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

Requirements:

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

Salary Benefits:

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

38 hours per week

De Boelelaan 1105