Dr. R. (Ronnie) de Jonge

Hugo R. Kruytgebouw
Padualaan 8
Kamer N205
3584 CH Utrecht

Dr. R. (Ronnie) de Jonge

Assistant Professor
Plant-Microbe Interactions
+31 30 253 6860

Team de Jonge (May 2022)


Current research projects

Unearthing rhizosphere competence in vivo

We use microbial genetics, microbiome metagenomics, computational modelling and molecular plant biology to identify microbial rhizosphere competence and root microbiome traits that affect rhizosphere competence of plant probiotics and the mechanisms through which root exudates affect plant-beneficial microbe interactions. Together with PhD candidates Sanne Poppeliers and Juan Jose Sanchez Gil, and with the bioinformatics team of Prof. Dr. Bas Dutilh. We found that diverse microbes are selected closer to the roots and selection, in part, is driven by the exudation of inositol that exerts microbe-specific effects including catabolization and behaviour. This role of inositol catabolism was published recently, 2023, in Current Biology back-to-back with work from our collaborator at Michican State, Dr. Sarah Lebeis.

Determining microbial host specificifity using synthetic communities

Project within the scope of the international CCRP program and InRoot project and in tight collaboration with the lab of Prof. Dr. Simiona Radutoiu. We use microbial synthetic communities built from different environments and host plants to identify the genetic traits underlying host specificity in Arabidopsis, Barley and Lotus. Involving PhD candidate Gijs Selten.

Discovery of plant genes, molecular processes and/or pathways enforcing root microbiome assembly

Together with Dr. Giannis Stringlis we study the role of plant processes in plant-beneficial root microbiome assembly. Recent emphasis on the role of endodermal barriers and root hairs together with guest researchers Jiayu Zhou and Jie Yin. We published a bioRxiv preprint on this topic Verbon et al. 2022 which is also available in published form in Molecular Plant as of 2023 here. We used root cell-type specific gene expression analysis following beneficial bacterium application to uncover a role for root hairs and the endodermis in establishing an optimal plant-beneficial bacterium association. Current investigation focuses on the role of root hairs in root microbiome assembly and activity.

Functional analysis of spinach downy mildew effectors

Together with Prof. Guido van den Ackerveken (Plant-Microbe Interactions and Translational Plant Biology) and Dr. Michael Seidl (Theoretical Biology and Bioinformatics) and spinach breeders across the Netherlands we investigate the evolution of spinach downy mildew virulence with an emphasis on effector. Together with PhD candidates Petros Skiadas at TBB and Melanie Mendel at Plant-Microbe Interactions and Translational Plant Biology.


Other topics:

Microbial inhibition of plant pathogens by toxin detoxification (e.g., mycotoxins)

Microbial genomics (genome comparisons, effector discovery, secondary metabolite discovery)




Brief summary of past research

I completed my Ph.D. research in November 2012 at Wageningen University with honors. Here I studied the role and evolution of fungal effectors during plant pathogenesis under the supervision of Prof. Pierre de Wit and Dr. Bart Thomma (current chair Phytopathology Wageningen UR). Get a digital copy of my thesis here.

I investigated the role and evolution of fungal effectors from the tomato pathogenic fungi Cladosporium fulvum and Verticillium dahliae. During colonization, both fungi secrete effectors that contribute to virulence. We showed that Ecp6 contributes to virulence by sequestering chitin oligosaccharides that otherwise elicit host immunity. In tomato, resistance towards race 1 isolates of V. dahliae is governed by Ve1, and we undertook an innovative next-generation sequencing approach to identify the corresponding avirulence gene. Computational analyses successively led to the identification of the race 1-specific gene Ave1. Ave1 activates Ve1-mediated resistance and contributes to fungal virulence. Similar to the region carrying Ave1, we identified multiple genomic regions with limited distribution among V. dahliae strains that coincide with large-scale interruptions of chromosome synteny and are enriched for effectors. This work led to several publications in leading international peer-reviewed journals.

As a postdoc at the VIB Plant Systems Biology department, I studied the genomes of plant pathogenic fungi. In collaboration with Melvin Bolton (USDA, Fargo) we used bioinformatics to infer the evolutionary history of toxin biosynthetic gene clusters in the sugarbeet pathogen Cercospora beticola


International activities

During my M.Sc. studies I worked for six months at the Scottish Crop Research Institute in Dundee, UK, under supervision of Prof. Paul Birch. During my period as a Ph.D. student at Wageningen University I visited the INRA-CNRS in Toulouse, France, under the supervision of Dr. Jérôme Gouzy twice for about three weeks in total to acquaint myself with the bioinformatics package Narcisse and Perl programming in general. In addition I worked for two weeks at the Max Planck Institute for Terrestrial Microbiology in Marburg, Germany with Dr. Eva Stukenbrock and Dr. Julien Dutheil to investigate population genetic structure of Verticillium dahliae genomes. I performed three years of postdoctoral research at the VIB Plant Systems Biology department in Ghent, Belgium and was a visiting scientist for two months at the USDA in Fargo, USA. 


Scholarships, grants and prizes

  • Rhico: Unearthing beneficial microbe rhizosphere competence traits in vivo (NWO Green II call; 2018-2023)
  • InRoot: Molecular Mechanisms and Dynamics of Plant-Microbe Interactions at the Root-Soil Interface (NNF CCRP; 2019-2025)
  • Understanding evolution of downy mildew virulence for knowledge-driven resistance breeding of spinach (TKI Agri T&U; 2020-2024)