Council members

PhD candidate,  Plant-Microbe Interactions, Utrecht University
Project: Mycoat: Creating sustainable seed coatings

About my research
Seeds are the foundation of global food production. Their viability, germination and resistance to stress are key to feeding the world. Conventionally, plant breeders coat the surface of seeds with extra materials to improve their handling and vitality, a process known as coating . The ingredients in seed coatings include nutrients, herbicides, fungicides, and insecticides. Seed coating promotes the rapid and uniform germination of seeds, ensures their survival against abiotic and biotic stress factors, and ensures a high crop yield. Seed coating technology is emerging as an alternative tool to conventional farming because seed coating uses minor amounts of chemical inputs during its application (Rocha et al., 2019). Despite their effectiveness, synthetic pesticides and fertilisers can accumulate in plants, soil and water, causing toxicity to microbial populations. Thus, we need less toxic and more biodegradable coatings.

Plant beneficial microbes (PBMs) can be an alternative to the use of agrochemicals in plant production. PBMs help plants maintain or increase plant growth, unlock nutrients for the plant, and reduce crop loss caused by pathogens, insects and abiotic stress. For example, Trichoderma and Pseudomonas strains added to agricultural soils can antagonise pathogens and induce resistance in plants against bacterial, viral and fungal pathogens.  In this project,  the chair groups of PMI, Microbiology and NMR  aim to  develop  sustainable seed coatings with plant-beneficial properties, based on fungal materials. We are looking at ways in which seed coating materials antagonize plant pathogens to protect emerging seeds from disease. Moreover, by using pathogen bioassays and digital plant phenotyping tools, we evaluate the contribution of our seed coatings to long-term plant health and resistance. We will also delve deeper into the modulation of the plant’s transcriptomic landscape and microbiome, when seeds interact with PBMs. This project can help us understand how fungal materials can be used in seed coating technology to support plant growth and resistance to pathogens.

PhD candidate, Plant-Environment Signaling, Utrecht University

About my research
Plants are able to perceive the quality and quantity of the light in their environment using several different light receptors, which enables them to respond adequately to their light environment and optimize light harvesting for photosynthesis. Via their phytochrome photoreceptors plants are able to detect shade. As a consequence, when a shade avoiding plant like Arabidopsis thaliana perceives shade its energy investment shifts away from processes like growth of the leaf lamina, root system and fruits towards an increased elongation of the stem and upwards growth of leaves. The shade avoidance response, which is also present in many crops, thus affects yield of edible and usable parts of said crops.

The shade avoidance response has been researched thoroughly in seedlings, and already some work has been done on adult plants. In my project I focus on adult plants, further elucidating growth responses upon spatial and temporal fluctuations in light quality and quantity in Arabidopsis thaliana and Solanum lycopersicum. For example monitoring leaf growth responses when only a small part of the leaf is shaded, but also investigating the effect of fluctuations in the light quality or quantity over time. The aim of my project will be to elucidate the molecular pathways underlying local light dependent growth responses and the effect spatial and temporal fluctuations in light quality and quantity have on leaf growth and development.

PhD candidate, Plant Hormone Biology, University of Amsterdam

Project title: Microbial recruitment by tomato and potato roots under nutrient deficiency

Under unfavorable conditions, plants exude a plethora of signaling molecules through complex series of biological mechanisms to recruit beneficial microbe(s). These beneficial microbes are involved in a range of processes from improving nutrient availability, providing growth hormones, and modulating the abiotic stresses response in plants to mitigating biotic stresses by inducing resistance and synthesizing antibiotics targeting pathogens. To facilitate this beneficial interaction, plants and their microbial partners have evolved a sophisticated chemical dialogue. Using small molecules, plants communicate with and modify the microbiome composition in their rhizosphere. My project aims to unravel potato/tomato-microbe chemical communications. For this, I am using multiomics approaches coupled with advanced analytical chemistry and molecular biology tools to identify the signalling molecules and their corresponding biosynthetic genes. The project will pave the ways toward reaching sustainable agriculture.

PhD candidate, Plant Systems Physiology, Radboud University
Project title: HeatGenes: toward a generic genetic framework for plant reproductive heat-tolerance.

About my research
As a consequence of climate change, weather extremes, such as heat waves, are expected to become increasingly frequent. As sessile organisms, plants are affected by these events in both the vegetative and reproductive phase. Heat stress during reproductive development leads to catastrophic yield loss in many food crops, imposing pressure on future food security. In the past, studies have shown during the reproductive stage, male gamete development is the most sensitive to high temperatures. However, past studies mostly focused on short extreme high temperature effects (heat shock) and few have investigated the effects of heat wave-like long-term mild heat (LTMH).

This is the fundamental drive of the HeatGenes project, a NWO (TTS)-funded study, performed in cooperation between the Radboud University and multiple companies involved in plant breeding. We expect the genetic basis of the reproductive heat-tolerance phenotype to be well-conserved among angiosperms. By performing genome-wide association studies (GWAS) on multiple plant species (e.g. Arabidopsis thaliana, tomato, common bean, carrot, and Brassica sp.), we are identifying quantitative trait loci (QTLs) and candidate genes associated with the heat-tolerance phenotype. A study in Arabidopsis thaliana will provide insights on molecular/physiological pathways involved, while studies in various commercially valuable crop species will directly provide germplasm for heat-tolerant lines. Additionally, we will develop reproductive heat-tolerance screening assays for plant species for which none existed previously.

PhD candidate, Laboratory of Molecular Biology / Plant Developmental Systems, Wageningen University & Research

About my research
Plants continuously grow through their main shoot, but certain signals during this growth will lead to budding of additional, lateral shoots. In tomato, these so-called axillary shoots compete for energy with fruit production, and to increase yield they are removed manually. However, their removal adds to labor costs and might cause an infection at the sites of the wound and is time-consuming. Molecular studies revealed a number of shoot outgrowth-suppressing genes, from the model plants Arabidopsis and tomato. In my project, we aim to elucidate the underlying mechanism of axillary shoot regulation in tomato. We are investigating regulatory network of shoot branching by using techniques such as CRISPR-Cas9, yeast-one-hybrid and RNA-seq.

PhD Candidate, Entomology, Wageningen University & Research
Project title: The double trouble of Insect attacks and water stress: how plants defend against insect herbivory while facing water stress.

About my research
Due to global climate changes, an increasing challenge in agriculture is to cope with more severe outbreaks of insects against the backdrop of more frequent drought and heavy rain events. The problem is magnified since an excess as well as a shortage of water not only reduces yield but may also reduce the resistance of plants to insect herbivores. Although plants in nature and agriculture commonly face combinations of biotic and abiotic stresses, responses to these stresses have usually been studied in isolation.

In my project I explore how a small group of different plant species from the Rorippa genus handle a combination of water stress and insect herbivory simultaneously. These plants are differently adapted to water stress but have an overlapping insect community, making it an interesting study system. The question is how these adaptations might help them cope in a simultaneous stress environment. I study this by combining a variety of experiments ranging from fieldwork to transcriptomics.

PhD candidate, Plant Developmental Genetics, Leiden University
Project title: Rejuvenator: the potential of regulating plant longevity

About my research
Polycarpic plants flower more than once in their lifetime, and need to resume vegetative development after flowering to continue growth and prepare for the next flowering cycle. Monocarps, on the other hand, do not resume this vegetative growth and die after flowering. Control of vegetative growth is of major agri- and horticultural interest, as it can help to improve the quality of leafy vegetables and the yield and quality of cuttings and flowers. Recently, the Arabidopsis REJUVENATOR/AHL15 transcription factor gene has been identified as a key regulator of vegetative growth. While striking phenotypes have been described in plants with altered RJV/AHL15 expression, the molecular mechanism of RJV/AHL15-induced vegetative growth remains unknown.

With this research, we aim to unravel the regulatory pathways surrounding RJV/AHL15 to gain understanding of vegetative development in plants. This will be done by studying different effects of RJV/AHL15 activity in Arabidopsis thaliana such as its effect on the transcriptome and its role in changing the epigenetic landscape of the genome, and the natural variation of RJV/AHL15 in different Arabidopsis ecotypes and other plant species. Understanding how vegetative development is regulated in plants will not only help breeding efforts in commercial crops, but also shed light on how the diversity of life history strategies has evolved in plants.

PhD candidate,  Laboratory of Biochemistry, Wageningen University & Research
Project: Redox-dependent extracellular interaction networks of Cysteine-Rich- and Leucine-Rich Repeat- Receptor Kinases.

About my research

Reactive Oxygen Species (ROS) are produced in intra- and extra-cellular compartments as response for any biotic and abiotic stresses. ROS also act as signal molecules in development and defence, however, the mechanisms and receptors by which extracellular ROS signals are perceived and integrated are still unclear. We propose that Cysteine-Rich Receptor-Like Kinases (CRKs), a family of Receptor Kinases (RKs) in Arabidopsis, can serve as extracellular ROS sensors. We propose that ROS modulate interactions between CRKs and Leucine-Rich Repeat Receptor Kinases (LRR-RKs) reflecting the redox state of the apoplast. We aim to elucidate how RKs signalling networks are modulated by ROS, and how this orchestrates responses to stresses by creating proteome-wide networks of interactions among extracellular domains (ECDs) of RKs in vitro.

The first part of the project will consist of building a Redox-dependent Interaction Network between the ECDs of LRR-RKs and CRKs of Arabidopsis using a large-scale interactome screen in different redox conditions (Smakowska-Luzan et al., 2018). The second part will assign a biological relevance to the redox-dependent CRKs interactions. Relevant candidates for redox-modulated interactions will be selected for further in-depth functional characterization using biochemical, molecular and cell biology approaches.

PhD candidate, Plant Physiology, Swammerdam Institute of Life Sciences, University of Amsterdam
Project title: Scensitive nature: Green leaf volatile perception in plants

About my research
Green leaf volatiles (GLVs) are an integral part of plant defense against biotic and abiotic stresses. They are emitted within seconds of damage to photosynthetic tissues and are known for their smell of cut grass. GLVs can have a direct or indirect defensive effect by repelling herbivores or pathogens or by attracting predatory insects. They also serve as within- or between-plant signals that either induce or prime plant defenses. However, it is still unknown how plants perceive volatile compounds and how the specificity of the volatile signal is transduced in the plant.

This research focuses on the GLV Z-3-hexenal and its isomer E-2-hexenal, as they are among the most abundant and influential volatiles in the GLV cluster. I aim to elucidate receptor candidates in Arabidopsis with forward genetics screens and proteomics approaches to further study plant GLV perception and implications for plant’s self-recognition and interactions with herbivorous insects and pathogens. Additionally, (3Z):(2E)-hexenal isomerases were recently identified in both insects and plants that convert Z-3-hexenal to E-2-hexenal. This change in the Z-3-/E-2-ratio affects the behavior of insects like foraging predators and host-seeking herbivores, and is expected to also alter plant defense response. For this part of my research I use potato, a crop species that unlike Arabidopsis has high isomerase activity, to study the role of hexenal isomerase in plants’ adaptive ability interact with its environment and its effect on ecological relations between plants and insects.

PhD candidate, Genetics, Wageningen University & Research

Project title: LettuceKnow Project 2.2 “Genetics of abiotic stress resilience in lettuce”

About my project:

It is well known that environmental factors such as light intensity, salinity levels and nutrient availability play an important role in plant growth and yield, yet the molecular mechanisms and genetic architecture that underline the responses of plants to said conditions are still largely unknown. With climate change causing erratic weather patterns, arable land with ideal environmental conditions is becoming an increasingly scarce resource. This necessitates the need to identify stress resilience loci and develop stress resistant crops. An important, yet underutilized avenue that can be used for identification of novel stress resilience loci is by mining the extended germplasm of crops thus exploring and exploiting its existing natural genetic variation. This approach has been used extensively in Arabidopsis thaliana but in the case of lettuce the use has been limited to the search for immunity related traits. With the advent of high throughput phenotyping technologies that can phenotype a large number of plants continuously across multiple days, phenotyping complex traits linked to abiotic stress can be more robustly captured. This, combined with powerful integrative bioinformatics and machine learning could help describe the genetic background of abiotic stress resilience in lettuce.

In a nutshell, my project a part of the larger LettuceKnow project aims “To identify and exploit natural variation in the LK500 population to improve lettuce resilience to abiotic stress conditions specifically fluctuating light and tipburn inducing growth conditions while reducing the trade-off towards plant growth”.

PhD candidate, Plant-Environment Signaling, Utrecht University

About my research

The abundance of molecular oxygen in our atmosphere allows plants to efficiently produce energy through mitochondrial respiration. Plants experiencing oxygen-limiting conditions, such as flooding and waterlogging, have to cope with these sudden energetic constrains by relying on fermentative metabolism and species-specific morphological adaptations. Therefore, scarcity of oxygen has traditionally been studied in the context of abiotic stress.

Surprisingly, meristematic tissues in plants were found to experience a condition of chronically low oxygen levels regardless of external oxygen availability. Specifically, stem cells hosted within the shoot apical meristem were shown to thrive in a state of constant hypoxia. In my research I mostly investigate the link between oxygen distribution, low-oxygen signaling and meristematic activity.

PhD candidate, Plant Microbe Interactions, Utrecht University
Project title: Data-driven SynCom scouting

About my research
The root microbiome is a highly complex and dynamic system in which millions of microbes interact with each other and with the plant root. Within a natural root microbiome, it is therefore hard to tell which microbes or which interactions lead to a specific plant phenotype or a shift in microbiome composition. Another way to study microbiomes is by inoculating plants with a self-assembled collection of microbes called a Synthetic Community or SynCom. This small collection of microbes makes it easier to map the interactions between plant roots and microbes, while being a simplified version of the natural root microbiome.

In this project, we aim to map the interactions between roots and microbes of three plant species concerning rhizosphere and endosphere colonization; Lotus, Arabidopsis and barley. For each of these plants we have a collection of hundreds of microbes that we can use in SynCom inoculations. We will observe which microbes are recruited by each plant and look more closely at the functional characteristics (or genes) of these recruited microbes. The data that will be produced shall be the driving factor to select potentially relevant microbes for more SynCom inoculation experiments.

PhD candidate, Laboratory of Entomology, Wageningen University & Research

About my research

Insect herbivores such as caterpillars and aphids can cause great damage to plants in the field, with disastrous consequences for plant fitness in terms of seed yield and quality. Apart from direct damage to flowers and seeds, herbivores affect yield and seed quality indirectly by changing plant-pollinator interactions or by reducing outcrossing rates due to favouring self-pollination under stressful conditions. A major knowledge gap in both fundamental and applied aspects of seed yield and quality is how they are affected by these indirect interactions between herbivores and pollinators.

My work aims to gain more insight into how insect herbivory affects various pollination processes and how plants integrate defense and reproduction strategies. I perform field experiments to study the effects of herbivory on Brassica rapa seed set and the response of the pollinator community in terms of attraction and behaviour; greenhouse studies to look more closely at the effects of herbivory on male fitness and self-incompatibility; and laboratory studies for a more mechanistic understanding of plasticity in self-incompatibility.

PhD Candidate, Plant Breeding, Wageningen University & Research
Project Title: Molecular breeding and evolution in allopolyploids: novel and applied methodologies

About my research
This research is focused on allopolyploids, organisms that harbour more than two copies of each chromosome and where each of these copies originates from a different ancestral species. Many agricultural crops have this condition, especially in the ornamental sector, and among those is Fragaria x ananassa, the garden strawberry. Applying standard analytical tools in these crops is in many cases not possible, meaning that adaptations to standard methods need to be designed an implemented.

In this project multiple technologies are being adapted to handle the anomalies of allopolyploid genetics. First, genotyping using whole-genome sequencing (WGS) data, particularly assessing the effect of sequencing depth on genotype accuracy, a special concern in allopolyploids. Secondly, linkage mapping using WGS genotypes, which is already a challenge without the added allopolyploidy. Thirdly, the study of ancestry in a wide range of strawberries, a relevant topic since the ancestors of allo-octoploid strawberry have not been fully identified yet. Lastly, quantitative-trait-locus (QTL) analysis of metabolic data in strawberries, aiming to characterize the wide aromatic variation in strawberry.