Researchers


Principal Investigators  


Harro Bouwmeester

Prof. dr. ir. Harro Bouwmeester

University of Amsterdam, Faculty of Science

My group investigates signalling molecules and their role in the communication of plants with other organisms, espec. below ground, such as parasitic plants, nematodes and the microbiome. We work on the discovery of new signalling relations using omics data, the importance of structural diversity in signalling molecules for biological specificity, elucidation of biosynthesis and perception mechanisms, and discovery of unknown roles of signalling molecules.

Further information

 

Marcel Dicke

Prof. dr. Marcel Dicke

Wageningen University, Plant Science Group

I am intrigued by how plants are an active key player in multitrophic interactions since my PhD on how plants ‘cry for help’. I am a PI of the MiCRop consortium, PI, coordinator of WP3 & WP5, coordinator of Excellence & Training, and supervisor of PhD candidates.

Further information

 

 

Christa Testerink

Prof. dr. Christa Testerink

Wageningen University, Plant Physiology

My group investigates abiotic stress in plants. Next to being a PI in the MiCRop consortium, I am also MiCRop coordinator of Research Synergy.

Further information

 

Toby Kiers

Prof. dr. Toby Kiers

VU University Amsterdam, Department of Ecological Science, Symbiosis Group

As one of the PIs of the consortium, I am mostly involved in WP 1 and 2. Next to that, I am also MiCRop coordinator of Outreach & Acceptance.

 

Corné Pieterse

Prof. dr. ir. Corné Pieterse

Utrecht University, Institute of Environmental Biology

I am one of the PI’s of the MiCROP consortium and coordinator of Ethics, Gender & Diversity. My group is interested in discovering novel concepts in plant-microbiome interactions and elucidating the underlying molecular mechanisms involved. With our discoveries we hope to contribute to sustainable agriculture through plant microbiome-based solutions.

Further information

 

Jos Raaijmakers

Prof. dr. Jos Raaijmakers

Netherlands Institute for Ecology, Microbial Ecology Department

I have conducted plant microbiome research over the past 15 years, with a focus on how plant domestication impacts the microbiome. My group is searching for the ‘missing plant microbes’ that were lost during domestication. I am a PI and member of the executive board of MiCRop consortium, coordinator of workpackages 2 and 4 and coordinator Utilisation & Knowledge Transfer.

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Data Analysis Team  


Bas Dutilh

Prof. dr. Bas E. Dutilh

Friedrich Schiller University Jena, Viral Ecology and Omics Group

Utrecht University, Metagenomics Group

I am PI of the Metagenomics Group and a member of the MiCRop data team. I have been studying metagenomics since 2004 and currently work on data-driven modelling of the microbiome.

Further information

 

Fred van Eeuwijk

Prof. dr. Fred van Eeuwijk

Wageningen University, Mathematical and Statistical Methods – Biometris

As part of the data analysis and statistics team I am involved in all work packages.

Further information

 

 

Anna Heintz Buschart

Dr. Anna Heintz Buschart

Assistant Professor

University of Amsterdam, Swammerdam Institute for Life Sciences, Microbial Metagenmics

I develop bioinformatics methods to analyse large scale meta-omics data and integrate multiple omics levels, to facilitate biological interpretations and predictions of microbial communities.

Further information

 

Marnix Medema

Dr. Marnix Medema  

Associate Professor

Wageningen University

My lab studies how to use genomic, transcriptomic and metabolomic data to identify metabolic pathways for plant specialized metabolites, including those involved in microbiome recruitment and modulation.

Further information

 

Age Smilde

Prof. dr. Age Smilde

University of Amsterdam, Swammerdam Institute for Life Sciences

Next to my work on MiCRop, I am leading a large systems biology research priority program of the Faculty regarding host-microbiome interactions. I am also involved in a UvA-research priority program around the oral microbiome.

Further information

 

Fentaw Abegaz

Dr. Fentaw Abegaz

University of Amsterdam, Swammerdam Institute for Life Sciences

I am a researcher involved in developing statistical methods for high dimensional data integration and modelling host-microbiome interactions.

Further information

 

Fred White

Fred White

University of Amsterdam, Swammerdam Institute for Life Sciences

As a bioinformatician, I am involved in developing / impementing data analysis pipelines.

Further information

 

Chrats Melkonian

Dr. Chrats Melkonian

Utrecht University & Wageningen University

I am a researcher driven by microbial ecology and evolution. As a postdoc in MICROP I will use multi-omics and modeling approaches with the aim to understand how host-microbiome interactions are involved in alleviation of plant stresses. I am interested in the governing principles behind microbial community assembly.

 

Arista Fourie

Dr. Arista Fourie

University of Utrecht

I am a microbiologist, interested in the interaction between microbes and their host as well as the interactions between microbes. My current focus is on traits that influence the rhizosphere competence of bacteria, such as secretion systems. I make use of metagenomics and metatranscriptomics to study these interactions in different plant species.

 

Mattias de Hollander

Mattias de Hollander

Netherlands Institute for Ecology

Bioinformatician

Further information

 

José Luis López

Dr. José Luis López

University of Utrecht

José's work focuses on seed endophytes and how they can be used to improve plant health. His current project focuses on microbial determinants that allow bacteria to colonise the rhizosphere, in particular he has expertise on codon usage bias and its use to estimate gene expression and bacterial growth rates.

Further information

 

 

 

Assistant Professors/UD/co-PIs  


Roeland Berendsen

Dr. Roeland Berendsen

Utrecht University, Plant-Microbe Interactions

I study the recruitment of benefical micro-organisms by plants in response to diseases. I am involved in WP 1, WP 3 and WP 4.

 

Lemeng Dong

Dr. Lemeng Dong

University of Amsterdam, Swammerdam Institute for Life Sciences, Plant hormone biology

As an assistant professor, I supervise PhD students, research, collaborate with other researchers in the consortium. My personal interest is to decode plant-microbiome languages and communications.

 

Paolina Garbeva

Dr. Paolina Garbeva

Netherlands Institute for Ecology

I am a researcher involved in PhD supervision (WP 4). I am fascinated by the power of how microbes interact with each other at their own microscopic scale.

Further information

 

Rumyana Karlova

Dr. Rumyana Karlova

Wageningen University, Laboratory of Plant Physiology

I'm an assistant professor at Wageningen University. We focus on Solanaceae and drought stress. For MiCRop, I am involved in WP 1 and mainly WP 3.

Further information

 

Karen Kloth

Dr. Karen Kloth

Wageningen University, Lab. of Entomology

I am involved in coordinating MiCRop at the Lab. of Entomology, WUR. I am mostly involved in WP1 and WP3, but also everywhere else WUR-Ent. plays a role.

 

Dr. Vasilis Kokkoris

Vrije Universiteit Amsterdam, Department of Ecological Science

I am an Assistant professor interested in the widespread mycorrhizal symbiosis. Specifically, I examine how the genetic organization of mycorrhizal fungi affects plant response and whether plants preferentially recruit specific genetic types of mycorrhizal fungi. I am mainly involved in WP1 and WP2.

 

James Weedon

Dr. James Weedon

Vrije Universiteit Amsterdam

I am assistant professor focussing on legumes. I have been studying soil microbes since 2008, and I am mostly interested in how bacterial and fungal community composition changes along environmental gradients, and the extent to which we can predict biogeochemical functions from compositional data.

Further information

 

Mark Zwart

Dr. Mark Zwart

Netherlands Institute for Ecology

My research group mainly studies the ecology and evolution of plant viruses. We are particularly interested in understanding why multipartite viruses exist and what the advantages of this strange genome organization are.

 

Kathrin Wippel

Dr. Kathrin Wippel

University of Amsterdam

My research aims to decipher mechanisms underlying the assembly and function of root-associated microbiota across different plant species, using reductionist approaches with microbial culture collections.


Postdocs  


Dr. Jié Hu

Netherlands Institute of Ecology (NIOO-KNAW)

In my research I aim to contribute to a sustainable agriculture via unleashing the power of plant-associated beneficial microorganisms. I am a postdoctoral researcher at NIOO, my role in MiCRop is to determine the impact of plant domestication on the taxonomic and functional diversification of the root microbiome, especially identifying ‘missing’ plant microbes, their genomes and biosynthetic genes.

 

Parvinderdeep Kahlon

Dr. Parvinderdeep S. Kahlon

Wageningen University, Lab. of Plant Physiology

I am involved in WP 3 and I am interested in understanding differences in above-ground tissue characteristics of wild and domesticated tomatoes in relation to the recruitment of beneficial micro-organisms under drought stress.

 

Rahul Jain

Dr. Rahul Jain

Plant-Hormone Biology group, Swammerdam Institute of Life Sciences, University of Amsterdam

Through my research I aim to contribute to understand how microbiome in plant rhizosphere communicate with the roots and respond under environmental stress to benefit plant partners. In MiCRop project, I will be looking for stress responsive chemical signals/metabolites secreted in the root exudates leading to recruitment of specific group of bacteria in the rhizosphere.


Márcio Fernandes Alves Leite

Dr. Márcio Fernandes Alves Leite

Plant-Hormone Biology group, Swammerdam Institute of Life Sciences, University of Amsterdam

In my research I use statistical models and quantitative approaches to understand how plant-microbiome interactions respond to changes in both managed and natural systems. In MiCRop project, I will take advantage of these models to gain insights on how different strigolactones affects the recruitment of the plant root-associated microbiome in Maize.

Further information

 


Technicians  


Deborah Cornado

Deborah Cornadó

The Netherlands Institute of Ecology (NIOO-KNAW)

As a microbiologist, I am involved in building and maintaining the microbial culture collection of the MiCRop project.

Further information

 

 

Rieta Gols

Dr. Rieta Gols

Wageningen University, Plant Science Group

I did my PhD on tritrophic insect interactions in wild and cultivated brassicaceous plant species. Based on my interest and expertise on this this topic, Marcel Dicke invited me to participate in MiCRop.

Further information


PhD students  


Dario Ramirez-Villacis

Dario X. Ramirez-Villacis

Utrecht University, Environmental Biology

I am a PhD student working with various species and varieties of potato in their center of origin (Ecuador), and studying the response of the root microbiome to Phytophthora infestans disease.

Further information

Research project

 

Davar Abedini

Davar Abedini

University of Amsterdam, Plant Hormone Biology

My project aims to unravel potato-microbes-PCNs chemical communications. I investigate the microbial recruitment by tomato/potato root under nitrogen deficiency.

Further information

Research project

 

Justin Stewart

Justin Stewart

VU University Amsterdam, Department of Ecological Science, Symbiosis Group

I am studying the evolutionary biogeography of underground networks and how microbial communities assemble. Specifically, I bring a background in geospatial analysis, statistics-machine learning, and microbial ecology.

Further information

Research project

 

Kris de Kreek

Kris de Kreek

Wageningen University, Lab. of Entomology

I investigate herbivore-induced recruitment of soil microorganisms and their effect on plant defence against herbivores. In contrast to most other projects in the MiCRop consortium, my project focuses on the intraspecific variation in microbiome recruitment in Brassica oleracea (cabbage).

Further information

Research project

 

Malin Klein

Malin Klein

VU University/University of Amsterdam

I study the stress-induced recruitment of microbes in the rhizosphere (legumes specifically). I bring a background in plant genetics and experience with arbuscular mycorrhizal fungi.

Further information

Research project

 

Marcela Aragon Gomez

Marcela Aragon-Gomez

Wageningen University, Lab. of Entomology

Further information

Research Project

 

Melissa Uribe Acosta

Melissa Uribe Acosta

Utrecht University, Institute of Environmental Biology

My research project focusses on evaluating how individual chemical and structural plant defense compounds can change rhizosphere and endosphere fungal and bacterial communities in Arabidopsis.

Further information

Research Project

 

Muhammad Rizaludin

Muhammad Rizaludin

The Netherlands Institute of Ecology, Microbial Ecology (NIOO-KNAW)

My PhD project investigates the mechanism underlying biotic-stress induced plant-microbe communication belowground via root-emitted VOCs (volatile organic compounds).

 

Further information

Research project

 

Roland Berdaguer

Roland Berdaguer

Wageningen University, Laboratory of Plant Physiology

My project aims at elucidating the mechanisms by which plants of the Solanaceae family, and more specifically tomato, recruit soil microbes that promote the plants’ resilience to drought stress. I bring a background in plant molecular biology and experience with root nodule symbiosis.

Further information

Research project

 

 

Sasiwimon Siricharoen

Sasiwimon Siricharoen

Wageningen University, Lab. of Plant Physiology

My PhD project aim to study the influence of maternal environment including different soil types and habitats on microbial communities of Arabidopsis thaliana seeds across different generations, and how these seed microbiome improve abiotic stress (drought and salt) tolerance during seed germination and seedling establishment.

Further information

Research project

 

Sebastian Jaupitre

Sébastien Jaupitre

University of Amsterdam, Plant Hormone Biology

I am a PhD student responsible for cucurbits work, and involved in WP 1 and WP 3. I’ve grown in a family of crop farmers and done a master in plant biology (plus I love eating them).

Further information

Research project

 

Stalin Sarango-Flores

Stalin Sarango-Flores

The Netherlands Institute of Ecology

I thrive to obtain the microbial information on wild tomatoes in their native habitat, and validate the microbe-plant liniking in modern tomatoes.

Further information

Research project

 

Zulema Carracedo Lorenzo

Zulema Carracedo Lorenzo

Wageningen University, Laboratory of Plant Physiology and Laboratory of Entomology

I am involved in WP1, WP3 and slightly in WP3. I work on identifying plant pathways of stress alleviating microorganism recruitment that could be targeted in plant breeding programs.

Further information

Research project

Sjors Huizinga

Sjors Huizinga

University of Amsterdam

My work is focused on the signaling that occurs between lettuce and the root-colonizing fungi Trichoderma and Fusarium in the soil. I am trying to identify which molecules are present in lettuce root exudate, how the composition of this exudate changes during stress, and which molecules can elicit biological responses from the fungi. Simultaneously, I am trying to identify and characterize the receptors that fungi use to perceive these signals.

Further information

Research project


Visiting scientists 


Imran Haider

Dr. Imran Haider

University of Amsterdam

I am a visiting researcher in the Plant hormone biology group, University of Amsterdam to investigate the mechanism underlying the regulation of strigolactone biosynthesis in crops, which could help to speed up Striga resistance breeding. In MiCRop project, I will explore the effect of strigolactones on recruitment of the plant root-associated microbiome.

Further information

 

Haikun Ma

Dr. Haikun Ma

Netherlands Institute for Ecology

I'm an assistant professor at Nankai University. I focus on how to use wild plant species to increase the disease resistance of crops. Not only identifying the beneficial microbes but also, from the community perspective, identifying the beneficial interactions.

Further information

 

Hemn Salehi

Hemn Salehi

University of Kurdistan

I am a Plant Biotechnologist at the University of Kurdistan in Iran. I am working as an advisor on projects focused on the impact of endophytic bacteria isolated from wild chickpeas and their influence on plant growth under drought conditions and work on the molecular analysis of alkaloid production in bacterial endophytes of endemic Papaver species in Iran. In MiCRop project, I investigate the endophytes effect on the root exudates metabolites under nitrogen deficiency.

Further information

 


Former colleagues  


Anouk Zancarini

Dr. Anouk Zancarini

Role: Assistant professor at University of Amsterdam

Further information

ResearchGate

 

Dr. Nejc Stopnisek

Role: Postdoc at NIOO-KNAW

Further information

ResearchGate

 

Giannis Stringlis

Dr. Giannis Stringlis

Role: Postdoc at University of Utrecht

 

Pedro Beschoren da Costa

Dr. Pedro Beschoren da Costa

Wageningen University, Lab. of Entomology

I’m a soil microbiologist working as a postdoc on the Entomology department. I will help establish and evaluate all of MiCRop’s microbiome related processes and pipelines within our group. I will also help coordinate collaborations between the consortium members, as I have done previously in other groups.

Further information