Two PhD positions Plant-Microbe Interactions (1.0 FTE)

The successful applicant will work as a PhD student on a NWO Green II-funded project entitled "Unearthing beneficial microbe rhizosphere competence traits in vivo". The selected candidate will work under supervision of Dr. R. de Jonge at the Plant-Microbe Interactions group.


The NWO Green II call focuses on research that provides the basis for a ground-breaking system change aimed at realising resilient and integrally sustainable plant and animal production systems, higher food security, and the conservation of nature and ecosystem services in the Netherlands.

The project summary is as follows:

Fixation of solar energy in plants through photosynthesis drives all life on our planet. Up to 20% of the carbohydrates produced by photosynthesis are released into the soil, making plants central players in the belowground food web. In nature, plant roots live in close association with countless microbes, also known as the root microbiome. Beneficial microbes provide plants with important services, such as enhanced nutrient uptake and protection against diseases. Because of their potential to sustainably improve crop production, increasingly microbial products are registered for biofertilization and biological control purposes in agriculture. However, despite their promise under controlled conditions, bioinoculant efficacy can vary in the field. This can be caused by variable environmental conditions that influence microbial performance, unidentified negative interactions with local microbiome communities, or a suboptimal match with plant genotype. Hence, an in-depth understanding of the microbial traits that influence rhizosphere competence is urgently needed for the development of more persistent microbial products for future crop improvement.

In this interdisciplinary project, which besides Utrecht University also involves Novozymes, world leader in the market of bioinoculants, we will combine microbial genetics, microbiome metagenomics, computational modelling and molecular plant biology to discover: microbial rhizosphere competence traits that influence the success of bioinoculants, root microbiomes traits that affect rhizosphere competence of bioinoculants, and the mechanisms by which root exudates affect plant-beneficial microbe interactions.

The two, successful PhD candidates will develop high-throughput, sequencing-based, microbial trait identification methodologies for beneficial microbes, based on transposon mutagenesis, gain-of-function expression libraries and experimentally evolved microbes to identify microbial rhizosphere competence traits in the context of naturally occurring microbial communities. Thus, experience in, and affinity with microbial molecular techniques, and computational/bioinformatics analyses of high-throughput sequencing data are imperative.