PhD Studentship: Designing Functional SynComs for Sustainable Agriculture

UK only

This 3.5-year PhD is fully funded by The University of Manchester for UK (Home) students only. Funding for this project covers tuition fees, UKRI minimum annual stipend (currently £20,780/annum) and up to a £2.5k/annum research training support grant. The PhD student can start in April 2026 or October 2026. 

Beneficial soil microbes can boost plant growth and help crops defend themselves against insect pests such as aphids, which cause damage by removing nutrients and spreading viruses. As chemical pest control becomes increasingly unsustainable due to environmental impacts and rising pest resistance, alternative strategies are urgently needed. Microbial inoculants offer a promising solution and form a rapidly growing sector in agriculture. However, their success in the field remains inconsistent. This is often because current approaches focus on adding lots of microbial diversity rather than identifying the specific microbial functions and network interactions that truly drive plant resilience.

With only a small fraction of soil microbial functions currently understood, there is a clear need to design evidence-based, functionally coherent microbial consortia to support sustainable agriculture in a changing climate.

Project Focus

Our research investigates beneficial rhizobacteria, which are root-associated microbes that improve plant nutrient uptake and trigger defence responses against pests. Using barley (Hordeum vulgare) as a model crop, we have shown that applying individual beneficial strains that suppress aphids can reshape the wider rhizosphere microbiome, recruiting additional helpful taxa from the soil.

This PhD project builds on that work by examining how single-strain inoculations initiate and structure microbial networks around plant roots. By identifying key interactions and functional synergies, you will design and test multi-strain microbial communities (SynComs) with consistent, predictable benefits for plants growing in complex soil environments.

Aims and Objectives

The overall aim is to design functional multi-strain inoculants that improve plant health across variable environments. As the PhD researcher, you will:

1. Use an existing culture library to test strain compatibility and co-inoculation effects, focusing on plant defence responses to aphids.
2. Identify additional soil bacteria that respond to inoculation with a focal strain, using BONCAT-FACS—an approach that labels and isolates the microbes that are actively growing or responding at the time of inoculation—together with root exudate profiling.
3. Design and test multi-strain synthetic microbial communities (SynComs) for plant growth and defence, and examine how well these communities transfer to other crop species.

Applicants should hold, or be about to obtain, a minimum upper second-class undergraduate honours degree (or equivalent) in a relevant discipline such as biology, ecology, microbiology, plant sciences, bioinformatics, or data science. The project is particularly suitable for students with experience or interest in plant–microbe interactions from an ecology or microbiology background, who are keen to develop computational and multi-omics skills. Likewise, students with a computational or data science background who have a strong interest in ecological and plant–microbiome questions and wish to gain lab-based experience are encouraged to apply. Candidates should demonstrate analytical thinking, curiosity for interdisciplinary research, and the ability to integrate experimental and computational approaches.

We recommend that you contact the main supervisor for this project before you apply; Dr Sharon Zytynska - sharon.zytynska@manchester.ac.uk. Please include details of your current level of study, academic background, and any relevant experience, along with a short paragraph outlining your motivation for pursuing this PhD project.

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