Postdoctoral Fellow in Computational Rhizobiome Analysis

Utrecht University


Postdoctoral Fellow Computational Rhizobiome Analysis, Utrecht University

Job description

Plants are key to future food security, but crop yields are threatened by climate change, anthropogenic input, and emerging pathogens. Beneficial root-associated microbes form a promising solution by protecting plants against stress and disease, but field applications are lagging behind due to varying ability of beneficial bacteria to colonize and survive in the rhizosphere. Ground-breaking experimental and computational approaches are opening up new possibilities to study the interactions between microbes and the plant and contribute to designing rhizosphere competent beneficial inoculants.

As a Postdoctoral Fellow you will work at the intersection of data science and plant-microbe interactions, embedded in two state-of-the art research groups. Within our interdisciplinary team, you will contribute to developing and applying innovative computational approaches to understand the rhizosphere microbiome. You will integrate diverse meta’omics big datasets, focusing on identifying traits that allow microbes to survive and thrive in the rhizosphere. By interpreting the identified traits in the context of cross-domain species interactions, you will make specific predictions about enhancing the functionality of beneficial microbes and contribute to preparing plants against future threats.


To excel in this role, you have:

an excellent scientific profile;
experience turning big data into knowledge;
translated bioinformatics to experiments and vice versa;
a PhD degree where computational analyses played a central role.

Collaboration with a great team and private partners including Novozymes;
Necessary support on all aspects of the project;
Full-time position for 2 years, part-time appointment can be discussed;
Full-time gross salary ranging from €3,255 to €4,274;
Benefits including 8% holiday bonus and 8.3% end-of-year bonus;
Pension scheme, partially paid parental leave, and flexible employment conditions based on the Collective Labour Agreement Dutch Universities.

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About the organization
In your future team, you will join an interdisciplinary and international team consisting of computational biologists, bioinformaticians, and plant microbiome researchers. You will benefit from collaborations with private partners to translate your promising results into applications. TBB: Many advances in biology are made possible by innovative computational analyses and models. Scientists in the Theoretical Biology and Bioinformatics group use bioinformatics, big data, and computational modelling to address fundamental questions in the life sciences. A selection of ongoing research lines includes metagenomics and viromics, host-microbiome modelling, root morphogenesis, and the principles of ecology and evolution.

Recent key publications:
Von Meijenfeldt et al. (2019) "Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT", Genome Biology 20: 217. DOI: 10.1186/s13059-019-1817-x.
Garza et al. (2018), "Towards predicting the environmental metabolome from metagenomics with a mechanistic model", Nature Microbiology 3: 456-460. DOI: 10.1038/s41564-018-0124-8.
Speth et al. (2016), "Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system", Nature Communications 7: 11172. DOI: 10.1038/ncomms11172.

PMI: Researchers in the Plant-Microbe Interactions group focus on understanding the fundamental mechanisms of plant-pathogen interactions, plant immunity and defense, and beneficial microbes. With our fundamental research, we contribute to developing sustainable, rational microbiome engineering strategies for next-generation crops.

Recent key publications:
Stringlis et al. (2018) “MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health”, PNAS 115: E5213-E5222. DOI: 10.1073/pnas.1722335115.
Berendsen et al. (2018) “Disease-induced assemblage of a plant-beneficial bacterial consortium”, ISME Journal 12: 71-173. DOI: 10.1038/s41396-018-0093-1.
Stringlis et al. (2018) “Microbial small molecules–weapons of plant subversion”, Natural Products Report 35: 410-433. DOI: 10.1039/C7NP00062F.

Utrecht University is a friendly and ambitious university at the heart of an ancient city. We love to welcome new scientists to our city – a thriving cultural hub that is consistently rated as one of the world’s happiest cities.

We are renowned for our innovative interdisciplinary research and our emphasis on inspirational research and excellent education. We are equally well-known for our familiar atmosphere and the can-do attitude of our people.

This fundamental connection attracts professors, researchers and PhD candidates from all over the world, making both the University and the Faculty of Science a vibrant international and wonderfully diverse community. The UU Faculty of Science is located at the Uithof campus just east of the city center. Research focus areas include Bioinformatics and Future Food.

Additional information
If you have any questions, please contact:
• Dr. Bas E. Dutilh:
• Dr. Ronnie de Jonge:

Everyone deserves to feel at home at our university. We welcome employees with a wide variety of backgrounds and perspectives. Are you interested?

Please apply for the position by clicking on the “Apply” button, enclosing:
• a letter of motivation;
• a curriculum vitae;
• names, telephone numbers, and email addresses of at least two references;
• a copy of your PhD certificate, or a letter from your university stating when your defence will take place.

If this specific opportunity isn’t for you, but you know someone who may be interested, please forward the link to them.

The application deadline is

In your application, please refer to


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