25.10.2024 - Wheat Alliance receives funding to boost sustainable wheat nutrition through microbes. The Novo Nordisk Foundation has awarded DKK 50 M to the Wheat Alliance project to harness the potential of plant-microbe interactions for exploring wheat genetics for improved nitrogen and phosphorus uptake and promote sustainable agriculture. The project includes partners from the Collaborative Crop Resilience Program (CCRP) at Aarhus University and University of Copenhagen in Denmark, Utrecht University in the Netherlands, and North Carolina State University in the USA, in addition to NIAB and the Crop Science Centre (CSC), both in Cambridge, UK.
As of 2015, our team is studying plant root - microbiome interactions and communication using various 'omics techniques in the Plant-Microbe Interactions group at the Department of Biology. Since 2023, the team is also associated with the AI Technology for Life group at the Department of Information and Computing Sciences (ICS) to use AI-based modeling to capture and predict the dynamics and assembly of root-associated microbial communities and bioinoculant success.
Current team members: Anneriet ter Burg (PhD candidate), Petra Matysková (PhD candidate; with prof. dr. Sanne Abeln), Gijs Selten (Predoctoral fellow), Melanie Mendel (PhD candidate; with prof. dr. Guido van den Ackerveken and dr. Michael Seidl), Ling-Yi Wu (PhD candidate at lab of prof. dr. Bas Dutilh), Jolanda Schuurmans (Technician)
Past team members (or completing): Petros Skiadas (PhD candidate at lab of Michael Seidl; with Guido van den Ackerveken), Sanne Poppeliers (PhD candidate), Juan José Sanchez Gil (PhD candidate), Hao Zhang (PhD), Erqin Li (PhD), Eline Verbon (PhD), Giannis Stringlis (Postdoctoral fellow), Yie Jin (Postdoctoral fellow), José Luiz López (Postdoctoral fellow at lab of Bas Dutilh), Arista Fourie-Fouche (Postdoctoral fellow at lab of Bas Dutilh).
Team photo (2022)
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 impact microbial metabolism and behavior. This role of inositol catabolism was published in 2023 in Current Biology back-to-back with work from our collaborator at Michigan State, Dr. Sarah Lebeis.
Project within the scope of the international CCRP program and InRoot project and in tight collaboration with the lab of Prof. Dr. Simona 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. We recently preprinted our findings here.
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.
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. Two preprints were published recently describing T2T P. effusa genomes and comparative genomics analysis thereof (Skiadas et al., 2024), and the development of a bacterial Type-3 secretion system for functional assays in spinach (Mendel et al., 2024).
Microbial inhibition of plant pathogens by toxin detoxification (e.g., mycotoxins)
Microbial genomics (genome comparisons, effector discovery, secondary metabolite discovery)
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.