PhD position: Plant root gene regulatory networks in host-microbiome interactions (1.0 FTE)

PhD position: Plant root gene regulatory networks in host-microbiome interactions (1.0 FTE)

Published Deadline Location
17 Apr 15 Jun Utrecht

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Your research will decipher how plants under pathogen attack engage root microbiota for enhanced protection and contribute to innovations in future agriculture.

Job description

Plants recruit and nurture billions of microbes on their roots, the so-called root microbiome. Microorganisms living inside plant tissue, the endosphere, have a largely unexplored functional potential to expand the genomic capabilities of their host by improving nutrient uptake, enhancing tolerance to environmental stress, and by providing protection against pests and diseases. Unraveling the beneficial functions of these endophytic microorganisms and the mechanisms involved in the interplay with their host provides enormous opportunities to address key societal problems of the 21st century, in particular the increased global demands for crops that are more resilient to (a)biotic stress and less dependent on fertilizers and pesticides. Exciting breakthroughs in this novel research field revealed that plants can "cry for help" from their root microbiota in response to leaf pathogen infection, therewith alleviating the stress through microbiome encoded functions. These discoveries sparked a number of vital questions in host microbiome research: Which plant genes/traits optimize microbiomes for host-supporting health functions? What microbiome functions are recruited by stressed host plants and how do they improve plant performance? As part of your PhD research, you will be using transcriptome studies in Arabidopsis to investigate the root gene regulatory networks that are key to how plants recruit beneficial microbes to their root system in response to pathogen attack, and decipher which plant traits (regulators of the networks and enzymes in biosynthetic pathways) are involved in optimizing root microbiomes for improved host supporting health functions. You will work closely with other members of the larger NWO-ENW-Groot consortium: a PhD student at Utrecht University (studying the recruited endophytes, how plants recruit them and how they impact the plant), and two Postdocs that work at NIOO-KNAW, Wageningen University and Utrecht University (integrating the transcriptome data with metabolome data and validating the predictions of these studies).


Utrecht University


We are looking for a highly motivated and creative PhD candidate with:

  • a Master's degree or an international equivalent in the relevant fields of Bioinformatics, Biology or Plant Science;
  • expertise in analyzing transcriptome data;
  • experience with plant molecular biology;
  • a strong interest in gene regulation and host microbiome research;
  • basic to intermediate statistical and mathematical skills;
  • excellent collaboration and communication skills (written and spoken);
  • a strong motivation to work in a multidisciplinary, international research team.

Conditions of employment

  • we offer a full-time position for four years in an international and interdisciplinary working environment and you will be provided with funding for research and training costs. This will provide you with an excellent basis and a strong network for a future career in the field of plant science and sustainable agriculture, in academia and industry.
  • a full-time gross salary starting at €2,325 and increasing to €2,972 per month during the appointment (scale P according to the Collective Labour Agreement Dutch Universities (cao)).
  • the salary is supplemented with a holiday allowance of 8% and an end-of-year bonus of 8.3% per year.
  • pension scheme, partially paid parental leave, and flexible employment conditions based on the Collective Labour Agreement Dutch Universities.

In addition to the employment conditions laid down in the cao for Dutch Universities, Utrecht University has a number of its own arrangements. For example, there are agreements on professional development, leave arrangements and sports. We also give you the opportunity to expand your terms of employment yourself via the Employment Conditions Selection Model. This is how we like to encourage you to continue to grow.

More information about working at the Faculty of Science can be found here.


Your PhD research will be conducted in the Plant-Microbe Interactions group of Profs Saskia van Wees and Corné Pieterse at Utrecht University. Your project will be part of the recently awarded NWO-ENW Groot programme “Unwiring beneficial functions and regulatory networks in the plant endosphere”. In this programme, 6 PhD candidates and 3 postdocs will be recruited who will integrate next generation ‘omics approaches with chemistry and advanced microscopy to i) identify functional traits and biosynthetic pathways involved in the beneficial activities of root endophytic microorganisms, ii) investigate the regulatory mechanisms and chemistry of the interactions between root endophytic microorganisms and their host plant, and iii) localize in situ the beneficial endophytic microorganisms and the molecular dialogue with their host plant. The research will be carried out in the labs of Profs Pieterse and Van Wees (Utrecht University), Van Wezel and Briegel (Leiden University), Medema (Wageningen University) and Raaijmakers (NIOO-KNAW). The consortium members operate at the global forefront of highly complementary disciplines that are crucial to move this emerging science field forward to generate a new blueprint of the molecular and chemical dialogues in the plant endosphere and to provide a fundamental basis for future engineering of plant microbiomes for enhanced crop resilience.

At the Faculty of Science there are 6 departments to make a fundamental connection with: Biology, Chemistry, Information and Computing Sciences, Mathematics, Pharmaceutical Sciences and Physics. Each of them is made up of distinct institutes which work together to focus on answering some of humanity’s most pressing problems. More fundamental still are the individual research groups - the building blocks of our ambitious scientific projects.

Utrecht University is a friendly and ambitious university at the heart of an ancient city. We love to welcome new scientists to our city – a thriving cultural hub that is consistently rated as one of the world’s happiest cities. We are renowned for our innovative interdisciplinary research and our emphasis on inspirational research and excellent education. We are equally well-known for our familiar atmosphere and the can-do attitude of our people. This fundamental connection attracts Researchers, Professors and PhD candidates from all over the globe, making both the University and the Faculty of Science a vibrant international and wonderfully diverse community.


  • Research, development, innovation
  • 36—40 hours per week
  • €2325—€2972 per month
  • University graduate
  • 1099508



Domplein 29, 3512 JE, Utrecht

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