Composition and Function of the Root Microbiome

root microbiome

The activity of microbes increases in the proximity to roots and thereby impact plant growth. We investigate the structure and function of this microbiota combining state-of-the-art DNA sequencing and cultivation-based manipulations in microcosms.

Composition and function of the Trifolium root microbiome

Because of its N-fixing capabilities, Trifolium pratense (red clover) is widely used as a grassland cover in Switzerland. However, little is known about the structure or function of its root-associated bacteria and fungal communities. We are combining culture dependent and independent methods for characterizing both the composition and ecological function of the root associated microbiota of T. pratense. Using standard microbiological techniques, we isolate bacteria and fungi belonging to a variety of taxonomic groups from the roots of this important agricultural plant species. In a second step, we generate community profiles of the root associated bacteria and fungal communities using DNA sequencing of phylogenetic marker genes. With this information, we compose synthetic microbe communities and test their ecological function in axenic microcosm experiments. Our specific research questions examine:

  • Consequences of the loss of microbial diversity
  • Contribution of certain microbial groups to nutrient cycling

Root microbiome dynamics in response to land management practices

Since 2009, the farming trial FAST has compared the effects of cropping systems, tillage, and cover crops on a variety of ecosystem services. We are interested in the consequences of organic versus conventional farming practices and different tillage regimes on the composition of the root-associated bacteria and fungal communities in wheat. By sequencing root samples of wheat plants grown under the various farming practices, we aim to shed light on the dynamics of the microbe communities as a function of the different land management practices. Specific research questions are:

  • Microbial communities in response to organic versus conventional farming practices
  • Responses of microbial communities to tillage treatments


Maize Influences Microorganisms to Repel Pests


Plants excrete antibodies from their roots into the soil. In this way, they influence the microbial communities in the soil, thereby improving the health of the next generation of plants.