PhD position in Microbial Community Genomics

PhD position in Microbial Community Genomics

Published Deadline Location
24 Apr 25 May Wageningen

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Job description

This project is part of the Gravitation Research Program SIAM - Soehngen Institute of Anaerobic Microbiology ( The PhD project will be developed at the Laboratory of Microbiology at Wageningen University & Research (WUR) under the supervision of Prof. Dr. Thijs J. G. Ettema.

Anoxic sediments host a wide diversity of microbial groups that are poorly characterized. Most of these groups currently lack cultured representatives, limiting detailed inferences about the physiological and cell biological properties of these lineages. One of such clades is the Asgard archaea, a deeply-branching archaeal superphylum that currently represents the closest prokaryotic relative of eukaryotes in the Tree of Life (e.g. see Spang et al, Nature 521, 173-178 (2015) & Zaremba -Niedzwiedzka et al. Nature 541, 353-357 (2017)). The aim of the current project is to employ various genomics strategies to gain insight in the physiology and metabolism of selected Asgard archaeal lineages that reside in anoxic environments. The PhD candidate will obtain sediment samples and isolate DNA to determine the microbial community composition using 16S rRNA amplicon sequencing and genome-resolved metagenomics analyses. In parallel, the PhD candidate will isolate community RNA and proteins from these sediment layers, which will be analysed using transcriptomics and proteomics approaches. Furthermore, enrichment cultures will be initiated and monitored using various advanced genomic and metabolic analyses. The collected genomic, transcriptomic and proteomic datasets will be used to investigate the physiology and genomic activity of Asgard archaeal lineages that reside in anoxic sediments.

We are looking for
We are looking for a highly motivated and curiosity-driven PhD candidate with an interest in microbiology, specifically on the integration of various 'omics' approaches (metagenomics, transcriptomics, proteomics) to study the microbial physiology of prokaryotes in anoxic marine and hot spring sediments. The optimal candidate should have a strong background in microbiology and in handing biological datasets using bioinformatics analyses. Other important personal qualities include: intrinsic motivation, well-organized, good communication skills and social skills (team-player).


Wageningen University & Research


  • Master in Biology, Microbiology or Bioinformatics or a related field;
  • Knowledge of molecular methods and microbial physiology is essential;
  • Programming experience with a language such as Python or Perl is required;
  • Experience in bioinformatics and analyses of large biological datasets, such as (meta)genomics, proteomics and/or transcriptomics data, is beneficial;
  • Fluency in English (both spoken and written) is a requirement. For international applicants (non-native English speakers) it is necessary to have: TOEFL internet-based 90 with a minimum of 23 for speaking, or IELTS (academic version) 6.5, with a minimum of 6.0 for speaking;
  • Good communication and presentation skills are required, as well as the ability to work together in teams.

Conditions of employment

We offer you the opportunity to obtain your PhD in 4 years by giving you a temporary position for a period of 1.5 years with extension of 2.5 years after successful evaluation. Gross salary per month € 2325,- in the first year rising up to € 2972,- per month in the fourth year.

Apart from offering a competitive salary we also provide good conditions for (study) leave and a pension of the ABP Pension Fund.

You are expected to dedicate some of your time to teaching by supervision of BSc and MSc students, and by participation in teaching activities.


Wageningen University & Research

The group of Microbial Evolution, headed by Prof. Dr. Thijs J. G. Ettema was recently established within the Laboratory of Microbiology at Wageningen University (see for details).
The Laboratory of Microbiology is engaged in research and education in the diversity, evolution, ecology, cell biology and physiology of microorganisms. Moreover, it contributes to the exploitation of the generated knowledge in the application areas of Health & Food, Bioproducts & Energy and Environment & Sustainability. The Microbial Evolution group studies the diversity, physiology and evolution of prokaryotes by using state-of-the-art (meta)genomics and cultivation approaches.

The Agrotechnology & Food Sciences Group is part of Wageningen University & Research where fundamental and applied sciences complement each other. As an important European player, we carry out top-level research and work alongside authoritative partners within the international business world as well as the government on "Healthy food in a biobased society". We have a crucial role in innovations within the market. Entrepreneurship and professionalism are what define us. In short, we are an interesting, international employer of stature.

Wageningen University & Research
Delivering a substantial contribution to the quality of life. That's our focus - each and every day. Within our domain, healthy food and living environment, we search for answers to issues affecting society - such as sustainable food production, climate change and alternative energy. Of course, we don't do this alone. Every day, 5000 people work on 'the quality of life', turning ideas into reality, on a global scale.

Could you be one of these people? We give you the space you need.

For further information about working at Wageningen University & Research, take a look at

Acquisition regarding this vacancy is not appreciated.


  • PhD
  • Natural sciences
  • max. 38 hours per week
  • University graduate
  • 499406


Wageningen University & Research

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