Bioinformatics Postdoc at UU/WUR: Map Metabolic Interactions in the Rhizosphere

Contribute to plant health and our understanding of the metabolic interactions between microbes and plants in the rhizosphere by computational modelling!

Job description

Are you a bioinformatician ready to start a postdoctoral fellowship to study metabolic interactions in the rhizosphere? We offer a joint position between two state-of-the-art bioinformatics research groups specialising in metabolism and metagenomics, with a shared interest in the plant-associated microbiome. The research groups are based at Utrecht University (UU) and Wageningen University & Research (WUR). Join us to work on computational approaches to study the interaction between microbes and the plant!

Your job
Plants are key to food security. Centuries of breeding has produced efficient and reliable crops, but little is known about the effects of domestication on the rhizobiome and the consequences for plant resilience to stress and disease. Ground-breaking experimental and computational approaches are opening up new possibilities to study the interactions between microbes and the plant. How does the plant recruit its microbiome and how do microbes colonise the roots?

As a postdoctoral researcher, you will contribute to developing and applying innovative computational approaches for analyzing primary and secondary metabolic traits in large genomic and metagenomic datasets from plant microbiomes. This will help elucidate how plants are able to recruit microbiomes with specific functions, and to design synthetic microbial communities to test the hypotheses resulting from these analyses. You will also collaborate with, co-supervise, and provide training for consortium partners, for example to interpret large metagenomic, metatranscriptomics and metabolomic datasets. This collaborative effort aims to advance our understanding of plant microbiomes. Together with other consortium members, our overall aim is to understand the role of microbial and plant metabolic interactions in shaping the rhizobiome, the response stress, and the microbial contributions to crop resilience in the face of a changing climate.

You will join an interdisciplinary and international team consisting of computational biologists and bioinformaticians at Utrecht University (UU) and Wageningen University & Research (WUR). This collaboration is part of MICROP, a government-funded research programme in the Netherlands that includes world-leading research institutes and private partners. You will benefit from interactions with a vibrant community of PhD candidates and postdocs who will jointly work on this topic, as well as from the rich datasets available within the consortium. The programme builds on and fosters many national and international collaborations with researchers studying plant and microbial metabolism, biotechnology, and (meta-) genomics.

You will be a member of two leading research groups: the Theoretical Biology & Bioinformatics group at UU and the Bioinformatics group at WUR. Your employment contract will be with UU, but the position involves close collaboration with WUR, ensuring active engagement with both teams.

Requirements

To excel in this role, you bring:

• a strong scientific profile with a relevant focus;
• experience with turning big data into knowledge;
• demonstrated experience with translating bioinformatics to experiments and vice versa;
• strong communication skills to ensure effective collaboration with consortium partners and smooth teamwork;
• a PhD degree where computational analyses played a central role.

Conditions of employment

We offer:

• collaboration with a great team and a large scientific consortium;
• necessary support on all aspects of the project;
• a full-time position for four years - initially a one-year contract with an extension for three more years after positive evaluation (part-time appointment of 0.8 - 1.0 FTE can be discussed);
• a gross monthly salary between €3,378 and €5,331 in the case of full-time employment (salary scale 10 under the Collective Labour Agreement for Dutch Universities (CAO NU));
• 8% holiday pay and 8.3% year-end bonus;
• a pension scheme, partially paid parental leave and flexible terms of employment based on the CAO NU.

In addition to the terms of employment laid down in the CAO NU, Utrecht University has a number of schemes and facilities of its own for employees. This includes schemes facilitating professional development, leave schemes and schemes for sports and cultural activities, as well as discounts on software and other IT products. We also offer access to additional employee benefits through our Terms of Employment Options Model. In this way, we encourage our employees to continue to invest in their growth. For more information, please visit Working at Utrecht University.

Employer

Universiteit Utrecht

A better future for everyone. This ambition motivates our scientists in executing their leading research and inspiring teaching. At Utrecht University, the various disciplines collaborate intensively towards major strategic themes. Our focus is on Dynamics of Youth, Institutions for Open Societies, Life Sciences and Pathways to Sustainability. Sharing science, shaping tomorrow.

Working at the Faculty of Science means bringing together inspiring people across disciplines and with a variety of perspectives and backgrounds. The Faculty has six departments: Biology, Pharmaceutical Sciences, Information & Computing Sciences, Physics, Chemistry and Mathematics. Together, we work on excellent research and inspiring education. We do so, driven by curiosity and supported by outstanding infrastructure. Visit us on LinkedIn and discover how you can become part of our community.

You will join the Theoretical Biology & Bioinformatics group (TBB) within the department of Biology: Many advances in biology are made possible by innovative computational analyses and models. Scientists in the TBB 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:

• López et al. (2023) "Growth rate is a dominant factor predicting the rhizosphere effect", ISME Journal 17: 1396-1405. DOI: 10.1038/s41396-023-01453-6.
• Hauptfeld et al. (2024) "Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes", Nature Communications 15: 3373. DOI: 10.1038/s41467-024-47155-1
• Von Meijenfeldt et al. (2023), "A social niche breadth score reveals niche range strategies of generalists and specialists", Nature Ecology and Evolution 7: 768-781. DOI: 10.1038/s41559-023-02027-7.

You will also be an active member of the Bioinformatics group (BIF) at Wageningen University & Research. The group focuses on fundamental and applied bioinformatics research in the green life sciences. In particular, they develop and apply novel computational methods for the analysis and integration of -omics data. The group has a strong track record in genome analysis, algorithm development and tool construction. An important research line focuses on plant microbiome analysis, and specifically the chemical language between plants and microbes, as well as between microbes mutually, that mediates microbiome-associated phenotypes of interest.

Recent key publications:

• Navarro-Muñoz et al. (2020) “A computational framework to explore large-scale biosynthetic diversity”, Nature Chemical Biology 16: 60-68. DOI: 10.1038/s41589-019-0400-9.
• Carrion et al. (2019) “Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome”, Science 366: 606-612. DOI: 10.1126/science.aaw9285.
• Jing et al. (2024) “Strategies for tailoring functional microbial synthetic communities”, The ISME Journal 18: wrae049. DOI: 10.1093/ismejo/wrae049.

Additional information

For more information, please contact Dr Bas E. Dutilh at b.e.dutilh@uu.nl or Dr Marnix H. Medema at marnix.medema@wur.nl.

Do you have a question about the application procedure? Please send an email to science.recruitment@uu.nl.