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.

Determining microbial host specificifity using synthetic communities

Project within the scope of the international InRoot program 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 recently: Verbon et al. 2022 . 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.

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 PMI.

Other topics:

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

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