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ERC Synergy Grant to study microbial communities: a step towards personalized agriculture

PRESS RELEASE - Microbiota, a term now familiar to most people, designates a community of microorganisms—bacteria, viruses, fungi—found on and in human beings, animals, and plants. The pathobiota, which is included in the microbiota, consists of diverse potentially pathogenic microorganisms. To further study the behaviour of pathobiota within their host, a team of researchers from INRAE, CNRS and the Toulouse INP-ENSAT (1) has received a 10 million euro Synergy Grant from the European Research Council. The winning team also includes researchers from the Institute for Developmental Biology in Tübingen and the Department of Ecology & Evolution of the University of Chicago (2). Their work will allow researchers to better predict the behaviour of plant diseases and pave the way for the development of personalized agriculture in the coming decades.

Published on 06 November 2020

illustration ERC Synergy Grant to study microbial communities: a step towards personalized agriculture

Combining observation, experimentation and modelling, these three words are key for the ECOGEN research team, created in 2013 in the Laboratory of Plant-Microbe Interactions (LIPM, INRAE/CNRS). This team just received an ERC Synergy Grant3 to fund their project on plant pathobiota: PATHOCOM. The international project, which combines ecology, quantitative genetics, and molecular biology4, will allow researchers to better understand plant-pathogen interactions. Scientists have been aware of the co-infection phenomenon that occurs in animals and humans for a few decades, but only recently did they start focusing on its presence in plants. This phenomenon could be the result of cooperative efforts between multiple pathogens to infect the host. For this reason, one of PATHOCOM’s main objectives is to quantify the different types of interactions taking place between pathogens within complex microbial communities, particularly cases of cooperation or competition. A secondary objective is to understand how the environment (climate, soil, etc.), plant communities and the genetics of the host and its microbiota influence these interactions. To achieve their objectives, the researchers will focus on the phytopathogenic bacteria of a laboratory model plant, Arabidopsis thaliana or thale cress5, which is a wild species commonly found in the countryside.

Synergy around three questions


To successfully complete their project in the next six years, the team has structured it around three complementary research questions. The first one aims to characterise in detail the pathobiota of several dozens of natural populations of Arabidopsis thaliana in France, Germany, and the United States. They will also characterise their environment (climate, soils, etc.), their microbiota and the plant communities in which these populations live. The second question consists of quantifying all the different types of interactions that occur between hundreds of strains of the three most abundant bacterial pathogens6 within A. thaliana. To do so, researchers will carry out individual laboratory analyses of—among others—more than 750,000 plants in less than 9 months! Finally, on the basis of this data, they will develop mathematical models as part of the third area of investigation. These models will allow researchers to predict the diversity and composition of pathogen communities. Their predictions will be compared to the observations made during the first stage.

Besides acquiring knowledge on the dynamics of diseases within natural plant communities, one of the long-term objectives of the project—based on the interactions between a wild host plant and its main pathogenic bacteria—is to develop innovative agrosystems that lead to more personalized agriculture. The results of the PATHOCOM project could allow researchers to guide farmers, helping them to choose the variety that they should grow according to the characteristics of their fields (microbial environment, and, particularly, pathogens).




1Team ECOGEN at the Laboratory of Plant-Microbe Interactions (LIPM)

2The winners are Fabrice Roux, researcher at the CNRS, from the LIPM, Detlef Weigel from the Max-Planck Institute in Tübingen and Joy Bergelson from the University of Chicago.

3  The European Research Council (ERC) opened calls on 24 July 2019 for the ERC Synergy Grant 2020, which has a global budget of 350 million euros and can therefore fund 39 grants. The objective of the call is to finance exploratory research projects lasting a maximum of 6 years and with a maximum budget of 10 million euro.

4 Molecular biology encompasses all the genetic engineering techniques regarding gene-modification. Quantitative genetics aims to use mathematical, statistical or informatics techniques to study the genetic architecture of phenotypic traits.

5  Reference species for plant research as well as for evolution, genetics and basic research. The first plant to have its entire genome sequenced.

6 Xanthomonas campestris, Pseudomonas syringae and Pantoea agglomerans


INRAE Press Office

Scientific contact

Fabrice Roux Laboratory of Plant-Microbe Interactions (LIPM)



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