Emergence, systematics and ecology of plant-associated bacteria


The aerial parts of terrestrial plants form an essential ecosystem for the biological equilibrium of the environment. This ecosystem hosts a microbiome in direct interaction with the aerial organs of plants, in particular the leaves, flowers and seeds. The components of this microbiota can be detrimental or beneficial for plant health. The goal of our research is to understand the controls at play in this microbiota to improve plant health.


  Twitter profile of the team: @Emersys_IRHS  




To reach this goal, we are seeking to:

1) Understand the drivers of the emergence of phytopathogenic bacteria belonging to the Xanthomonas and Xylella fastidiosa 

2) Interfere with the transmission of phytopathogenic strains by/to seeds

            To identify the drivers of the emergence of phytopathogenic bacteria, we are combining comparative genomics and microorganism phenotyping, including non-pathogenic strains and specimens from the areas of origin or diversification of host plant species. This work is conducted on the Xanthomonas genus, but also on Xylella fastidiosa following its discovery in 2013 for the first time in Europe (Projects EU POnTE et XF-ACTORS). This research is leading us to frequently revisit the phylogeny of some groups of plant pathogens, by revising the taxonomy and improving the tools used for the detection, identification and typing (eg. Dupas et al. 2020, Portier et al. 2019). These approaches also enable to retrace the events that triggered the pathogenic convergence of phylogenetically distant strains (eg. Denancé et al. 2019, Ferreira et al. 2019). The molecular determinants involved in host adaptation identified by comparative genomics, are then experimentally validated by reverse mutagenesis and high-throughput phenotyping in containment chambers (Plateforme PHENOTIC).

          Another important research theme of the team focuses on the transmission of pathogenic bacteria by seeds and the role of the seed microbiome. If the presence of phytopathogenic microorganisms inside seeds has been documented for more than a century, the microbial diversity associated to this habitat has been largely underestimated or even ignored. Using metabarcoding and metagenomics, we have recently discovered the presence of hundreds of microbial species on seed samples (Rochefort et al. 2019, Torres-Cortés et al. 2019). Changes in seed microbiome composition were correlated to differences in germination vigor of some seed samples. Thus, to develop strategies to manipulate seed microbiome composition, it is important to decipher the ecological and biological processes involved in the assembly of this microbiome and its dynamic during germination-emergence. After the analysis of molecular determinants of seed transmission with targeted approaches (Darrasse et al. 2018), we are developing global approaches of transcriptomics in planta. This research is conducted on the pathosystems X. citri pv. fuscans - X. phaseoli pv. phaseoli on bean.

           Finally, the team is transferring its results to socio-economic partners in the frame of collaboration contracts and provision of services.  For instance, we are involved in projects on a Pseudomonas pathogen responsible of the zucchini vein clearing disease (Lacault et al. 2020), or on a phytopathogenic Clavibacter (Osdaghi et al. 2020). In this context, the team is hosting a biological resource center (CRB) dedicated to microorganisms associated to plants: the CIRM-CFBP, the French collection of plant-associated bacteria. More than 7000 strains and their metadata are available in the CIRM-CFBP. The team is also closely involved in the development of the phenotyping platform  PHENOTIC, in particular with the development of tools and skills (Phenoplant) enabling a high-throughput analysis of plant-pathogen interactions.

In terms of partnership and networks, we are the founding members and animators of the FNX network for French Network of xanthomonads  since 2008. This network gathers all the French research teams having xanthomonads as research model. We are participating to the activities of the COST action EuroXanth aiming to stimulate science on Xanthomonadaceae for integrated plant disease management in Europe. We are also involved in the international Phytobiomes alliance and the national animation group PhytoMic who gathers research laboratories studying plant-associated microbial communities. Finally, we are participating to the coordination committee of the INRAE HoloFlux Metaprogram.


Matthieu Barret : matthieu.barret@inrae.fr

See also


In this folder

CIRM-CFBP preserves more than 7200 bacterial accessions, strategic resources for plant health.

Modification date: 20 December 2023 | Publication date: 11 May 2011 | By: CD