Understanding and predicting PATHOgen COMmunities

Project Information

PATHOCOM

Grant agreement ID: 951444

DOI

10.3030/951444

EC signature date 30 June 2021

Start date 1 July 2021

End date 30 June 2028

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 9 945 744,00

EU contribution

€ 9 945 744,00

Coordinated by

MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
Germany

Periodic Reporting for period 3 - PATHOCOM (Understanding and predicting PATHOgen COMmunities)

Reporting period: 2024-07-01 to 2025-12-31

Summary of the context and overall objectives of the project

Infectious disease is often the major selective agent in nature, and we cannot understand how populations evolve without understanding their pathogenic microbes. Beyond host immunity, an important factor determining the ability of pathogens to invade a host is how pathogens interact with other pathogens as well as background microbiota. This project investigates these questions in plants. Previous work has largely focused on pairwise interactions between one plant host and one pathogen, leaving a large gap in our understanding of how different types of interactions between microbes, and especially pathogens, determine the outcome of host-pathogen interactions in the real world. This project integrates large-scale field observations of microbes in the plant Arabidopsis thaliana with ultra-high-throughput experimental tests of host-dependent interactions among microbes, allowing experiment-informed modeling of pathogenic microbe-microbe interactions. These models, which will be improved through an iterative process of data collection with synthetic communities, will illuminate how interactions, from pairwise to higher-order, shape microbial community composition and structure. In the final step, the resulting models will be tested against and refined with field data. Together, these efforts will transform the study of plant pathogens by applying deep analyses of microbial interactions in an ecological context to explain patterns in nature. The ultimate goal is to refashion plant-pathogen-microbiome studies into a predictive science.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Natural populations of the plant Arabidopsis thaliana have been extensively characterized for ecological variables across two plant life cycles from fall 2021 to spring 2023. The microbiota and pathobiota in and on these plants as well as on companion species and soil is well advanced, as is the genetic characterization of the plants. A subset of plants has been processed for gene expression analyses, to determine the effects of microbial colonization on the immune status of wild plants. The analysis of these data is also well advanced.

Both plant and microbe strains have been barcoded, and sequencing methods for ultra-high-throughput analyses of barcodes from infected plants are being refined. Instrumentation for massively parallel bacterial infections by spraying has been developed. Large-scale infection trials are currently ongoing.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Previous work has largely ignored the impact of interactions between pathogens, the pathobiota. This project will provide the first large-scale experimental data set accurately describing the range of interactions, including higher-order interactions, that drive complex microbial communities in the plant phyllosphere.

Pseudomonas bacteria invading a plant leaf through stomata (Copyright: Sonja Kersten, Detlef Weigel)