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24, chemin de Borde Rouge –Auzeville – CS52627
31326 Castanet Tolosan CEDEX - France

Dernière mise à jour : Mai 2018


Laboratory of Plant-Microbe Interactions - LIPM

Laboratory of Plant-Microbe Interactions

Research themes - Symbiotic functions, genome and evolution of rhizobia

Experimental evolution of the plant pathogen Ralstonia solanacearum into a legume symbiont

More than ten years ago, our team launched a pioneering evolution experiment, aiming at replaying the evolution of a new rhizobium genus under laboratory conditions. This experiment, based on the natural evolutionary history of rhizobia, consisted in the introduction of the symbiotic plasmid of the β-rhizobium Cupriavidus taiwanensis into the plant pathogen Ralstonia solanacearum. This chimeric strain was evolved under the C. taiwanensis host plant (Mimosa pudica) selection pressure to successively activate and/or improve the different symbiotic stages, nodulation, infection, bacterial maintenance in infected cells and tentatively mutualistic nitrogen fixation. This experiment and its analysis have already provided major achievements. We i) showed that the two first symbiotic steps, nodulation and nodule infection, were rapidly acquired and optimized in 17 cycles (Marchetti et al., 2017), ii) revealed that the transition to intracellular symbiosis relies on the rewiring of regulatory circuits (Marchetti et al. 2010, Guan et al. 2013, Capela et al. 2017, Tang et al. 2020), iii) uncovered a mechanism of co-transfer of symbiosis and mutagenesis genes accelerating the evolution of rhizobia (Remigi et al. 2014), iv) predicted conditions that allow the fixation of emerging mutualistic variants among a non-mutualistic population (Daubech et al. 2017), and v) evidenced parallels between natural and experimental evolution of Mimosa symbionts (Clerissi et al. 2018).

This experiment is going on with a view to pursue bacterial adaptation to endosymbiosis and possibly reach mutualism. This experiment is now analyzed in a more dynamic and exhaustive way by combining bacterial population sequencing, medium throughput reconstruction of mutations, phenotyping and modeling. This project aims at deciphering the genetic bases of bacterial adaptation and the pathogeny-symbiosis transition as well as identifying the selective forces that drove the evolution of legume symbionts.

Shaping new bacterial symbionts

Plant transcriptomic responses to bacterial adaptation to endosymbiosis

The objective of this project is to harness the unique biological material generated by experimental evolution to study the plant responses to bacterial evolution. A collection of nearly isogenic Ralstonia mutants is being constructed as mutations responsible for the acquisition or improvement of a symbiotic trait is identified. Mimosa transcriptomes in response to the progressively adapted Ralstonia mutants are analyzed and compared to the M. pudica transcriptomes in response to its natural symbiont C. taiwanensis. Our study focus on transcription factors whose expression profile is associated with a phenotypic change and putatively involved in the control of the different symbiotic steps (nodulation, infection, persistence or mutualism). Analyses of these plant responses may help to predict the sequence of molecular events that have accompanied the genesis of rhizobium-legume symbiosis.


Our main collaborators are P.M. Delaux (LRSV, Toulouse), J.B. Ferdy (EDB, Toulouse), C. Pouzet and A. Leru (Imaging platform Toulouse), E. Rocha (Pasteur Institute, Paris) and D. Roche (Genoscope-CEA, Evry).

 Current fundings

SPE INRAE (2021-2022) Impact des modifications épigénétiques dans l’adaptation bactérienne à un nouveau mode de vie. Partner: A. Guidot (LIPME), 15 k€.

FRAIB DYNAMIC (2021-2022) Evolutionary dynamics of bacterial adaptation to symbiosis with legumes. Partner: J.B. Ferdy (EDB, Toulouse), 15 k€.

ANR REPLAY (2017-2021) Replaying the evolution of rhizobia: towards a conceptual and practical framework for the design of new nitrogen-fixing plant symbionts. Partners: Genoscope (D. Roche), IP Paris (E. Rocha), 460 k€.