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Ecology and Genetics of Plant(s) - Microbiota - Bioagressors Interactions • PMB Team

Context and Issues

Pathogens are a threat to agricultural production. One of the current challenges in agriculture is to reduce the use of pesticides and harmful agrochemicals, in particular by developing agroecological solutions and combining them with varietal resistance. Promising results show that the untapped diversity of soil microbiota can influence plant tolerance/resistance to pests. It is recognised that communities of organisms associated with plants (microbiota, nematofauna) contribute to the extended phenotype (health and performance) of the plant. This paradigm shift implies exploiting the full biodiversity of the soil and identifying the factors involved in the assembly of communities and the ecological networks of the soil microbial biodiversity.


However, our knowledge of how the complex tripartite interactions between plants, root parasites and plant-associated microbiota determine disease development needs to be further developed. It is therefore necessary to study the interactions between crop plants, associated communities and pests to better understand these interactions and mobilise them in crop health.


The two objectives of the team are:


  1. To describe and understand the diversity and the assemblages of microbial and nematode communities associated with plants, and the functional traits modulating the direct and/or indirect resistance of plants to different soil-borne pests;
  2. To identify and validate the genetic basis of plant-microbiota interactions in relation to plant health and the adaptation of soil-borne pests to varietal resistance. 

To achieve these objectives, the team is developing an interdisciplinary approach to identify the traits involved in tripartite interactions and the evolutionary processes of these interactions.


The team's research project is organised into three interconnected thematic axes.

Axis 1 - Analysis of the assembly rules and interaction networks of rhizospheric communities associated with plants.

The aim is to describe and understand the assemblages of soil and rhizosphere communities, and the interaction networks within the diversity of microbiota and nematodes. The factors that drive these interactions under different soil and climatic conditions and different agronomic practices (crop rotation, crop diversity and diversification, soil management), as well as their consequences on the adaptation of plants to different biotic stresses (fungi, protists, nematodes and insects) are studied.


Studying of the spatial and temporal dynamics of this diversity will reveal the factors involved in the "Microbial Associated Phenotype" in relation to the modulation of the plant resistance phenotype (e.g. biological regulations and/or modulation of plant immunity).


 Axis 2 - Functional analyses of beneficial and deleterious interactions.

This approach of functional ecology of interactions aims to (i) identify the genes and metabolites (of the microbiota, the plant and/or the bioaggressor) involved in the modulation of the tripartite dialogue, (ii) validate the functional role of these genes and metabolites, and (iii) identify the chemical signaling between these different factors. We are interested in the functional network (including metabolites and mRNAs) involved in the plant-microbiota-bioagressor dialogue in order to identify the active species and microbial functions that confer plant resistance and limit the development of pests. This knowledge will contribute to the development of future biocontrol methods based on the identification of species and functions of the microbiota that modify the perception of signals exuded by the plant and/or the plant-pathogen dialogue.


Axis 3 - Co-adaptation / co-evolution of interactions in a holobiont context.

The adaptive and selective processes at the origin of the co-evolution between plant - microbiota - bioaggressor are studied via the identification of loci in the plant, microbiota and bioaggressor that are under selection. The identification of such loci is a step forward in the selection of new plant genotypes with long-lasting resistance characteristics and capable of interacting positively with soil microbial communities. Experimental evolutionary approaches under controlled conditions are being carried out to identify both plant and microbiota loci that show evidence of selection and modulate host resistance to bioagressors. As pest populations also evolve in response to host responses, experimental evolutions in which these populations - showing a different degree of virulence - are followed for several successive cycles under contrasting microbiota diversity.


For the different co-evolution studies, microbiota diversity is reconstructed using synthetic communities obtained by culturomics from native communities.

Les 3 axes permettront d’identifier des outils innovants, comme des consortia élites de microbes, des gènes, des fonctions ou encore des métabolites modulant les interactions plante / microbiote / bioagresseur.

Skill and Expertise

The PMB team brings together a multidisciplinary team of researchers (5 researchers and 4 engineers) and technical staff (9 permanent staff) with complementary expertise in soil ecology, the study of plant-microbiota interactions, nematology, population genomics, metagenomics, metabolomics, (meta)transcriptomics, molecular biology, microbiology (culturomics), bioanalysis, bioinformatics, biostatistics, instrumentation, monitoring of physical measurements, and IoT.

The team has the skills to conduct in situ and experimental approaches, as well as 'meta' and 'synthetic communities' approaches to address our three axes.



The INRAE Phytomic and NEMALLIANCE (INRAE and ANSES alliance) networks are led by researchers from the team and reinforce our research project.

Nem alliance


Montarry J., Mimee B., Danchin E.G.J., Koutsovoulos G.D., Ste-Croix D.T., Grenier E. (2021) Recent Advances in Population Genomics of Plant-Parasitic Nematodes. Phytopathology 111(1), 40-48.

Gautier C., Martinez L., Fournet S., Montarry J., Yvin J. C., Nguema-Ona E., Guillerm-Erckelboudt A. Y., Piriou C., Linglin J., Mougel C. & Lebreton L. (2020). Soil microbiota effect on the efficiency of root exudates to induce suicide hatching of cyst nematodes. Frontiers in Microbiology, 11, 2489.

Ourry M., Lopez V., Hervé M., Lebreton L., Mougel C., Outreman Y., Poinsot D. & Cortesero A. M. (2020). Long lasting effects of antibiotics on bacterial communities of adult flies. FEMS Microbiology Ecology, 96(4).

Daval S., Gazengel K., Belcour A., Linglin J., Guillerm-Erckelboudt A. Y., Sarniguet A., Manzanares-Dauleux M. J., Lebreton L. & Mougel C. (2020). Soil microbiota influences clubroot disease by modulating Plasmodiophora brassicae and Brassica napus transcriptomes. Microbial Biotechnology, 13( 5), 1648– 1672.

Thevenoux R., Folcher L., Esquibet M., Fouville D., Montarry J. & Grenier E. (2020). The hidden diversity of the potato cyst nematode Globodera pallida in the south of Peru. Evolutionary Applications, 13(4), 727-737.

Daval S., Belcour A., Gazengel K., Legrand L., Gouzy J., Cottret L., Lebreton L., Aigu Y., Mougel C. & Manzanares-Dauleux M. J. (2019). Computational analysis of the Plasmodiophora brassicae genome: mitochondrial sequence description and metabolic pathway database design. Genomics, 111, 1629-1640.

Lebreton L., Guillerm-Erckelboudt A. Y., Gazengel K., Linglin J., Ourry M., Glory P., Sarniguet A., Daval S., Manzanares-Dauleux M. J. & Mougel C. (2019). Temporal dynamics of bacterial and fungal communities during the infection of Brassica rapa roots by the protist Plasmodiophora brassicae. PLoS ONE, 14(2), e0204195.

Montarry J., Bardou-Valette S., Mabon R., Jan P. L., Fournet S., Grenier E. & Petit E. J. (2019). Exploring the causes of small effective population sizes in cyst nematodes using artificial Globodera pallida populations. Proceedings of the Royal Society B-Biological Sciences, 286(1894).

Eoche-Bosy D., Gautier M., Esquibet M., Legeai F., Bretaudeau A., Bouchez O., Fournet S., Grenier E. & Montarry J. (2017). Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida. Molecular Ecology, 26(18), 4700-4711.

Fournet S., Eoche-Bosy D., Renault L., Hamelin F. M. & Montarry J. (2016). Adaptation to resistant hosts increases fitness on susceptible hosts in the plant parasitic nematode Globodera pallida. Ecology and Evolution, 6(8), 2259-2568.

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