Microbial genomics of plant-associated microbes

Ronnie de Jonge

Our Research

Beneficial microbes provide plants with important services, such as enhanced mineral uptake, nitrogen fixation, growth promotion and biocontrol, and thus contribute to plant health. Alike their pathogenic counterparts, they can be recognized by the plant immune system through detection of their common microbe associated molecular patterns or MAMPs, thereby triggering basal immunity. Thus, successful colonization depends on active interference with the plant immune system. Plants in turn need to distinguish between beneficial and pathogenic microbes to facilitate only those that are advantageous. Such establishment of plant-microbe symbioses requires the exchange of specific signalling molecules to fine tune immunity and promote colonization.

Understanding the molecular mechanisms of plant-microbe interactions are at the heart of our research. In order to understand how microbes, be it pathogenic or beneficial, interact with the plant we make extensive use of sequencing data and comparative, evolutionary genomics as well as transcriptomics approaches. Secreted small molecules play an important role in many such interactions and we have recently revealed the genetic basis of one such molecule: cercosporin, a polyketide toxin (https://doi.org/10.1101/100545). Also, plants make use of small organic molecules to interact with their surrounding microbes, and we investigate how exudation of such molecules directs microbiome assemblage and microbial competitiveness on the plant root.

In our research we make use of large variety of ‘omics’ techniques such as: genome sequencing, metabarcoding, metatranscriptomics, metagenomics, comparative genomics, and transposon mutagenesis sequencing (TN-Seq). We conduct evolutionary experiments to highlight genetic features of microbial adaptation; see these two recent preprints: https://www.biorxiv.org/content/10.1101/2020.12.01.407551v2 & https://www.biorxiv.org/content/10.1101/2020.12.07.414607v1.

Research Group

Ronnie de Jonge
Group name: Team de Jonge
Research field: Microbial genomics of plant-associated microbes
Genomics, Genome Biology


Padualaan 8
3584 CH
Office: N.205
Building: Kruyt Buiding