Microorganisms that colonize the aboveground and the underground parts of a crop plant are generally called the microbiome. They largely influence the growth and the vulnerability of plants towards pathogens. Interesting for us is how plants respond to the colonization and how we can influence the composition of the microbiome. In addition, transfers of antibiotic resistances or human pathogens, that may be present in the plant’s microbiome, are of high interest to the consumers.

Interactions between crop plants and pathogens were traditionally seen as a direct interrelation between the plant and the pathogen. Today, we understand that the composition of the microbiome has a significant effect on the plant’s response to pathogen attack. Many of the microorganisms enriched in the rhizosphere (roots) or the phyllosphere (leaves and shoots) can weaken the pathogens directly or indirectly, via the induction of plant’s defense mechanisms, and support the development of healthy plants. The plant provides the microorganisms with up to 40% of its assimilated nutrients, actively influencing the composition of the microbiome.  

At the Institute for Epidemiology and Pathogen Diagnostic, we examine how diverse factors such as plant species, its variety, the soil type or location determine the composition and function of the microbiome. At the same time, several practices such as plowing, use of biological control strains or plant strengtheners or use of organic fertilizer also affect the microbiome. Plant defense mechanisms are of particular importance to us. Those can be influenced by microbiome, which is therefore an important key for a successful suppression of pathogens’ growth. We study also the presence of transferable antibiotic resistance genes and human pathogens. Further, we investigate the interactions between the microbiome and the plant using new DNA or RNA-based analyses and the newest "omics" and microscopy techniques.  

The aim of our research is better microbiome-based approaches in crop plant production, which means better control of the microbiome on one hand, and incorporation of those findings into new agricultural practices on the other hand.