Two PhD positions Plant-Microbe Interactions Utrecht University, Plant-Microbe Interactions group Netherlands

Two PhD positions Plant-Microbe Interactions (1.0 FTE)


Job description

The successful applicant will work as a PhD student on a NWO Green II-funded project entitled “Unearthing beneficial microbe rhizosphere competence traits in vivo”. The selected candidate will work under supervision of Dr. R. de Jonge at the Plant-Microbe Interactions group.

The NWO Green II call focuses on research that provides the basis for a ground-breaking system change aimed at realising resilient and integrally sustainable plant and animal production systems, higher food security, and the conservation of nature and ecosystem services in the Netherlands.


The project summary is as follows:


Fixation of solar energy in plants through photosynthesis drives all life on our planet. Up to 20% of the carbohydrates produced by photosynthesis are released into the soil, making plants central players in the belowground food web. In nature, plant roots live in close association with countless microbes, also known as the root microbiome. Beneficial microbes provide plants with important services, such as enhanced nutrient uptake and protection against diseases. Because of their potential to sustainably improve crop production, increasingly microbial products are registered for biofertilization and biological control purposes in agriculture. However, despite their promise under controlled conditions, bioinoculant efficacy can vary in the field. This can be caused by variable environmental conditions that influence microbial performance, unidentified negative interactions with local microbiome communities, or a suboptimal match with plant genotype. Hence, an in-depth understanding of the microbial traits that influence rhizosphere competence is urgently needed for the development of more persistent microbial products for future crop improvement.

In this interdisciplinary project, which besides Utrecht University also involves Novozymes, world leader in the market of bioinoculants, we will combine microbial genetics, microbiome metagenomics, computational modelling and molecular plant biology to discover: microbial rhizosphere competence traits that influence the success of bioinoculants, root microbiomes traits that affect rhizosphere competence of bioinoculants, and the mechanisms by which root exudates affect plant-beneficial microbe interactions.

The two, successful PhD candidates will develop high-throughput, sequencing-based, microbial trait identification methodologies for beneficial microbes, based on transposon mutagenesis, gain-of-function expression libraries and experimentally evolved microbes to identify microbial rhizosphere competence traits in the context of naturally occurring microbial communities. Thus, experience in, and affinity with microbial molecular techniques, and computational/bioinformatics analyses of high-throughput sequencing data are imperative.



- A MSc in Microbiology and/or Experimental Plant Sciences, and demonstrated training in Bioinformatics;

- A strong background in computational analyses and programming as well as genetic and molecular techniques;

- Excellent English oral, written and presentation skills.



The candidate is offered a full-time position for 1 year with an extension for a further three years if the evaluation is positive. The gross salary is in the range between €2,222 and maximum €2,840 per month. Salaries are supplemented with a holiday bonus of 8 % and a year-end bonus of 8.3 % per year. We offer a pension scheme, collective insurance schemes and flexible employment conditions (multiple choice model). The research group will provide the candidate with necessary support on all aspects of the project. More information is available at: working at Utrecht University.

About the organization

A better future for everyone. This ambition motivates our scientists in executing their leading research and inspiring teaching. At Utrecht University, the various disciplines collaborate intensively towards major societal themes. Our focus is on Dynamics of Youth, Institutions for Open Societies, Life Sciences and Sustainability.

Utrecht University is one of the oldest universities in the Netherlands and one of the largest in Europe. Established March 26, 1636, Utrecht University has an enrolment of over 30,000 students, employs over 5,000 faculty and staff, and is consistently ranked among Europe’s best universities for both education and research. The city of Utrecht is a central hub within the Netherlands, known for its vitality, medieval city center and cultural wealth.


The Faculty of Science consists of six departments: Biology, Chemistry, Physics and Astronomy, Mathematics, Information and Computing Sciences, and Pharmaceutical Sciences. The Faculty, which is located at the Uithof campus, is home to 4,500 students and over 1,000 staff and is internationally renowned for the quality of its research. The Faculty's academic programmes reflect developments today.


The Plant-Microbe Interactions group aims to explore and exploit the plant's natural immune system. Our research is focused on understanding the molecular and biological details of how pathogens infect plants, how resistant plants successfully defend themselves, and how beneficial microbes in the root microbiome promote plant growth and defense. The research goals are being achieved by using model and crop plant species in combination with state-of-the-art techniques and methods in phytopathology, microbiology, molecular biology, biochemistry, genetics, genomics and bioinformatics. With our fundamental research we aim to provide a rational basis for developing sustainable strategies for disease resistance in next-generation crops.


Additional information

Additional information about the vacancy can be obtained from Dr. R. de Jonge, +31 30 253 68 60 or


To apply please attach a letter of motivation, curriculum vitae and (email) addresses of at least two referees. Also provide a copy of the highest academic degree certificate, and a list of courses (including marks) followed during your BSc and MSc programmes.


It is requested to address the following aspects in your motivation letter:

  • What is your motivation for doing a PhD?
  • What makes you a suitable candidate for this project?
  • What questions came to your mind when reading the project summary?


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The application deadline is

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