Linking soil microbiome with increased crop and food quality
Soil microbiomes are increasingly recognized as a key driver of sustainable agriculture, not only because they support crop productivity, but also because they can influence the nutritional quality of our food. Soil physicochemical properties (such as organic matter, pH, nutrient availability, and structure) interact closely with soil microbial communities, shaping nutrient cycling and plant–microbe interactions. However, the relationships between soil microbiome composition, soil properties, and final crop nutritional quality remain insufficiently understood.
This PhD project aims to investigate how soil microbiomes and physicochemical soil conditions jointly influence plant development and food quality. The project will explore whether targeted soil inputs, such as amendments, biofertilizers, and/or microbial inoculants, can steer these interactions toward improved plant health and enhanced the nutritional value of our crops. The work will contribute to the development of evidence-based strategies for sustainable farming.
Research challenges
Although many soil amendments and biological products are commercially available, how they influence plant performance and nutritional quality, but also how they influence the soil microbiome, and in turn, how this influences plant nutritional quality is often inconsistent across soils, crops, and environmental conditions. One key challenge is to identify groups of organisms in the microbiome that influence the nutritional quality of the plant and to find ways to stimulate these microbes. Another challenge is that soil microbiomes are complex and resilient ecosystems: introduced microorganisms may fail to establish, and the effects of amendments can vary depending on existing microbial communities and soil chemistry. This project aims to move beyond causal relationships and work towards actionable activities that can realistically increase food quality at field scale such as improved management practices or detection tools.
Your assignment
You will collect and analyze soil and plant samples from crop field and you will also design and perform controlled experiments to evaluate how different soil inputs (including amendments, biofertilizers, and microbial inoculants) influence soil physicochemical properties and soil microbial community dynamics. You will assess plant performance and quantify food quality parameters, with a focus on nutrient content and relevant food quality indicators.
Using a multidisciplinary approach, you will integrate microbiome analysis with soil chemistry and plant chemical measurements, aiming to identify key mechanisms and interactions. You will measure micronutrients with ICP techniques and specific nutritional characteristics with GC and HPLC techniques. The project will be developed in collaboration with research partners and is expected to include interaction with industry stakeholders, allowing alignment with real-world agricultural needs and opportunities for implementation. You will be located at Wetsus, in Leeuwarden, and you will be registered as PhD candidate at Leiden University.
Your profile
You hold an MSc degree in soil science, biology, ecology, environmental sciences, microbiology, biotechnology, agronomy, plant sciences, or a related field. You have an interest in experimental work and interdisciplinary research. Experience with soil or plant analysis, microbial ecology, molecular biology techniques, or plant growth experiments is considered a plus. You are motivated to work in an applied research environment and collaborate with both academic and industry partners.
Keywords: Soil ecology, soil microbiome, plant nutritional quality, plant chemistry, soil amendments, microbial inoculation, food quality, sustainable agriculture
Professor/University group/Wetsus supervisor(s):
University promotor and co-promotor: Prof. Dr. Martijn Bezemer;
Wetsus supervisor(s): Dr. Ángel Velasco Sánchez
Project partners: Soil
Only applications that are complete, in English, and submitted via the application webpage before the deadline will be considered eligible.
Guidelines for applicants: https://phdpositionswetsus.eu/guide-for-applicants/
