Center for Plant Molecular Biology

Deconstruction and Reconstruction of the Plant Microbiota, DECRyPT

This is a project within the priority programme SPP 2125: Deconstruction and Reconstruction of the Plant Microbiota, DECRyPT

SPP Project: Ecology of the Microbiota in Lotus corniculatus

The SPP Project on Lotus corniculatus explores the diversity, structure, and function of microbiota in this widely distributed grassland legume. Our research aims to reveal how environmental factors, plant-specific traits, and organ-specific environments contribute to the assembly and stability of microbial communities. Through this project, we aim to build foundational knowledge for the ecological role of plant microbiota in promoting resilience, adaptability, and health in natural plant populations.

Project Goals

This project is guided by three main objectives:

  1. Determine the Environmental Drivers of Microbiota Composition
    Investigate the role of abiotic and biotic environmental factors in shaping L. corniculatus microbiomes across various habitats.
  2. Understand Organ-Specificity in Plant Microbiota
    Explore how different plant organs (roots, shoots, flowers, and seeds) act as unique habitats for microbiota, each with distinct microbial communities.
  3. Develop Predictive Models for Microbiome Dynamics
    Use insights from field studies and synthetic community experiments to model microbiota dynamics under changing environmental conditions.

Research Focus

1. Impact of Environmental Factors on Microbial Community Composition
This area investigates how external factors like soil properties, climate, and local biodiversity affect microbiota in L. corniculatus populations.

  • Recent Findings: Our research shows that environmental factors such as soil temperature, air temperature seasonality, and soil microbiome composition are critical drivers of microbiota composition. We identified microbes like Burkholderia and Sulfuritalea that display unique, organ-dependent responses to environmental conditions, offering new insights into how site-specific factors influence the distribution and structure of microbial communities in different plant parts​ (Lutap et al., in preparation).

2. Organ-Specificity of Microbial Communities
In this area, we explore how each plant organ in L. corniculatus (roots, shoots, flowers, seeds) harbors unique microbiota influenced by the organ’s environment and function.

  • Recent Findings: Our findings show that microbial communities vary significantly between plant organs, influenced by the organ’s physical environment and functional role. For example, roots are enriched with nitrogen-fixing bacteria such as Mesorhizobium, which supports nutrient acquisition, while the aboveground organs, including flowers and seeds, show a prevalence of microbes like the leaf pathogen Setosphaeria and necrotrophic fungus Botryotinia. This organ-specific microbial structure highlights the selective nature of each plant compartment, acting as a distinct habitat for beneficial, neutral, or pathogenic microbes​ (Lutap et al., in preparation).

3. Predictive Modeling of Microbiome Dynamics and Host-Microbiome Interactions
This area focuses on integrating data from microbial community studies to develop predictive models that explain microbiome dynamics in response to environmental shifts.

  • Recent Findings: Using metacommunity theory, we characterize plant organs as interconnected but distinct microbial communities that interact within the plant’s overall ecosystem. Our research has identified core microbial species that consistently appear across seasons and locations, suggesting a potential for these microbes to be used in predictive models that inform on plant resilience and health under varying environmental conditions​ (Lutap et al., in preparation).

Innovative Approach

Our approach combines metacommunity theory with ecological data from natural plant populations to provide a comprehensive understanding of plant-microbiome dynamics. By studying microbial communities in their natural habitat, we aim to identify critical environmental and biological factors that shape plant microbiomes at multiple scales. This research can inform sustainable plant management practices, promoting resilience and adaptation in plants exposed to environmental stressors.

Significance and Future Impact
The SPP Project on Lotus corniculatus enhances our understanding of plant-microbiome interactions in a natural context, providing valuable insights into ecological stability and adaptation. By identifying and characterizing key microbial species, this project supports sustainable agriculture and ecosystem management, with potential applications for enhancing plant health, resilience, and productivity.

Main investigator: Eric Kemen

Collaboration: Oliver Bossdorf, Eve Institut, Universität Tübingen