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.

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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.

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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.

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Dr. Karen Kloth

Wageningen University, Lab. of Entomology

Together with my team I study insect-plant-microbiome interactions. We investigate how microbes can help plants in suppressing insect herbivory and boost interactions with beneficial insects.

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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.

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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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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.

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Prof. dr. Christa Testerink

Wageningen University, Plant Physiology

My group investigates abiotic stress in plants. As co-PI in the MiCRop consortium, I am also MiCRop coordinator of Diversity & Inclusion.

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Prof. dr. Aalt-Jan van Dijk

Universiteit van Amsterdam, Swammerdam Institute of Life Sciences

Research scientist with broad interest in bioinformatics, systems biology and computational biology. Strong expertise in application and development of machine learning approaches to analyze biological datasets, modelling dynamics of gene regulation networks, prediction of protein functions, and computational analysis of protein functional sites.

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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.

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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.

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.

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Dr. Anna Heintz Buschart

Assistant Professor University of Amsterdam, Swammerdam Institute for Life Sciences, Microbial Metagenomics

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.

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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.

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Dr. Johan Westerhuis

University of Amsterdam, Swammerdam Institute for Life Sciences

I am part of the Data Analysis team and I develop statistical methods for integration of high-dimensional data to explore interaction between host plants and microbial communities.

Gijs Selten

Utrecht University

My research focuses on the studying root microbiome assembly through disentangling the chemical communication between plant and microbes. As part of the data team, I employ data analytical methods on microbiome, metagenomics, and bacterial genomics data to achieve this.

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Dr. Arsheed Sheikh

Utrecht University, Plant-Microbe Interactions

I study how plants use beneficial microbes to overcome sulfur deficiency, an emerging constraint on crop productivity and nitrogen-use efficiency. Using soybean as a model system, my work integrates microbiome profiling, immunometabolism, and signaling pathways to uncover how plant–microbe interactions enhance sulfur acquisition and promote sustainable nutrient use.

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Dr. Rieta Gols

Wageningen University, Plant Science Group

I am interested in the ecology of plant-herbivore-natural enemy interactions. In MiCRop we investigate how microorganisms, in particular those in the soil, affect these insect interactions with the plant and whether we can manipulate the soil microbiome to improve plant health.

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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.

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Dr. Viviane Cordovez

NIOO-KNAW

My research focuses on the impact of plant-associated microorganisms on plant growth and health by coupling culturomic, metabolomic and genomic approaches. I am involved in WP4 and WP5, investigating the functional potential of wheat phyllosphere and rhizosphere microbiomes for biotic stress resilience.

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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.

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Prof. 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.

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Dr. Alexander Haverkamp

Wageningen University, Lab of Entomology

Plants communicate with mutualist such as pollinators but also antagonists like herbivores in multiple different ways and microbes often play an important role in this communication. My research focuses on the sensory ecology of plant-pollinator interactions and how this communication is influenced by the microbiome in a flower.

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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.

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Prof. dr. Christa Testerink

Wageningen University, Plant Physiology

My group investigates abiotic stress in plants. As co-PI in the MiCRop consortium, I am also MiCRop coordinator of Diversity & Inclusion.

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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.

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Prof. dr. Bregje Wertheim

Wageningen University, Lab of Entomology

Since September 2024, I am the Chair of the Laboratory of Entomology at Wageningen University. My research focus is on the complex gene networks that coordinate ecologically relevant traits in insects, and how genomes change during evolution. My aim is to unravel the molecular principles of evolutionary innovation and functional diversification of gene regulatory networks. We study this for various traits and interactions, including insect immunity, insect defenses against toxic fungi, sexual conflict, social behaviour and insect-microbiome interactions.

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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.

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Prof. Dr. Erik H. Poelman

Wageningen University, Laboratory of Entomology

My team studies community ecology and evolution of plant-insect interactions. We study adaptations of wild Brassicaceae in their defence against attack by multiple herbivores and maintenance of beneficial interactions with pollinators. We unravel how micro-organisms modulate such interactions including those between plants, herbivores, parasitoids and hyperparasitoids.

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Prof. dr. Ronald Pierik

Wageningen University, Laboratory of Plant Physiology

My group studies the molecular pathways that operate to regulate plant plasticity in response to light cues that represent neighbour proximity. Within the Microp consortium we contribute our experience on rice research, planting density, and molecular biology to study plant plasticity.

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Dr. Brandon Ford

Plant Microbiome Interactions, Utrecht University

I am a microbiologist working to identify and investigate the genetic factors influencing the recruitment of beneficial microbes protective against plant pathogens, using high-throughput transposon insertion mutant sequencing screens towards this aim.

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Dr. Masato Homma

University of Amsterdam

My research focuses on the evolutionary dynamics of strigolactone production in plants in response to environmental cues, and on how these signaling molecules influence the composition and functional properties of the root microbiome. To achieve this, I aim to identify specific plant-produced strigolactones, elucidate their biosynthetic pathways, and manipulate their profiles using representative species from diverse plant families, including Solanaceae, Cucurbitaceae, Fabaceae, and Poaceae.

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Dr. 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.

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Dr. 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.

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Dr. 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).

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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.

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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.

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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.

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Dr. Melissa Uribe Acosta

Wageningen University and Research

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.

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Dr. Ton Winkelmolen

Wageningen University

I will focus on the effect of shade on rice and its interaction with salt. The focus of my project will be mainly on the molecular players involved in these pathways and how these affect the rice plant.

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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.

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Kai Cartwright

Vrije Universiteit Amsterdam

I support diverse projects exploring the ecology and network biology of arbuscular mycorrhizal fungi. My interests include microbial diversity, symbioses and holobiont perspectives.

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Camila Fornaguera

Wageningen University

My project focuses on investigating how floral microbiomes influence plant–pollinator interactions in Brassicaceae. By examining microbial effects on nectar chemistry and floral signaling. I aim to understand how these interactions shape pollinator behavior, pollinator health and plant reproductive success, with the goal of supporting the development of microbial-based approaches to enhance pollination efficiency in agricultural systems and promote pollinator resilience in ecosystems.

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Rick Temminck

NIOO-KNAW

My PhD research is mainly focused on how to apply different yeast species to wheat plants as a replacement for Fungicides though the development and application of synthetic communities (SYNCOMS). Finding functional replacements for commonly overused fungicides is an important way to reduce resistance development in medically relevant strains and to lower reduced yields and mycotoxin exposures around the globe.

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Syb Hopkoper

Wageningen University

My research focuses on the assembly of the plant microbiome associated with cabbage root fly infestation. I aim to understand the spatial and temporal dynamics of this microbiome, its health-promoting functions, and the drivers of its assembly.

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Toine Massar

University of Amsterdam

With the help of bacterial synthetic communities (SynComs) that closely represent the natural composition of the plant root microbiome, I will be researching the effects of (a)biotic stress on microbiome recruitment (WP1). Through a multi-omics approach, I aim to find molecular mechanisms on both the plant side (WP3) and on the microbial side (WP4) which co-ordinate the relationship between plant and microbiome. At the end of my research project, I aim to have developed a SynCom which improves stress-resilience in crops, with which seeds can be coated before sowing in agriculture (WP5).

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Wietze Metzelaar

Utrecht University

My research focuses on enhancing nutrient use efficiency in crops by improving sulfur nutrition. The aim is to harness plant-associated microbiomes to mediate sulfur acquisition and optimize its utilization. Specifically, I investigate the genetic and molecular mechanisms that govern crop interactions with soil microbial communities under sulfur-limited conditions.

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Simon van Staalduine

Vrije Universiteit

I work on large-scale flow extraction of AMF networks and to uncover the decisions that are made where nutrients should be transported. This requires the use of large amounts of data to track a high number of networks in automated microscopes. I obtained my Msc in Nanobiology at the TU Delft, where my research project involved revealing orientation structures in tissue samples using computational scattered light imaging.

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Bianca Turcu

Vrije Universiteit Amsterdam

I am involved in maintaining the mycorrhizal fungi collection of the MiCRop project and in assisting with molecular biology procedures like DNA extractions and ddPCR.

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Nicky van der Wielen

Wageningen University

My interests lie in studying the interplay between stress resilience in crops and their microbiome. I aim to explore and understand these plant-microbiome interactions and ultimately translate this into advancements in agricultural practices.

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Alberto Arrè

Utrecht University, Plant-Microbe Interactions

In my research project I want to explore host-microbiota specificity in plants under stress conditions. The main goal is combining synthetic communities (SynComs) experiments, machine learning and other bioinformatic approaches to explore both microbe-microbe interactions and microbial recruitment at the rhizosphere level, comparing closely related plant species, and with a focus on biotic and abiotic stress.

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Tim Verhoeven

University of Amsterdam

My research explores the interactions between soybean plants, the soil microbiome, and the parasitic soybean cyst nematode (SCN). Specifically, I focus on the biological function of plant-exuded compounds that trigger SCN hatching. Because inducing a pest's hatching seems counterproductive for the plant, we believe these molecules offer a greater trade-off, such as recruiting beneficial microbes.

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Marcela Aragon-Gomez

Wageningen University, Lab. of Entomology

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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.

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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.

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Sébastien Jaupitre

University of Amsterdam

My PhD project aims at studying the chemical recruitment of beneficial microorganisms in Cucurbitaceae under abiotic and biotic stresses and the functions associated with a beneficial microbiome.

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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

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.

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Melissa Uribe Acosta

Wageningen University and Research

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.

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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).

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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.

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Atharv Ambekar

University of Amsterdam

I aim to understand the mechanisms of how rhizosphere microbes can modify compounds exudated by roots. I use culture-dependent as well as independent approaches, coupled with metabolomics, to understand mechanisms of microbial modulation of rhizospheric signals.

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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).

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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.

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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.

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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.

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Fred White

University of Amsterdam

My PhD involves statistical method development in designed multiblock studies. I am working with statisticians and biologists who aim to investigate plant microbe interactions in order to improve sustainability in agriculture. My work involves data simulation, methods testing and development.

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Dr. Justin Stewart

Vrije Universiteit Amsterdam

Justin Stewart is an evolutionary ecologist studying how plant–microbe symbioses vary across spatial scales. His work focuses on mycorrhizal fungi and aims to quantify the global distribution of biodiversity, functional traits, and biomass in soils. He integrates field sampling, microscopy, DNA sequencing, robotics, and remote sensing to link micron scale processes with global ecological patterns. His research also examines how natural and agricultural soils differ in microbiome composition and function. Justin applies AI and machine learning approaches to harmonize large datasets and produce global predictive maps. He splits his time between the group of Dr. Vasilis Kokkoris at VU Amsterdam and the fungal non-profit SPUN

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Mingxiao Zhang

University of Amsterdam, plant hormone biology group

My project focuses on understanding how plants shape the assembly of their root microbiome. I investigate how plant transcription factors regulate interactions with commensals and influence host-specific microbial community composition. By combining synthetic microbial communities, plant genetics, and microbiome analysis, I aim to uncover the molecular mechanisms that regulate plant-microbe associations.

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Prof. Dr. Rodrigo Mendes

Embrapa Environment, Brazil

My group focuses on decoding the "cry for help" hypothesis to uncover how the rhizosphere microbiome comes to the rescue of plants facing nutrient scarcity, drought, and pathogen attack.

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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.

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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.

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Jelle Spooren

Utrecht University

Associated PhD: Plant-driven assembly of disease-suppressive microbiomes.

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Dr. Pim Goosens

Utrecht University

Plant-microbe interactions

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Pof. dr. Age Smilde

University of Amsterdam

Emeritus data-team leader

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