DOCTORAL SCHOOL E2M2: E2M2 COMPETITIVE RECRUITMENT FOR DOCTORAL CONTRACTS /CAMPAIGN 2023, Subject : Functional changes in Pseudomonas PGPR during experimental evolution in the rhizosphere.
Scientific research theme :
- Bio-mathematics, bio-informatics, evolutionary genomics
- Community ecology, ecosystem functioning, ecotoxicology
- Evolutionary biology, population biology, ecophysiology
- Micro-organisms, interactions, infections
- Paléoenvironnements and evolution
To apply contact the PhD supervisor: Prof. PRIGENT-COMBARET
Co-supervisor: Dr. MULLER at Research at unit: UMR5557 Microbial Ecology
E-mail : claire.prigent-combaret@univ-lyon1.fr
E-Mail : daniel.muller@univ-lyon1.fr
Scientific context: Plant hosts interact with a wide variety of microbial species that make up their microbiota. Many recent studies have shown that microbiota are able to influence the growth, behaviour and health of their host and form an ecological unit with their host called the plant holobiont (Vandenkoornhuyse et al. 2015 New Phytol 206:1196).
Within this microbiota, certain bacteria, known as PGPR (Plant Growth-Promoting Rhizobacteria), are capable of stimulating plant growth and protecting it against disease (*Vacheron et al. 2013 Front Plant Sci 4:356). Indeed, they are able to express several plant-beneficial traits involved in:
(i) the improvement of plant mineral nutrition (nitrogen fixation, phosphate solubilisation, iron bioavailability, etc.), (ii) the modulation of plant hormone balance, (iii) the production of antimicrobial compounds and the induction of plant defence responses (*Vacheron et al. 2013 Front Plant Sci 4:356; *Lemanceau et al. 2017 Trends Plant Sci 22:583). Although these bacteria perform a wide range of beneficial functions for plants, inoculation of PGPRs does not always result in significant beneficial effects on the host.
Indeed, the adaptive mechanisms that lead to the establishment of PGPR populations in the rhizosphere and their ability to express their traits are still largely unknown. One of the main constraints that beneficial plant populations have to overcome is that they have to colonise a niche that might be occupied by other populations that make up the root microbial community.
They must participate in a variety of interactions i.e. with the host plant and with the other members of the root microbial community. In the case of root microbiota, the importance of these interactions in the adaptation of plant-beneficial populations to the rhizosphere of a plant has not been sufficiently considered. We still do not know how PGPR interact with other members of the rhizomicrobiota and with the plant.
We believe that taking these interactions into account, as part of an experimental evolutionary approach, could provide a better understanding of how plant-bacteria interactions work and provide ways to better exploit the beneficial effects of plant-beneficial inoculants on the plant (*Manriquez et al. 2021 Front. Microbiol. 12:619122). Therefore, in order to understand the adaptive mechanisms involved in plant-bacteria cooperation and between bacteria in the rhizosphere,
Our group has developed an approach of experimental evolution, carried out on a synthetic community (SynCom) composed of 10 PGPR belonging to different species of the fluorescent Pseudomonas, evolving in the presence and absence of plants for over 400 generations. Metabarcoding analysis allowed us to study the evolutionary dynamics of the SynCom. We observed rapid changes in the composition of the synthetic community.
The population dynamics are different when the SynCom micro-evolves with the plant compared to in vitro conditions, showing that the plant influences the selection of Pseudomonas PGPR populations. We now need to understand what functional characteristics of the PGPR allow these ‘evolved’ bacteria to adapt to the rhizosphere.
Host team:
Rhizosphere group (RHIZO) – UMR5557 Microbial Ecology. This project will be co-supervised by C. Prigent-Combaret and D. Muller and will also involve scientific collaborations with T. Lurthy (post-doc; expertise in plant protection against broomrape) and G. Desbrosses (professor at IPSiM, Montpellier; expertise in plant defence and signalling responses in Arabidospis).
The PhD project will therefore aim to understand which genomic and phenotypic changes have occurred in PGPR populations that evolved for 400 generations with plants during an experimental evolution study. We hypothesize that these traits are key for the adaptation of PGPR to the host plant and its rhizosphere, and for the full expression of their beneficial properties on the plant (regarding plant development, plant nutrition, plant protection against pathogens, and elicitation of plant defense).
The first step of the project will focus on comparing about fifty isolates, selected after 400 generations, with their ancestral parents in terms of their genomic characteristics (available genomes), their metabolic profiles, their functional traits (with particular attention to traits important in the interaction with the plant, and in microbial interactions) and their competitiveness in the rhizosphere.
The second step will be to evaluate their interaction with plants in terms of plant growth promotion and plant protection against fungal diseases and plant parasites (like broomrape). We expect the ‘evolved’ isolates to interact better with plants, resulting in improved resistance to biotic stresses.
To test whether this trait is generic, their association with plants and against a wide range of pathogens will be assessed. In addition, the responses of signalling pathways involved in root development, plant nutrition and immunity will be investigated, particularly in the model plant Arabidopsis.
The third step will be to analyze the interactions that ‘evolved’ isolates will share with other members of a defined bacterial rhizosphere community (artificial rhizomicrobiota), using metabarcoding and metatranscriptomic approaches to compare the structure of the community at a taxonomic level and its functioning. (* indicates publication from the RHIZO group).