PhD position on modelling of anaerobic synthetic communities

Gepubliceerd op
7 mei 2018
Locatie Wageningen
Expertisegebied Natural Sciences
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We are looking for

The Netherlands Organisation for Scientific Research (NWO) Domain Applied and Engineering Sciences (AES), recently granted a four-year research project “Syngas to High-Value Chemicals” within the context of the NWO program 'Closed cycles - Transition to a circular economy' ( This project involves research groups from the University of Wageningen & Research (WUR) and from the University of Amsterdam (UvA). The aim of the project is to develop combined biological and chemical/enzymatic processes for the production of chemicals from syngas or carbon-monoxide rich waste streams. There will be three PhD candidates working on the project each of them focused on: (1) wet-lab approaches and physiology of anaerobic mixed cultures, (2) dry-lab approaches, namely the construction and validation of multiple genome-scale constraint-based, (3) chemical and enzymatic upgrading of the molecules generated in the biological process.

Syngas is an alternative feedstock for fermentation; a vast array of carbonaceous materials, including recalcitrant wastes or lignocellulosic materials, can be used to produce syngas. Syngas fermentation is a sustainable alternative to conventional sugar-based fermentation. Research performed within this project will advance knowledge on the functioning of synthetic microbial communities, and open new possibilities for syngas fermentation. We will develop processes to produce a range of alcohols (and fatty acids ) [such as propanol, butanol, hexanol, heptanol, nonanol and their corresponding acids], which are currently produced mainly through chemical approaches. Long-chain alcohols and organic acids are building block for the chemical industry and key compounds for biobased (CO2-neutral) jet fuels. A major innovation lies in the model-driven, modular construction of synthetic microbial consortia to increase the product range/versatility so that different module (microorganism) combinations can be used for converting different gaseous mixtures or creating different interdependencies.

The PhD project (2), open for application, will be developed at the Laboratory of Systems and Synthetic Biology (SSB) and the Laboratory of Microbiology (MIB) at Wageningen University & Research.

Vitor Martins dos Santos, Peter Schaap (WUR-SSB); Diana Z. Sousa (WUR-MIB)

We are looking for
We are searching for an enthusiastic and motivated PhD candidate to perform dry-lab activities within project (2). Dry-lab tasks include: construction of multiple genome-scale constraint-based (CB) metabolic models, validation of CB models with experimental data, analysis of carbon-flows (and other metabolites) in the consortia, generation of hypotheses for improving the performance of the microbial consortia.

We ask

- Master in Bioinformatics / Computational Biology with strong computational/bioinformatics affinity.
- knowledge on bioinformatics, genome and transcriptome analyses, metabolic modelling.
- Knowledge on anaerobic microbial physiology as  is a plus.
- Fluency in English (both spoken and written).
- Good communication and presentation capabilities.

We offer

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 € 2222,- in the first year rising up to € 2840,- per month in the fourth year. 

We not only offer a competitive salary but also good (study) leave and a pension of the ABP Pension Fund.

More information

For more information about this position, please contact Dr. Peter Schaap, associate professor,  telephone number +31 317485142.
For more information about the contractual aspects, please contact Mrs. J. van Meurs, HR advisor, telephone number +31 317480101.

You can apply online at until the 30th of May 2018.

Please submit:
- motivation letter, including interests, and strong scientific abilities,
- curriculum vitae including degree certificates, abstract of master thesis,
- A minimum of two references we can contact directly.

Interested candidates should submit their application containing the above mentioned documents in one PDF file at

Review of applications will be done until end of May or until an optimal candidate is selected.

We are

The Agrotechnology & Food Sciences Group is part of Wageningen University & Research, an organisation that brings together fundamental and applied scientific research. We work on creating ‘healthy food in a biobased society’ with private sector companies, research institutes and government agencies in the Netherlands and abroad. Our innovations play a crucial role in solving the major issues which affect society today. Entrepreneurship and professionalism are key in all that we do. In short, we are a major international employer offering considerable potential for your career.

Wageningen University & Research
Delivering a substantial contribution to the quality of life. That's our focus – each and every day. Within our domain of good and safe food & food production, food security and a healthy 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.

The Laboratory of Systems and Synthetic Biology (SSB) at the Wageningen University develops and applies theoretical frameworks supporting experimental research towards the systems understanding of the hierarchies and dynamics of cellular networks. These frameworks are used for directed cellular reprogramming, with applications to health, industry and the environment. The lab has made acknowledged contributions to large-scale genome engineering of designer microbes and to cellular-reprogramming for the tailored production of valuable chemicals and deagradation of toxic compounds.

We are the group of Microbial Physiology within the laboratory of Microbiology (MIB) of Wageningen University.The Laboratory of Microbiology is engaged in research and education in biotransformations and interactions of microorganisms as well as their control. Moreover, it contributes to the exploitation of the generated knowledge in the application areas of Health & Food, Bioproducts & Energy and Environment & Sustainability. Microbial physiology group is especially interested in microbial transformations in anoxic conditions with strong interest in syntrophy, reductive respiratory processes and bioproduction of interesting molecules.

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.