2025-B24 Linking oak genetics and the microbiome: effects on plant growth and disease suppression

Project highlights

Plant genotype can influence the recruitment of beneficial microorganisms

This phenomenon is barely understood in tree species

This project investigates links between oak genetics and microbiome composition and its role in health and disease

Overview

Trees are essential components of terrestrial biomes but face significant threats from climate change and disease. Plant genomes encode genes associated with disease resistance and susceptibility, but due to the sessile and long–lived nature of tree species, they are disproportionately impacted by climate change and encounters with pathogens that they have not co-evolved with. In recent years, numerous studies have demonstrated the importance of plant–associated microbiota in extending the phenotypic repertoire of plant hosts, including microbial-mediated plant beneficial traits such as growth promotion, stress tolerance and disease suppression. Multicellular tree hosts and their associated microbiota may therefore express a variety of phenotypes (e.g. stress tolerance). Recent studies have also demonstrated that specific plant genes can shape the assembly and function of microbial communities in the plant host. Consequently, understanding the link between plant genetics and the encoded metabolic pathways that direct the assembly of the plant–associated microbiome provides new opportunities to identify tree genotypes with desirable traits such as resistance to disease and environmental stress. Whilst this interaction has been observed for model plant and crop species, the links between tree genetics and microbiome assembly is barely understood. This collaborative and interdisciplinary project will utilise oak genome data and microbiome profiles for the same individual oak trees, already generated by the supervisory team, to identify oak genotypes associated with specific microbial taxa. Subsequently, the impact of oak genotype on microbiome assembly (recruitment of inoculated microorganisms) and beneficial traits (growth promotion, drought tolerance, and disease resistance) will be validated experimentally in controlled glasshouse experiments with oak seedlings of known genotype. This project is a partnership between the University of Birmingham, Kew Gardens and Forest Research and will provide the candidate with a multidisciplinary training in tree health. Engineering tree microbiomes through the selection of host genotypes that direct the recruitment and assembly of beneficial microbiota is an important emerging area of research with potential to enhance the success of tree planting initiatives and safeguard global forest biomes and the societal, ecological and economic services they provide.

Figure 1: Collection of oak leaf tissue samples at a woodland site for oak genome and microbiome analysis.

Host

University of Birmingham

Theme

Climate and Environmental Sustainability
Organisms and Ecosystems

Supervisors

Project investigator

Prof James McDonald (University of Birmingham; [email protected])

Co-investigators

Prof Richard Buggs (Kew Gardens; [email protected])
Dr Sandra Denman (Forest Research; [email protected])

How to apply

Each host has a slightly different application process.
Find out how to apply for this studentship.
All applications must include the CENTA application form.
Choose your application route

Methodology

This project combines field, laboratory and computational approaches in both microbiology and plant biology to address an important knowledge gap surrounding the link between tree genetics and microbiome composition. The candidate will apply a range of techniques, including computational analysis of oak genome and microbiome data, propagation of oak seedlings for glasshouse experiments, metabolome analysis of oak accessions, working with oak-associated microbial cultures using our extensive isolate collection and setting up glasshouse experiment to test the impact of oak genotype on microbiota recruitment, plant growth, stress tolerance and disease suppression.

Training and skills

DRs will be awarded CENTA Training Credits (CTCs) for participation in CENTA-provided and ‘free choice’ external training. One CTC can be earned per 3 hours training, and DRs must accrue 100 CTCs across the three and a half years of their PhD.

The PhD candidate will join a dynamic research partnership enabling a diverse and interdisciplinary training in a variety of skills and techniques, including computational analysis of oak genome and microbiome datasets, working with microbial isolates and culture collections, glasshouse experiments with oak seedlings, metabolome analysis of oak tissue samples, and oak infection assays. The project may also include fieldwork in oak woodlands in the UK. The candidate will also have access to training opportunities (genome/microbiome analysis), seminars, symposia and research events at the partner institutions and opportunities to present their research at appropriate research conferences and workshops with project partners.

Partners and collaboration

This project is a partnership between the University of Birmingham (James McDonald – oak microbiome), Kew Gardens (Richard Buggs – oak genomics) and Forest Research (Sandra Denman – oak pathology), with support from Action Oak. The candidate will be primarily based in James McDonald’s group at the University of Birmingham but will be co-supervised and supported by project partners at Kew Gardens and Forest Research. There will be opportunities to visit both external partners for training and completion of project tasks and for interaction with the supervisory team’s wider network of collaborators.

Further details

For further details regarding this PhD position, please contact Prof. James McDonald ([email protected])

Supervisor webpages:

Professor James McDonald – School of Biosciences – University of Birmingham

Professor Richard J A Buggs | Kew

Sandra Denman – Forest Research

 To apply to this project: 

You must include a CENTA studentship application form, downloadable from: CENTA Studentship Application Form 2025.

You must include a CV with the names of at least two referees (preferably three) who can comment on your academic abilities.

Please submit your application and complete the host institution application process via: https://sits.bham.ac.uk/lpages/LES068.htm.   Please select the PhD Bioscience (CENTA) 2025/26 Apply Now button. The CENTA Studentship Application Form 2025 and CV can be uploaded to the Application Information section of the online form.  Please quote CENTA 2025-B24 when completing the application form.

 Applications must be submitted by 23:59 GMT on Wednesday 8th January 2025.  

Possible timeline

Year 1

Computational identification of plant gene-microbial taxon co-occurrence and metabolic pathways responsible.

Experimental validation of oak metabolome differences associated with each genotype.

Year 2

Glasshouse experiment to validate microbial recruitment based on tree genotype/metabolome.

Data analysis, preparation of manuscript(s) for publication, thesis writing.

Year 3

Glasshouse experiment to validate impact of oak genetics and microbial recruitment on (i) plant growth, (ii) drought tolerance, (iii) disease resistance.

Data analysis, preparation of manuscript(s) for publication, thesis writing.