Are you looking for a PhD position focusing on the interplay between insects and their microbiomes? Are you a bioinformatician who wants to develop and apply computational methods for microbiome analysis and virus discovery using sequencing data sets? Then this PhD vacancy might be of interest to you.

Like all organisms, insects have a native microbiome, including bacteria, fungi, and insect viruses. Many insects also serve as vectors to transmit viruses among animals or plants and the insect microbiome potentially influences this virus transmission. Therefore, the focus of insect virus research expanded from individual virus-host systems to metagenomics, i.e., bulk sequencing the genetic content of environmental samples without the need for prior virus isolation.

In this project, we will study whiteflies, a diverse group of agriculturally important insects that feed on plants and can transmit a variety of plant viruses. Whiteflies pose a severe threat to many plant crops, both in greenhouses and open fields. The management of this pest currently relies on insecticides; however, most whitefly species have already developed insecticide resistance. Biological control based on microorganisms is a promising tool; however, this requires fundamental understanding of the microbiome of whiteflies and its impact on virus transmission.

In this PhD project, you will contribute to developing bioinformatics approaches for microbiome analyses in insects, with a focus on the virome. You will discover the microbiome players and reconstruct virus genomes from metagenomics sequencing data of individual whiteflies. You will then associate this information with additional meta-data (such as geographic location and host plant) and, additionally, zoom in on the co-occurrence of different microorganisms in individual whiteflies to reveal possible synergistic or antagonistic effects. This project will thus contribute to understanding the factors that shape the viromes of insects.

You will integrate data from public sources, from international collaborations and from individual insects to be sampled in the Netherlands. Beyond the scientific and potential application merits, you will build a network for your future career both within and outside Wageningen University.

You will work here
The research is embedded in two chair groups at Wageningen University: the Bioinformatics Group led by prof. Dick de Ridder and the Laboratory of Virology led by prof. Monique van Oers. Your daily supervisors will be dr. ir. Astrid Bryon and dr. Anne Kupczok, with complementary expertise: insect virology, virome analysis, and agricultural entomology (Astrid Bryon) and bioinformatics, comparative genomics, and molecular evolution (Anne Kupczok). The position is for four years and you will join the graduate school PE&RC.

• a successfully completed MSc degree in bioinformatics or a related field
• demonstrable experience in high-throughput sequencing data analysis and comparative genomics;
• proficiency in programming (e.g., python);
• affinity with virology, ecology, and molecular evolution;
• enthusiasm for working in close collaborations with experimental biologists;
• a proactive attitude and teamwork skills and are committed to obtaining a PhD;
• a very good level of oral and written English. You are required to show a certification of English skills. For more information about the required level please take a look at this link.

Wageningen University & Research offers excellent terms of employment. A few highlights from our Collective Labour Agreement include:

• Partially paid parental leave;
• working hours that can be discussed and arranged so that they allow for the best possible work-life balance;
• the option to accrue additional compensation / holiday hours by working more, up to 40 hours per week;
• there is a strong focus on vitality and you can make use of the sports facilities available on campus for a small fee;
• a fixed December bonus of 8.3%;
• excellent pension scheme.

In addition to these first-rate employee benefits, you will receive a fully funded PhD position and you will be offered a course program tailored to your needs and the research team.

The gross salary for the first year is € 2.770 - per month rising to € 3.539,- in the fourth year in according to the Collective Labour Agreements for Dutch Universities (CAO-NU) (scale P). This is based on a full-time working week of 38 hours. We offer a temporary contract for 18 months which will be extended for the duration of the project if you perform well.

There are plenty of options for personal initiative in a learning environment, and we provide excellent training opportunities. We are offering a unique position in an international environment with a pleasant and open working atmosphere.

You are going to work at the greenest and most innovative campus in Holland, and at a university that has been chosen as the “Best University” in the Netherlands for the 19th consecutive time.

Coming from abroad
Wageningen University & Research is the university and research centre for life sciences. The themes we deal with are relevant to everyone around the world and Wageningen, therefore, has a large international community and a lot to offer to international employees.

Because we expect you to work and live in the Netherlands our team of advisors on Dutch immigration procedures will help you with the visa application procedures for yourself and, if applicable, for your family.
Feeling welcome also has everything to do with being well informed. Wageningen University & Research's International Community page contains practical information about what we can do to support international employees and students coming to Wageningen. Furthermore, we can assist you with any additional advice and information about for example helping your partner to find a job, housing, or schooling. Finally, certain categories of international staff may be eligible for a tax exemption on a part of their salary during the first five years in the Netherlands.

Wageningen University & Research

The mission of Wageningen University & Research is “To explore the potential of nature to improve the quality of life”. Under the banner Wageningen University & Research, Wageningen University and the specialised research institutes of the Wageningen Research Foundation have joined forces in contributing to finding solutions to important questions in the domain of healthy food and living environment. With its roughly 30 branches, 7,600 employees (6,700 fte) and 13,100 students and over 150,000 participants to WUR’s Life Long Learning, Wageningen University & Research is one of the leading organisations in its domain. The unique Wageningen approach lies in its integrated approach to issues and the collaboration between different disciplines.

Read the 5 reasons why your future colleagues enjoy working at WUR and watch the video below to get an idea of our green campus!

We will recruit for the vacancy ourselves, so no employment agencies please. However, sharing in your network is appreciated.

For more information about this function, please contact Astrid Bryon (staff member of the WU Laboratory of Virology; astrid.bryon@wur.nl) and Anne Kupczok (staff member of the WU Bioinformatics Group; anne.kupczok@wur.nl) by e-mail. Applications are only accepted using the apply button on the vacancy page.

For more information about the procedure, please contact vacaturemeldingen.psg@wur.nl.

General information about the Bioinformatics Group can be found on https://wur.eu/BIF. General information about the Laboratory of Virology can be found on https://wur.eu/VIR.

Do you want to apply?
You can apply directly by uploading your CV and motivation letter, using the apply button on the vacancy page on our website which will allow us to process your personal information with your approval.
This vacancy will be listed up to and including Monday 10 June 2024. We hope to schedule the first job interviews on 21 and 22 June 2024.

In this first round, please only send your resume and motivation letter. Any other documents will not be taken into consideration at this stage.

Equal opportunities
Wageningen University & Research (WUR) employs a large number of people with very different backgrounds and qualities, who inspire and motivate each other. We want every talent to feel at home in our organisation and be offered the same career opportunities. We therefore especially welcome applications from people who are underrepresented at WUR. A good example of how WUR deals with inclusiveness can be read on the page working at WUR with a functional impairment.