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).