Postdoc position on integrative omics of plant-microbe interactions

Published on
September 29, 2020
Location Wageningen
Respond Click here to respond

We are looking for

Plant microbiomes represent an untapped resource of microorganisms and natural bioactive compounds that significantly contribute to plant resilience to pathogens and abiotic stresses. In this project, you will implement innovative omics integration strategies to systematically connect genes and their expression patterns to metabolites that play key roles in host-microbe interactions within endosphere microbiomes. For example, you will use transcriptomic and metabolomics data to link plant co-expression modules to metabolites and their mass-spectrometric fragmentation patterns from root exudates, and analyse the effects of these pathways/molecules on microbiome composition.
This is a joint project between Wageningen University (Marnix Medema) and Utrecht University (Saskia van Wees / Corné Pieterse) and is also linked closely to the Netherlands Institute of Ecology (Jos Raaijmakers). Throughout the course of the project, you would be expected to spend time in both Wageningen and Utrecht (the latter facilitated through a guest appointment), in order to fully interact with the groups at both locations. The expertise of the Medema research group lies in developing computational approaches to identify biosynthetic pathways and connect them to specific molecules and phenotypes, whereas the Van Wees group has much experience in plant transcriptomic analysis and reconstruction of the gene regulatory networks that underlie such pathways.
This project will play a key role in integrating multiple types of omics data from both plant and microbes generated within a larger ENW Groot consortium between NIOO-KNAW, Wageningen University, Utrecht University and Leiden University. You will work closely with PhD students and postdocs appointed at these institutes, which will make it possible to unravel the chemical products and physiological roles of the pathways you identify. In the end, the research is projected to lead to fundamental new insights into microbe-microbe and plant-microbe interactions in the endosphere microbiome, and may result in the industrial development of novel crop protection solutions for agriculture.

We ask

We are looking for an ambitious, enthusiastic team player and result-driven scientist with:

  • An excellent academic record (PhD) in bioinformatics or computational biology.
  • Affinity with plant-microbe biology and metabolism.
  • Demonstrable expertise in working with transcriptomic and/or metabolomic data.
  • Proven proficiency in programming (in, e.g., Python).
  • Basic to intermediate statistical and mathematical skills.
  • This position requires an excellent English language proficiency  (a mininum of CEFR C1 level). For more information about this proficiency level, please visit our special language page.

We offer

A challenging position with, depending on your experience, a competitive salary from €  3217,- for a full working week of 38 hours in accordance with the Collective Labor Agreement Dutch Universities (scale 10).
In addition, we offer:

  • 8% holiday allowance;
  • a structural year-end bonus of 8.3%;
  • excellent training opportunities and secondary employment conditions;
  • flexible working hours and holidays can possibly be determined in consultation so that an optimal balance between work and private life is possible;
  • excellent pension plan through ABP;
  • 232 vacation hours, the option to purchase extra and good supplementary leave schemes;
  • a flexible working time;
  • a choice model to put together part of your employment conditions yourself, such as a bicycle plan;
  • a lively workplace where you can easily make contacts and where many activities take place on the Wageningen Campus. A place where education, research and business are represented;
  • use the sports facilities on campus (IF APPLICABLE)
Wageningen University & Research stimulates internal career opportunities and mobility with an internal recruitment policy. There are ample opportunities for own initiative in a learning environment.
We offer a versatile job in an international environment with varied activities in a pleasant and open working atmosphere.
We offer the research environment of a young and dynamic group with a strong international profile; a state-of-the-art computational infrastructure; close national and international collaboration with other PhD students and researchers; and the possibility to further develop your scientific education with courses, training and conferences. There will also be opportunities to be involved in teaching at workshops or courses.

More information

For more information about this position, please contact dr. Marnix Medema (, tel. +31 317 480 944) or Saskia van Wees (, tel. +31 30 253 6861).
For information on the selection procedure, please consult  

Applications can only be submitted online, at; please do not mail material directly to the persons above.
You can apply up to and including October 31, 2020.

We are

The mission of Wageningen University & Research is “To explore the potential of nature to improve the quality of life”. Within Wageningen University & Research, nine specialised research institutes from the Wageningen Research Foundation and Wageningen University have joined forces to help answer the most important questions in the domain of healthy food and living environment.

With approximately 30 locations, 6,000 employees, and 12,000 students, Wageningen University & Research is one of the leading organisations in its domain worldwide. An integrated approach to problems and the cooperation between various disciplines are at the heart of the unique approach of Wageningen.

For further information about working at Wageningen University & Research, take a look at the special career site.

Equal opportunities employer
We are an employer that offers equal opportunities. We are happy to receive applications from all suitably qualified people regardless of race, gender, functional impairment, religion / belief, sexual orientation or age.
We believe that a diverse and inclusive working environment makes us a more relevant, competitive and resilient organization. Click here for more information about working at WUR with a functional impairment.

Wageningen UR has a global reputation for its ground-breaking research and innovative education in the fields of food and health, sustainable agrosystems, the rural environment, and societal development - all of which make an essential contribution to the quality of life, i.e. the supply of safe and healthy food and drink, on the one hand, and the chance to live, work and play in a balanced ecosystem with a large variety of plants and animals on the other. Within Wageningen UR, the Plant Sciences Group (PSG) brings together science education and scientific, strategic and applied research in the fields of biology, of plants in relation to their environment, of plant-related organisms and of plant production. This project will be carried out at the Bioinformatics Group within PSG. This rapidly expanding research group focuses on fundamental and applied bioinformatics research in the green life sciences. In particular, they develop and apply novel computational methods for the analysis and integration of –omics data. The group has a strong track record in genome analysis, algorithm development and tool construction. There are many national and international collaborations with researchers studying plant and microbe metabolism, biotechnology and genomics.

You will closely collaborate with the Plant-Microbe Interactions group at Utrecht University. The Plant-Microbe Interactions group aims to unravel at the molecular level how the plant immune system orchestrates interactions with beneficial members of the root microbiome, pathogens and insects. This provides a rational basis for developing sustainable strategies for disease resistance in next-generation crops that produce more, with less input of fertilizers or pesticides.

Apply now