Vera Hesen

Vera Hesen MSc

PhD Candidate


Droevendaalsesteeg 10
6708 PB Wageningen

+31 (0) 317 47 34 00

The Netherlands



As a plant biologist I connect ecology to molecular biology by studying natural populations of molecular model plant Arabidopsis thaliana in secondary soil succession. Although challenging, it is fascinating to work on the interface of these fields!


Field picture 2018
Vera Hesen
Collecting samples from secondary succession fields

I have completed both my BSc and MSc Biology both at Wageningen University. In my BSc (organismal and developmental biology) I became more and more interested in developmental biology as well as the interplay with the local environment. With my MSc (gene regulation and molecular development) I deepened my knowledge on this subject and moved towards the plant biology world. Both my MSc thesis (carried out at Plant Developmental Biology, Wageningen University) and MSc internship (carried out at Estelle laboratory, University of California San Diego) trained my to become a critical and independent scientist with a passion for fundamental research.

After I finished my studies I got the opportunity to write my own PhD research proposal as part of the Experimental Plant Science graduate program. In this proposal I moved with my background in molecular plant biology towards the turbulent world of terrestrial ecology. Together with Prof. Wim van der Putten (Terrestrial Ecology, NIOO-knaw) and Dr. Viola Willemsen (Plant Developmental Biology, Wageningen University) I wrote a proposal about linking ecology and molecular biology through studying natural population of Arabidopsis thaliana during secondary soil succession. As of June 2018 I am carrying out the proposal as an PhD student part of both Terrestrial Ecology and Plant Developmental Biology. The project is extremely multidisciplinary ranging from soil chemistry and microbiome composition to root architecture studies and whole genome sequencing. It is amazing to work in both departments and experience much support and input to carry out this adventurous project!

Speaking at Netherlands Experimental Plant Science conference April 2022
Vera Hesen
Speaking at Netherlands Experimental Plant Science conference April 2022

PhD Project description

In spite of recent advances in molecular biology and ecology, we still do not understand mechanistically how plant life history strategies are shaped by environmental factors. Here I will study how plant-soil interactions influence adaptation of these strategies. My aim is to unravel how soil development during secondary succession influences the selection of plant life history strategies. I will study natural populations of Arabidopsis thaliana and how they are influenced by successional changes in biotic-abiotic soil conditions in a well-described time series of abandoned ex-arable fields. During secondary succession, the plant community shifts from pioneer to later succession species under influence of changes in both the abiotic and biotic composition of the soil. I will test the hypothesis that belowground changes contribute to adaptation of plant roots to their specific soils. Arabidopsis is a well-established molecular model plant and has many favorable characteristics. Studying sequence variation within this species will allow me to describe selection at the genetic level. Specific gene editing experiments will test and validate roles for root architecture in adaptation. In this research, I will integrate soil ecology and molecular plant biology studying genomes, expression patterns, plant-soil feedback effects and root architecture. These findings will provide fundamental knowledge on root traits of crops adapted to sustainable soil management in agriculture.

This project is a collaboration between Department of Terrestrial Ecology (NIOO-KNAW) and Plant Developmental Biology (Wageningen University) under the guidance of:

Prof. dr. ir. Wim van der Putten (Terrestrial Ecology - NIOO-KNAW)
Prof. dr. ir. Ben Scheres (Plant Developmental Biology - Wageningen University)
Dr. Viola Willemsen (Plant Developmental Biology - Wageningen University)

Rhizotron system with Arabidopsis plant and root
Vera Hesen
Arabidopsis root system in rhizotron system
Top view Arabidopsis rosettes
Vera Hesen
Natural variation in Arabidopsis rosettes
Arabidopsis thaliana
Vera Hesen
Natural populations of Arabidopsis thaliana

The hidden half of the plant world


Peer-reviewed publicaties

  • Environmental microbiome

    Pioneer Arabidopsis thaliana spans the succession gradient revealing a diverse root-associated microbiome

    Vera Hesen, Yvet Boele, Tanja Bakx-Schotman, Femke van Beersum, Ciska Raaijmakers, Ben Scheres, Viola Willemsen, Wim H. van der Putten

    BACKGROUND: Soil microbiomes are increasingly acknowledged to affect plant functioning. Research in molecular model species Arabidopsis thaliana has given detailed insights of such plant-microbiome interactions. However, the circumstances under which natural A. thaliana plants have been studied so far might represent only a subset of A. thaliana's full ecological context and potential biotic diversity of its root-associated microbiome.

    RESULTS: We collected A. thaliana root-associated soils from a secondary succession gradient covering 40 years of land abandonment. All field sites were situated on the same parent soil material and in the same climatic region. By sequencing the bacterial and fungal communities and soil abiotic analysis we discovered differences in both the biotic and abiotic composition of the root-associated soil of A. thaliana and these differences are in accordance with the successional class of the field sites. As the studied sites all have been under (former) agricultural use, and a climatic cline is absent, we were able to reveal a more complete variety of ecological contexts A. thaliana can appear and sustain in.

    CONCLUSIONS: Our findings lead to the conclusion that although A. thaliana is considered a pioneer plant species and previously almost exclusively studied in early succession and disturbed sites, plants can successfully establish in soils which have experienced years of ecological development. Thereby, A. thaliana can be exposed to a much wider variation in soil ecological context than is currently presumed. This knowledge opens up new opportunities to enhance our understanding of causal plant-microbiome interactions as A. thaliana cannot only grow in contrasting soil biotic and abiotic conditions along a latitudinal gradient, but also when those conditions vary along a secondary succession gradient. Future research could give insights in important plant factors to grow in more ecologically complex later-secondary succession soils, which is an impending direction of our current agricultural systems.
  • Genes

    Nature and nurture

    Merijn Kerstens, Vera Hesen, Kavya Yalamanchili, Andrea Bimbo, Stephen Grigg, Davy Opdenacker, Tom Beeckman, Renze Heidstra, Viola Willemsen

    Root development is crucial for plant growth and therefore a key factor in plant perfor-mance and food production. Arabidopsis thaliana is the most commonly used system to study root system architecture (RSA). Growing plants on agar-based media has always been routine practice, but this approach poorly reflects the natural situation, which fact in recent years has led to a dramatic shift toward studying RSA in soil. Here, we directly compare RSA responses to agar-based medium (plates) and potting soil (rhizotrons) for a set of redundant loss-of-function plethora (plt) CRISPR mutants with variable degrees of secondary root defects. We demonstrate that plt3plt7 and plt3plt5plt7 plants, which produce only a handful of emerged secondary roots, can be distinguished from other genotypes based on both RSA shape and individual traits on plates and rhizotrons. However, in rhizotrons the secondary root density and the total contribution of the side root system to the RSA is increased in these two mutants, effectively rendering their phenotypes less distinct compared to WT. On the other hand, plt3, plt3plt5, and plt5plt7 mutants showed an opposite effect by having reduced secondary root density in rhizotrons. This leads us to believe that plate versus rhizotron responses are genotype dependent, and these differential responses were also observed in unrelated mutants short-root and scarecrow. Our study demonstrates that the type of growth system affects the RSA differently across genotypes, hence the optimal choice of growth conditions to analyze RSA phenotype is not predetermined.