Postdoc Position in AI: Foundation Models for Crop Microbiomes

successful crop microbiome engineering.

Your job

Plant-associated microbiomes can strongly influence crop growth, nutrition and resilience, but their behaviour depends on the crop, soil, environment and the surrounding microbial community. NOAH aims to make these context-dependent interactions learnable and predictable. At the centre of the project is ARCA (AI-guided Root microbiome engineering for ClimAte-resilient and nutritious crops), a crop microbiome foundation model trained on large-scale public and newly generated datasets.

As Postdoctoral Researcher in AI, you will take a leading technical role in developing ARCA. You will explore which model architectures and learning objectives work best for sparse, high-dimensional and heterogeneous microbiome data, and turn the selected approaches into robust trainable models. Your work will cover both foundation-model pretraining and downstream predictive and generative applications.

Your main responsibilities are to:

• design, implement and benchmark foundation-model architectures for microbiome data, including transformer-based and masked-autoencoder approaches and relevant architectures adapted from related biological domains;
• develop representations that integrate microbial identity and abundance with genomic or functional information and contextual metadata such as crop genotype, soil and environmental conditions;
• define and evaluate self-supervised learning objectives and embedding strategies, and benchmark their added value against simpler machine-learning baselines;
• train and evaluate ARCA on large-scale microbiome datasets, with attention to sparsity, batch effects, scalability, generalisation across studies and uncertainty in downstream predictions;
• fine-tune ARCA for tasks including microbial root competence and crop-relevant outcomes, and iteratively improve the model using experimental Design-Build-Test-Learn data generated by NOAH partners;
• develop a generative ARCA component, exploring autoencoder- and/or diffusion-based approaches for generating ecologically plausible microbiome configurations;
• apply interpretable and explainable AI approaches to identify microbial taxa, functions and contextual features driving model predictions;
• develop reproducible training and evaluation workflows and work with project partners to make models and associated tools usable beyond the immediate research setting.

You will not work on an isolated AI benchmark. ARCA predictions will be tested experimentally in greenhouse and field settings and the resulting microbiome and crop phenotype data will feed back into model development. This gives you the opportunity to develop new AI methodology while seeing how model predictions perform in a real biological and agricultural system.

In this position you will part of an interdisciplinary research environment spanning the AI Technology for Life and Plant-Microbe Interactions groups, with close interaction with bioinformatics, microbial ecology and experimental crop research at the UU and NOAH partners. You will have access to Utrecht University GPU/HPC infrastructure and large, curated microbiome and microbial genome datasets. Additionally, you will collaborate closely with NOAH partners at Aarhus University, Niab, INRAE and The Hyve, including experimental teams that will directly test model predictions.

Requirements

We are looking for a postdoctoral researcher who enjoys developing methods for complex biological data and working closely with experimental scientists. You meet the following criteria:

• a PhD, or a PhD close to completion, in machine learning, artificial intelligence, computational biology, bioinformatics, computer science or a closely related field;
• strong hands-on experience with deep learning and modern representation learning, preferably including transformers, self-supervised learning, foundation models, autoencoders or related architectures;
• strong programming skills in Python and experience with a deep-learning framework such as PyTorch, including training and evaluating models on GPU/HPC infrastructure;
• experience working with high-dimensional biological, omics, ecological or similarly sparse and heterogeneous data, or a clear motivation to develop this expertise;
• an interest in interpretable AI, rigorous benchmarking and reproducible research, together with the ability to collaborate across AI, bioinformatics, microbiology and crop science.

Experience with microbiome data, microbial genomics, metagenomics or multimodal biological data is an advantage, but is not required if you bring strong machine-learning expertise and are motivated to learn the biology.

Additional Information

Benefits

• a central role in developing ARCA, the core AI technology of the five-year EIC Pathfinder project NOAH;
• a position available from January 2027, initially for 1 year, extended with 3 years after a positive evaluation;
• a gross monthly salary, depending on qualifications and expereince, between €3.706 and €5.760 (salary scale 10 under the Collective Labour Agreement for Dutch Universities (CAO NU)). The salary is based on a 38-hour working week;
• 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 set out in our collective labour agreement, we offer attractive additional benefits, including opportunities for personal and professional growth, flexible leave arrangements, and extra vacation days. Through the UU Terms of Employment Options Model, you can tailor your employment package to your needs. In this way, we encourage you to grow in what you do, both in your work and in your development. Read more about our terms of employment.

Selection process

At Utrecht University, we strive to be a place where everyone feels at home. We value colleagues with different backgrounds, perspectives and identities, including differences in culture, religion or ethnicity, gender, sexual orientation, neurodiversity, disability and age. We are committed to creating a safe and inclusive environment where everyone can thrive and contribute. Read more about our commitment to diversity and inclusion. If you have any questions about accessibility, for example regarding your workplace Hugo R. Kruytgebouw, the application process or your work, please contact us via our HR contact page.

Knowledge security screening can be part of the selection procedures of academic staff. We do this, among other things, to prevent the unwanted transfer of sensitive knowledge and technology.

If you are enthusiastic about this position, apply via the “Apply now” button. Please enclose:

• your curriculum vitae, clearly demonstrating your relevant experience for this position (based on the criteria under “ Your qualities”;
• your letter of motivation, specifically explaining: (1) how your relevant, demonstrable expertise aligns with the project’s goals; (2) how you would approach the described task(s);
• the names and contact details of at least two references;
• a copy of your PhD certificate or a letter stating when your defence will take place.

If this specific opportunity is not for you, but you know someone else who may be interested, please forward this vacancy to them.

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Additional comments

For more information, please contact Dr Ronnie de Jonge at r.dejonge@uu.nl.

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