collaborations within the EU project (France, Portugal, Austria, Italy...). The work is also anchored within an ongoing bilateral collaborative project CNRS-IRP with Nanjing Agricultural University (China). Because of its international nature, the recruited PhD will have to work within the developed international network (~20 % of the PhD aboard). English B2 or C1 is thus mandatory
Available financial Resources
Fundings to develop the PhD work are available within the ongoing EU project Microbe4Climate' The PhD work will benefit from the latest developments performed at the EcogenO platform on microbial single cell analyses and all the state-of-the-art high throughput genomics equipments. The PhD work will also benefit of the Genouest bioinformatics infrastructure for all the computational work, and of the existence of in house developed bioinformatic workflows dedicated to microbial single cell DNA analyses.
Available technical Resources
Key technical ressources to succeed are available. The EcogenO platform (leaded by P Vandenkoornhuyse) has all the required state of the art instruments, human resources and molecular biology expertise to ensure that the sequence data production will be efficient. The University of Rennes / CNRS has an important bioinformatic platform (GenOuest) and privileged access to allow all the computational work to be performed. The ECOBIO lab has also technical services to allow all the required experimental ecology and molecular ecology labwork. Extreme climatic events such as droughts and heatwaves, are becoming more frequent and intense and are now key acute stressors for agricultural soil microbiomes (Bardgett & Caruso, 2020, Bei et al., 2023; Philipp et al., 2025). Drought and associated heat generally reduce microbial biomass and extracellular enzyme activities (Qu et al., 2023). Overall, extreme climatic events restructure networks and functions (Castro et al., 2019 ; Philipp et al., 2025) and can push agroecosystem soils toward smaller and more vulnerable microbial pools with impaired nutrient cycling. Under this framework it is also important to emphasize that soil microorganisms also contain the plant microbial symbiotic pool. About 90% of the root endosphere microbiota is filtered from the rhizosphere, which itself represents a subset of the pool of species in bulk soil (Xiong et al., 2021a). Hence, the plant microbiota is not assembled randomly but is structured, tissue-dependent, and deterministically composed (Xiong et al., 2021b). These microbiota/plant interactions affect plant development (e.g. Streitwolf-Engel et al., 1997; Wagner et al., 2014, Vandenkoornhuyse et al., 2015; Trivadi et al., 2020, Turanoglu et al., 2025), notably by modifying the plant's ability to acquire resources, to reproduce and to resist to biotic and abiotic constraints (Vandenkoornhuyse et al., 2015; Trivadi et al., 2020). The facilitation processes and related plant functional plasticity involve multiple mechanisms primed by the plant microbiota (e.g. Vandenkoornhuyse et al., 2015).
Known effects of heat and drought on soil microorganisms...
Drought sharply reduces the growth of most bacteria/archaea. In grassland soils >90% of taxa stop dividing, leaving a small set of drought-tolerant specialists (notably Actinobacteriota, Streptomyces) as the active core (Metze et al., 2023; Ochoa-Hueso et al., 2018). Community composition typically shifts from drought sensitive Proteobacteria, Acidobacteria and Verrucomicrobia toward more stress tolerant Gram positive taxa (Actinobacteriota, Firmicutes, Gemmatimonadota) and specific drought-tolerant fungi, with changes propagating from bulk soil into rhizosphere and root endosphere (Gao et al., 2022; Bei et al., 2023; Metze et al., 2023). Combined heat-drought events (heat waves) are supposed to intensify drought effects on bacterial diversity and reduce recovery after rewetting, even when community composition is less affected (Von Rein et al., 2016; Wang et al., 2020).
Observed heat and drought effects on soil microorganisms... but unknown population selection processes!
Heat and especially drought act as ecological filters that reduce overall microbial activity and diversity, but favor a subset of Gram-positive, spore-forming, drought- and heat-tolerant taxa. The hypothesis #1 of the PhD project is that selection processes and evolution of soil microbial populations under extreme environmental constraints are expected to drive a reduction of soil microbial richness and diversity, but an increase in proportion of generalist microorganisms (bigger genomes hypothesized containing a higher number of genes allowing to buffer environmental stresses).
Heterogeneity processes are also expected as a stress response
The hypothesis #2 of the PhD project is that heterogeneity in microbial stress responses is expected, even among genetically identical cells in uniform environments. This cell-to-cell variability would be driven by differences in gene expression, growth rate, metabolic state, and local interactions would play a crucial role in how populations adapt and survive under stress from 2 main mechanisms and sources of heterogeneity: - Phenotypic heterogeneity is hypothesized with individual microbes if variable activation of stress response pathways, such as the SOS response or oxidative stress defenses, due to noisy gene regulation as conceptualized recently (Lopez and Wingreen, 2022). - Short-range interactions, such as shielding from reactive oxygen species, can generate collective phenotypes where some cells protect others, enhancing overall survival (Alnahhas & Dunlop, 2023). The hypothesis #3 of the PhD project, is that the existence of ecological and functional drivers which provides population- and community-level selective advantage for heterogeneity would rely on: - Division of labor, where subpopulations specialize in different tasks to maximize survival (Alnahhas & Dunlop, 2023; Spratt & Lane, 2022; Wang et al., 2014). - Subpopulations with slower growth or altered gene expression can survive harsh conditions, allowing regrowth after stress removal and contributing to resistance (Wang et al., 2014; Sampaio et al., 2020; Alnahhas & Dunlop, 2023). - Microbe-microbe interactions and cross-feeding that further modulate stress responses, influencing resilience and adaptation (Mataigne et al., 2022; Spratt & Lane, 2022: Alnahhas & Dunlop, 2023).
Testing the hypotheses:
Advances in microbial single-cell RNA and DNA sequencing, are transforming our understanding of microbial communities by revealing cellular heterogeneity, rare taxa, and functional dynamics that bulk methods cannot resolve. Single-cell microbiota analyses represent a paradigm shift in microbiome research, enabling the study of individual microbial cells within complex communities. Unlike traditional bulk sequencing, which averages signals across populations and often misses rare or functionally distinct microbes, single-cell approaches provide high-resolution insights into microbial diversity, function, and interactions. These methods have uncovered previously hidden heterogeneity, allowed for the identification of low-abundance or uncultured taxa, and enabled the direct linkage of genotype to phenotype at the cellular level. Recent advances in microfluidics, high-throughput sequencing, and cell sorting have made it possible to analyze thousands of individual microbial cells from diverse environments, including the human gut, oral cavity, marine ecosystems, and engineered systems like wastewater treatment plants (Rosenthal et al., 2017; Woyke et al., 2017; Chijiiwa et al., 2019; Pachiadaki et al., 2019; Hatzenpichler et al., 2020; Lloréns-Rico et al., 2022; Zheng et al., 2022; Madhu et al., 2023; Hosokawa & Nishikawa, 2023). As the field rapidly evolves, single-cell analyses are poised to address fundamental questions in microbial ecology, host-microbe interactions, and disease mechanisms, while also presenting new technical and analytical challenges. Based on both an experimental work at Ecotron Ile-de-France and sampling of soil and plants from a long-term field experiment located in China (see for instance Xu et al, 2024), single cell microbial community analyses will be performed to address the hypotheses. Both the wet-lab and in silico workflow are mastered in the laboratory and are ready to use (Mauger et al., 2025).
Publiée le 05/05/2026 - Réf : cd1ff06f2dcde6effd11815ef3452496
