PhD candidate Effect of Agriculture on the Plant Microbiome (Vacancy closed)


In the NWO-KIC project MicroHealth, we will study the role of the microbiome in the relationship between soil, agricultural products and health of humans. This relationship has enormous societal implications because agriculture has a large impact on our environment and food is the number one driver of human health. 


In MicroHealth, with a team of plant and human biologists, sociologists and data analysts, we will establish the connection between the impact of agriculture on the soil and plant quality/microbiome and the consequences for the health of humans, as well as the social and political context of this connection. 


We will achieve this by (1) studying the impact of farming strategies on the soil and crop microbiome and nutritional composition; (2) through advanced data analysis this will be coupled to human health through an intervention study in the HELIUS cohort tracing microbiome changes and its relation to health status; (3) this is embedded in research on opportunities and conflicts in policies and stakeholder-networks and microbiome-related health practises at the household level. 


For activity 1) we are looking for a PhD student, who, with help by a technician, will be responsible for field and greenhouse research into the effects of fertiliser use on the microbiome and nutritional composition of a number of open field crops. You will collaborate with other PhDs and postdocs who will work on the other activities.


If you enjoy working in an interdisciplinary research team and are eager to contribute to the understanding of how plants interact with other organisms, then the Plant Hormone Biology group, which is part of the Swammerdam Institute for Life Sciences in the Faculty of Science at the University of Amsterdam, is the place to be. 


The mission of the Plant Hormone Biology group is to understand the chemical communication of plants with other organisms in their environment. With an international and diverse team of post-docs, PhDs and technicians with expertise varying from analytical chemistry to biochemistry and molecular biology we study how plants use signaling molecules to affect the behaviour of other organisms in the rhizosphere. This includes communication with microbial communities that have been shown to play a crucial role in the protection of plants against a range of stresses. 


Our research is aimed at understanding the biological relevance of this chemical communication and use it as a basis for improving resistance and harnessing the potential of beneficial root microbes resulting in improved stress resilience in crops for sustainable food production with reduced inputs.


What are you going to do?

You will plan, carry out and analyse experiments under field and greenhouse conditions in which we will determine what the effect is of fertiliser use on the microbiome and nutritional composition (using metabolomics analysis) of a number of open field vegetable crops. Part of the field produced crops will be used in an intervention study in the HELIUS cohort by team members at AUMC. In the controlled conditions experiment you will investigate the mechanisms underlying the effects of the different fertilisers on microbiome recruitment and nutritional composition, for example identify the signalling molecules that drive differences in the microbiome. 


Tasks and responsibilities:
•    complete a PhD thesis within the official appointment duration of four years; 
•    perform your experiments in a systematic and well controlled manner and keep accurate records by 

     properly documenting and organizing your work;
•    be an active member of the research group and take responsibility for shared tasks. Discuss your work

     with group members and during consortium meetings. Incorporate feedback and give input to others; 
•    report your results to the MicroHealth consortium;
•    present your work at (inter)national scientific meetings;
•    take a leading role in writing and publishing manuscripts;
•    participate in the Faculty of Science PhD training program and the training program of the

     Experimental School of Plant Sciences;
•    assist in teaching and supervising Bachelor and Master theses and tutoring students;


What do you have to offer?

You are passionate about science and have a particular interest in experimental plant biology and the plant microbiome. You enjoy performing experimental work (in field and greenhouse), as well as data analysis. You enjoy working in a multidisciplinary team and are a team player. You have good communication skills as you will be expected to discuss your results with a large group of partners and in (inter)national meetings.


Your experience and profile 
•    a PhD in Biology or Plant Science;
•    experience with experimental work involving plants;
•    experience with omics analysis (especially microbiome and metabolomics);
•    familiar/experience with programming such as in R;
•    affinity with plant metabolism and the plant microbiome;
•    fluency in English, both written and spoken.


Our offer

A temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). The preferred starting date is as soon as possible. This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.


Your salary will range between €2,770 in the first year to €3,539 gross per month in the last year of employment, on the basis of a full working week of 38 hours. This sum does not include the 8% holiday allowance and the 8.3% year-end allowance. A favorable tax agreement, the 30% ruling, may apply to non-Dutch applicants. The Collective Labour Agreement for Dutch Universities (CAO NU) is applicable.


Besides the salary and a vibrant and challenging environment at Science Park we offer you multiple fringe benefits:
•    232 holiday hours per year (based on fulltime);
•    multiple courses to follow from our Teaching and Learning Centre;
•    a complete educational program for PhD students;
•    the possibility to follow courses to learn Dutch;
•    help with housing for a studio or small apartment when you’re moving from abroad. 


Are you curious to read more about our extensive package of secondary employment benefits, take a look here.


About us

The University of Amsterdam is the Netherlands' largest university, offering the widest range of academic programmes. At the UvA, 30,000 students, 6,000 staff members and 3,000 PhD candidates study and work in a diverse range of fields, connected by a culture of curiosity.


The Faculty of Science has a student body of around 8,000, as well as 1,800 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works, be it elementary particles, the birth of the universe or the functioning of the brain. 


The Swammerdam Institute for Life Sciences (SILS) is one of the Faculty of Science’s largest institutes. Its approximately 240 scientists and staff members work in 17 research groups that perform excellent research centered on four themes: Neurosciences, Cell & Systems Biology, Microbiology and Green Life Sciences.


Do you want to know more about our organization? Read more about working at the University of Amsterdam.


Any questions?

Do you have any questions or do you require additional information? Please contact:

         T:  +31 20 5256476


Job application

If you feel the profile fits you, and you are interested in the job, we look forward to receiving your application. You can apply online via the UvA website. We accept applications until and including 17 December 2023. 


Applications should include the following information (all files besides your cv should be submitted in one single pdf file):

•    a detailed CV including the months (not just years) when referring to your education and work experience;
•    a letter of motivation;
•    the names and email addresses of two references who can provide letters of recommendation.


Only complete applications received within the response period via the link below will be considered.


A knowledge security check can be part of the selection procedure.
(for details: National knowledge security guidelines).


The interviews will be held in the course of December 2023 and January 2024. 



The UvA is an equal-opportunity employer. We prioritise diversity and are committed to creating an inclusive environment for everyone. We value a spirit of enquiry and perseverance, provide the space to keep asking questions, and promote a culture of curiosity and creativity.