Plant microbiomes

Plants, the primary source of human food, host microbiomes on their roots and leaves. These microbiomes influence crop production, tolerance to stress and plant protection against disease. An informed use of microbiomes associated with plants has great potential for a sustainable agriculture of the future.

Bacteria, viruses and fungi can cause plant disease and heavy crop loss. On the other hand, key microbes, such as mycorrhizal fungi and nitrogen-fixing rhizobia, help plants uptake nutrients and grow. However, most of the plant microbiome is not well studied and it is unclear how both beneficial and harmful microbes interact with the rest of the plant microbiome.

The objectives of WP3 are to:

  • Understand the structure and function of plant microbiomes by reverse engineering approaches
  • Achieve targeted microbiome manipulation by introduction of plant beneficial microbes
  • Achieve prevention of invasion of a pathogen into a plant microbiome

WP3 focuses on Arabidopsis thaliana as laboratory model and wheat as relevant crop in the greenhouse and in the field. WP3 will identify key microbes that improve plant growth and protection. Predictive models derived from experiments will help engineer microbiomes for improved plant health. Findings will be applicable in the future to improve food production and food security in the face of growing human population and climate change.

Work Package Leader
Prof. Ian Sanders
University of Lausanne

Latest publications

Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags
Daniel, B. B. J., Steiger, Y., Sintsova, A., Field, C. M., Nguyen, B. D., Schubert, C., Cherrak, Y., Sunagawa, S., Hardt, W.-D., Vorholt, J. A. (2024).
mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations
Sintsova, A., Ruscheweyh, H.-J., Field, C. M., Feer, L., Nguyen, B., Daniel, B., Hardt, W.-D., Vorholt, J. A., Sunagawa, S. (2024).
Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens
Pfeilmeier, S., Werz, A., Ote, M., Vorholt, J. A., et al. (2024).