PhD Position on Predictive Plant–Microbiome–Pathogen Interactions

How does the microbiome surrounding a plant determine whether a pathogen can successfully invade? And can we predict disease outcomes from microbiome composition and plant phenotypes? Join us as a PhD candidate to investigate how the potato microbiome influences interactions with two major plant pathogens: Phytophthora infestans and Ralstonia solanacearum. You will combine high-throughput plant phenotyping, microbiome profiling, predictive modelling and targeted experimental validation to identify the microbial factors that make plants more resilient to disease.

Your job
You will join the Plant-Microbe Interactions group and work within the NWO Vici project ResistoBiome: Predictive microbiome modelling for resilient and sustainable potato cropping systems.

In this project, you will investigate why the same pathogen can cause severe disease in one microbial environment but establish poorly in another. You will work with a unique collection of 100 Dutch agricultural soil microbiomes and grow potato plants in the automated phenotyping facilities of the Netherlands Plant Eco-phenotyping Centre (NPEC). Using high-resolution imaging, you will follow plant growth, physiology and disease development after infection with Phytophthora or Ralstonia.

You will combine these phenotyping data with bacterial and fungal microbiome profiles to build predictive models of pathogen invasion and plant performance. Working in close collaboration with with a postdoctoral researcher and a fellow PhD candidate, you will identify microbial taxa and microbial interactions that are most strongly associated with disease resistance or susceptibility.

A key part of your project will be to move from prediction to biological understanding. You will select promising microbes emerging from the models, isolate and experimentally test them, and investigate how they influence pathogen establishment and plant health. This will allow you to ask not only which microbes predict disease outcomes, but also why they matter.

During your PhD, you will:

• perform large-scale potato experiments using 100 contrasting soil microbiomes;
• use automated high-throughput phenotyping to quantify plant growth, physiology and disease development;
• profile root and leaf microbiomes using amplicon sequencing;
• analyse integrated microbiome and phenotyping datasets;
• contribute to machine-learning models predicting pathogen invasion success and plant resilience;
• identify microbial taxa and interactions associated with contrasting disease outcomes;
• isolate and experimentally validate selected candidate microbes;
• design follow-up experiments to understand how protective microbes influence plant–pathogen interactions;
• collaborate closely with researchers in microbiology, plant pathology, phenotyping, bioinformatics and predictive modelling.

The project gives you the opportunity to work across scales: from thousands of plants and complex microbiome datasets to mechanistic experiments with individual microbial isolates.