PhD Position on Phage Ecology in Microbial Communities

Microbial communities are essential to the functioning of ecosystems, from the oceans to the human gut. Within these communities, phages infect vast numbers of bacteria every day and outnumber bacteria about 10 to 1. Currently, we lack a quantitative understanding for how phages impact community composition and function, and conversely, how a complex community context shapes the action of phages on their specific hosts.

In this PhD project, you will study marine bacteria and their phages in isolation and in communities, from simple synthetic communities to enrichments of natural communities. Combining high-throughput characterization methods and state-of-the-art bioreactor technology with metagenomic sequencing and mathematical modelling, your research will lead to a quantitative understanding of the effects of phages on microbial communities and the ecosystem functions they provide. Beyond a better understanding of phage-bacteria interactions in marine microbial communities, this project will also yield insights and methods that will be applicable to other environments such as soils and industrially relevant communities (wastewater treatment, food microbiology), as well as for phage therapy to treat antibiotic resistant bacterial infections.

Your duties

• create and quantitatively characterize a phage bank for key marine bacteria
• measure the effects of phage infection in different community and environmental contexts
• obtain and analyze amplicon and metagenomic sequencing data
• optional: construct mathematical (kinetic) models of phage-bacteria interactions in complex communities
• assist in teaching, including the supervision of BSc and MSc internship students
• communicate your research in local and international conferences
• write a dissertation leading to a PhD degree towards the end of the 4-year project

This project is highly interdisciplinary; ideal candidates should have a subset of the required skills (microbiological/phage laboratory skills, programming, modelling, bioinformatics) and a strong willingness to learn new skills.

• you have a MSc or equivalent degree in systems biology, (micro)biology, (bio)physics, or a similar field
• you have good experimental skills, and preferably experience with basic microbiological laboratory skills
• you have experience with programming (e.g., Python, Mathematica or R)
• excellent ability to communicate in both spoken and written English

A challenging position in a socially involved organization. The salary will be in accordance with university regulations for academic personnel and amounts €2,541 (PhD) per month during the first year and increases to €3,247 (PhD) per month during the fourth year, based on a full-time employment. The job profile: is based on the university job ranking system and is vacant for at least 1 FTE.

The appointment will initially be for 1 year. After a satisfactory evaluation of the initial appointment, the contract will be extended for a duration of 4 years.
Additionally, Vrije Universiteit Amsterdam offers excellent fringe benefits and various schemes and regulations to promote a good work/life balance, such as:

• a maximum of 41 days of annual leave based on full-time employment
• 8% holiday allowance and 8.3% end-of-year bonus
• child daycare facilities available on campus
• optional model for designing a personalized benefits package

The ambition of Vrije Universiteit Amsterdam is clear: to contribute to a better world through outstanding education and ground-breaking research. We strive to be a university where personal development and commitment to society play a leading role. A university where people from different disciplines and backgrounds collaborate to achieve innovations and to generate new knowledge. Our teaching and research encompass the entire spectrum of academic endeavor – from the humanities, the social sciences and the natural sciences through to the life sciences and the medical sciences.

Vrije Universiteit Amsterdam is home to more than 31,000 students. We employ over 5,000 individuals. The VU campus is easily accessible and located in the heart of Amsterdam’s Zuidas district, a truly inspiring environment for teaching and research.

Diversity
We are an inclusive university community. Diversity is one of our most important values. We believe that engaging in international activities and welcoming students and staff from a wide variety of backgrounds enhances the quality of our education and research. We are always looking for people who can enrich our world with their own unique perspectives and experiences.

The Faculty of Science
Working at the Faculty of Science means working together with students, PhD candidates and scientists who are focused on their discipline, yet also have a broad view of the world. We are proud of the collegial working environment within the faculty, which is characterised by an ambitious and pragmatic attitude with commitment to the bigger picture. At the Faculty of Science, scientists and students work on fundamental and complex social issues for a sustainable and healthy future. From forest fires to big data, from obesity to malnutrition, from genetics to pharmaceuticals and from molecules to the moon: our teaching and research cover the full breadth of the natural sciences. Scientific teaching and research is highly experimental, technical, computational and interdisciplinary in nature. This is why we collaborate extensively with leading research institutes and industry. The faculty has over 11,000 students studying across 40 educational programmes and employs over 1,600 staff spread over 10 scientific departments, making us the largest science faculty in the Netherlands.
About the department, institute, project
The mission of A-LIFE is to advance the fundamental understanding of the interplay between life and its environment through innovative and curiosity-driven science. The department seeks to connect properties and emergent behaviours from micro to global scales, from molecules to ecosystems, including human populations. We aim to inspire our students and apply our expertise to shape a sustainable future and support healthy living.