The Netherlands Institute of Ecology (NIOO-KNAW) is a top research institute of the Royal Netherlands Academy of Arts and Sciences (KNAW). NIOO-KNAW focuses on fundamental and strategic research on individual organisms, populations, communities, and ecosystems. The Department of Microbial Ecology offers a


PhD position (Vacancy number ENWGroot-PhD-ME-20-005)


Project title:  Unwiring beneficial functions and regulatory networks in the plant endosphere


Project descriptions: Plant roots are colonized by billions of microorganisms that affect plant growth and tolerance to (a)biotic stresses. Recently we discovered that plants infected by fungal pathogens actively recruit microbes inside their root tissue, the endosphere, for protection. Here we will investigate how plants under siege communicate with their microbiome and characterize the protective endophytic microbes, their genes and metabolites. The obtained fundamental knowledge will provide a strong basis for developing innovative strategies that integrate microbiomes in plant breeding and sustainable crop protection. The overall aim of the PhD project is to characterize the endophytic bacteria and protective functions that are activated by plants under attack by a fungal pathogen.


Job description:

  • Isolate and characterize endophytic bacteria from plants under siege
  • Conduct bioassays and develop tools and markers to monitor endophytic colonization
  • Identify microbial genes and biosynthetic pathways activated in plants under siege
  • Elucidate the activities and structure of compounds encoded by identified pathways
  • Present your work at (inter)national meetings and publish scientific articles
  • Supervise MSc students in the ENW Groot project



  • MSc degree in plant-microbe interactions, microbiology
  • Hands-on experience in data mining and microbiome analyses, molecular microbiology, plant bioassays, mutational analyses of microbes
  • Experience in bioinformatics (R and Python) and/or (bio)chemistry will be of added value
  • Willing to work at two different locations (NIOO-KNAW, Leiden University)
  • Language skills: fluency in English writing and speaking required


Appointment: the PhD position will be hosted at the Department of Microbial Ecology of the Netherlands Institute of Ecology (NIOO-KNAW) and will work closely together with the Molecular Biotechnology group at the Institute of Biology, Leiden University. We offer the research environment of a dynamic group with a strong international profile; state-of-the-art laboratory and greenhouse 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. The position is full-time (38 hours/week), initially for 1 year, after which a go/no-go decision will be taken on extension with another three years. The gross salary in the first year is € 2.325,00 per month rising to € 2.972,00 in the fourth year for a full-time appointment.


Starting date: September 2020


Principal supervisors: Prof. Jos M. Raaijmakers (NIOO-KNAW); Dr. Victor Carrion (Leiden University)


Application: NIOO-KNAW wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background. Please send your application, in English, including complete curriculum vitae and names and contact details of three professional referees to, and mention “ENWGroot-PhD-ME-20-005” in the subject header.


Closing date for application: Monday 15 June 2020. Applications received later than this date will not be considered.


Information: General information about the ENW Groot program can be found at:

Specific information about the PhD position can be obtained from Prof. Jos M. Raaijmakers;; +31 317-473497




Application deadline:
Start date:
Location: NIOO-KNAW, Wageningen, The Netherlands