Engineering microbial consortia in green house crops using sustainable carriers
The plant-associated microbiome plays a fundamental role in plant growth, resilience to stress, nutrient acquisition, and overall crop quality. Beneficial microorganisms have therefore attracted increasing attention as nature-based solutions to improve crop performance in a sustainable way. However, despite promising laboratory results, microbial inoculation strategies often fail under realistic conditions because introduced strains do not persist. In many cases, inoculated microorganisms are rapidly outcompeted by native microbial communities, limiting their long-term impact.
This PhD project aims to develop engineering solutions for effective steering and targeted inoculation of plant microbiomes. The central hypothesis is that successful microbiome engineering depends not only on the selection of beneficial strains, but also on delivery methods, ecological compatibility, and the design of suitable carrier systems.
Research challenges
One of the major challenges in microbial inoculation is the low establishment of introduced microorganisms in complex water, soil and rhizosphere environments. Native microbiomes are very robust, resilient and redundant and environmental fluctuations further reduce inoculum survival. In addition, the choice of carrier material strongly influences microbial viability, colonization efficiency, and spatial distribution in the root zone.
A systematic evaluation of inoculum formulation, carrier materials, and ecological interactions is therefore needed. Understanding how introduced microorganisms interact with resident communities — whether through competition, cooperation, or niche differentiation — is key to designing robust inoculation strategies that deliver measurable benefits to crop health and nutritional quality.
Your assignment
You will investigate the establishment and performance of selected beneficial microbial strains or consortia under controlled conditions at different scales (laboratory, greenhouse and field). Different carrier materials such as extra-polymeric substances and inoculation approaches will be tested to evaluate their influence on microbial survival, colonization, and functional impact on plants and soils. Alternatively, you will develop slow-release systems for dedicated inoculation strategies. The project will combine microbiological experiments including molecular and analytical techniques to monitor microbiome dynamics and plant responses, with designing and engineering new release systems
The work will contribute to the development of effective and scalable nature-based technologies for sustainable crop production and will be in close collaboration with plant growers.
Your profile
You hold an MSc degree in microbiology, biotechnology, plant sciences, environmental sciences, soil sciences or a related discipline. You have an interest in biotechnological engineering, microbial ecology and experimental research. Experience with molecular biology techniques, microbiome analysis, or plant–microbe interaction studies is considered an advantage. You are motivated to work at the interface of fundamental microbiology and applied agricultural innovation.
Keywords: Microbiome engineering, microbial inoculation, carrier materials, plant–microbe interactions, sustainable agriculture, microbial ecology, nature-based solutions, soil
The team
University promotor/University group: prof. dr. ir. Martijn Bezemer. Leiden University
Wetsus co-promotor and daily supervisor: dr. Inez Dinkla
Wetsus senior advisor: dr. Caroline Plugge
Project partners: Engineered soil amendments – Wetsus
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/
