Introduction:
Microbial communities play a crucial role in the health and development of various organisms, including humans and plants. The human gut microbiome aids in digestion and protects against pathogens, while plant microbiomes on roots and leaves promote growth and defend against harmful bacteria. Understanding the factors that shape these microbial communities is essential for harnessing their potential in agriculture and other applications. Researchers led by Professor Julia Vorholt from ETH Zurich have identified an organizing principle for the bacteria residing on the leaves of Arabidopsis thaliana (thale cress), shedding light on the mechanisms behind leaf surface microbiome formation.
Decoding Leaf Microbiome Formation:
In previous work, Vorholt's group observed remarkable similarity in microbial communities on plant leaves, indicating an underlying mechanism governing leaf microbiome composition. Building on this knowledge, the researchers developed models to predict how individual bacterial strains on leaf surfaces interact and compete with one another based on their nutrient preferences and metabolic abilities. The study, conducted in collaboration with colleagues from EPFL, has been published in the journal Science.
Resource Competition and Interactions:
The research team focused on the metabolic capabilities of bacteria and how they interact in a competitive environment. By studying the ability of more than 200 representative strains of bacteria from Arabidopsis thaliana leaves to grow using different carbon sources, they identified extensive overlap in food niches, indicating intense competition for resources. Using these carbon profiles, the researchers built metabolic models for all bacterial strains and simulated interactions between thousands of pairs of bacteria. The simulations revealed predominantly negative interactions, where competition led to the decrease in population of at least one of the strains.
Cooperation and Resource Exchange:
Despite the prevalence of competition, the metabolic models also predicted positive interactions among bacteria. Further analysis showed that cooperative interactions were linked to the exchange of organic and amino acids. Plant experiments confirmed these predictions, validating the accuracy of the models at 89%. The unexpected reliability of the models suggests that metabolic characteristics indeed play a significant role in shaping leaf microbiomes.
Applications in Microbiome Design:
The predictive capabilities of these models have significant implications for microbiome design, particularly in agriculture. Currently, seed companies and agricultural chemical producers rely on trial and error to identify microbes that support crop protection sustainably. The findings of Vorholt's team provide valuable insights for targeted microbiome design, enabling the supplementation of unbalanced communities with beneficial microbes, the removal of specific species, and the potential treatment of diseases using combinations of bacteria with specialized functions.
Harnessing the Potential of Microbiomes:
Julia Vorholt, as Co-Director of the Swiss National Centre of Competence in Research (NCCR) Microbiomes, leads a network of 20 research groups dedicated to unraveling the mysteries of microbiomes in various organisms. Their ultimate goal is to harness the immense potential of microbiomes for health, agriculture, and the environment. Predictive models, like the ones developed in this study, will be instrumental in achieving this objective.
Conclusion:
The research led by Julia Vorholt and her team provides insights into the organizing principles behind the microbial communities that populate plant leaves. By understanding how bacterial strains interact and compete based on their metabolic characteristics, scientists can improve the design of microbiomes for agriculture and other applications. This research opens up possibilities for harnessing the potential of microbiomes to enhance crop protection and advance sustainable agricultural practices. The predictive models developed pave the way for targeted microbiome design and contribute to the growing field of microbiome research across different organisms.
