Center for Plant Molecular Biology

DeCoCt

Knowledge based design of complex synthetic microbial communities for plant protection (DeCoCt)

This project is funded by a European Research Council (ERC) Consolidator Grant, supporting innovative research to advance our understanding of microbial community dynamics.

The DeCoCt Project: Designing Competitive, Stable Microbial Communities for Plant Protection

The DeCoCt project, funded by the European Research Council, is pioneering a new approach to plant protection. Our focus is on developing and supporting stable, protective microbial communities (also known as microbiota) that naturally inhabit plant leaves and help plants resist pathogens and environmental stresses. Using the model plant Arabidopsis thaliana, we aim to uncover how plant-microbiome-microbe interactions contribute to plant health, resilience, and adaptability.

Project Goals

The DeCoCt project focuses on three main objectives:

  1. Identify Key Drivers of Microbiota Dynamics
    Discover the microbial and environmental factors that shape the structure and behavior of plant microbiomes.
  2. Uncover Mechanisms that Stabilize Microbial Communities
    Understand how microbial communities resist disturbances, ensuring stability and protective functions over time.
  3. Construct Synthetic Microbial Communities for Plant Protection
    Create tailored synthetic microbial communities (SynComs) that can reliably enhance plant defenses against pathogens and adapt to environmental challenges.

Research Focus

1. Drivers of Microbiota Dynamics
This area investigates how specific microbes and environmental factors contribute to microbial community changes, stability, and plant health.

  • Recent Findings: Using machine learning tools such as linear discriminant analysis effect size (LEfSe) and random forest models, we identified critical microbes that influence community shifts. Key insights include the identification of biofilm-related genes being essential for microbial resilience in the plant phyllosphere. Our studies further highlighted the presence of antimicrobial proteins in the plant apoplast, released from the hub microbe Albugo, which help reshape microbial communities by selectively inhibiting certain bacteria in the phyllosphere. Additional studies have shown that abiotic factors such as radiation, wind, and drought significantly impact microbial diversity and abundance across seasons (Chaudhry et al., in preparation; Gomez-Perez et al., New Phytologist, 2023; Mahmoudi et al., ISME Communications, 2024).

2. Stability of Dynamic Communities
This area explores community resilience by investigating how microbial communities respond to both natural conditions and environmental or biological disruptions.

  • Recent Findings: A core set of microbes, especially Pseudomonas species, plays a central role in maintaining microbial community stability by modulating the functions of other species. Pseudomonas also acts to suppress antagonistic behaviors in other microbes, such as Bacillus, thereby enhancing overall community resilience. This mechanism highlights a path toward creating balanced and resilient microbial communities. Collaborations with research groups, including those led by Nadine Ziemert and Heike Brötz-Oesterhelt, have not only helped identify these key microbes but also enabled deeper exploration into the mechanisms essential for community stability (Almario et al. mBIO, 2022; Höhn, ISME Communications, 2024; Chaudhry et al., in preparation). 

    In addition to prokaryotes, eukaryotic organisms also play a significant role in fostering stable communities. We found that the eukaryotic protist and plant pathogen Albugo releases antimicrobial proteins—particularly those enriched with intrinsically disordered regions (IDRs)—which selectively inhibit certain bacterial strains to control microbial diversity. These insights open new possibilities for predicting and utilizing antimicrobial proteins to develop targeted, microbiome-based plant protection strategies (Agler et al., PLOS Biology, 2016; Gomez-Perez et al., New Phytologist, 2023)

3. Synthetic Biology for Microbial Community Design
In this area, we design and test synthetic microbial communities to establish practical applications for plant protection.

  • Recent Findings: By analyzing microbial communities in Arabidopsis, we identified several species with strong pathogen-suppressive abilities. For instance, Pseudomonas and Sphingomonas bacteria, as well as basidiomycete yeasts and protists, have shown the potential to protect plants from various pathogens, including Albugo laibachii, the causal agent of white rust. This redundancy across microbial types supports a robust defense mechanism adaptable to diverse conditions (Mahmoudi et al., bioRxiv, 2024).

Innovative Approach

Our approach to plant health integrates advanced computational modeling, synthetic biology, and ecology. By combining high-resolution genomics data, field observations, and laboratory experiments, we are breaking new ground in sustainable agricultural practices. Our findings will help in future to develop plant microbiomes that enhance plant resilience to disease and environmental stresses, ultimately offering sustainable alternatives to chemical pesticides.

Significance and Future Impact
The DeCoCt project represents a paradigm shift in how we understand plant-microbe interactions. By designing and testing synthetic communities that can integrate with natural microbiota, we lay the foundation for new agricultural practices that promote crop health naturally and sustainably. The research outcomes promise to advance plant protection in agriculture, with applications extending to medicine, ecology, and biotechnology.

Main investigator: Eric Kemen

NEWS

attempto online 30.11.2018

Two consolidated grants of the European Research Council go to researchers of the University Tübingen
The biochemist Ana Jesus García-Saéz is investigating programmed cell death; the biologist Eric Kemen is working on new methods for plant protection based on the microbiome. Both will each receive €2 million for the consolidation of their research group.

ATTEMTO Ausgabe/Issue 51/ 2019

Microbes at the service of agriculture