Professor James McDonald

Supervisor Details

Contact Details

Professor James McDonald

School of Biosciences, University of Birmingham

Scientific Background

Research Interests

Research in Professor McDonald’s group focusses on the following broad themes:

Investigating the role of the oak microbiome in health and disease, characterising microbial disease suppression, engineering the oak microbiome to future-proof tree health and combat tree disease.
Characterising the microbial processes of waste biomass conversion to biogas in landfill sites and anaerobic digestion plants to develop engineered microbiomes for enhanced waste conversion to biogas.
Integrating knowledge on microbiome engineering and microbiome science across diverse systems (e.g. plants, humans, industrial systems) to identify key scientific principles that underpin microbiome assembly and function.

Supervision Style

In three words or phrases: Supportive; committed; focussed on your development as a researcher.

Provision of Training

In my lab we apply a variety of techniques to address our research goals. Consequently, training will be provided by a combination of myself, co-supervisors, or other experienced postgraduates or postdocs in our research teams, or through attending external training courses. In some instances, there will be a need to learn and develop new skills or methods independently, with support from myself and the team.

Progression Monitoring and Management

I am a ‘hands on’ supervisor and like to maintain regular contact with my team members to hear how the research is progressing. My aim is to help you to reach your full potential and I will support you on that journey. I will also expect you to take ownership of your project and drive it forward, with support from myself and the team.

Communication

Strong communication is critical for a successful research team. Our research group interacts via a full team lab meeting every 4 weeks, and fortnightly 1-to-1 meetings with me (or small group meetings for researchers working on the same project) in addition to ad hoc meetings when required and informal updates and during the week (either in person, or via Email or WhatsApp). We also have a lab WhatsApp group and socialise outside of work both as a research team and with other research groups.

PhD Students can expect scheduled meetings with me:

In a group meeting

At least once a week

In year 1 of PhD study

At least once a week

In year 2 of PhD study

At least once a fortnight

In year 3 of PhD study

At least once a fortnight

These meetings will be a mixture of face to face and via video chat or telephone, and I am usually contactable for an instant response (if required) every working day.

Working Patterns

Work in my lab requires being present on site (be it in a laboratory or at a field site) during the core hours.

Notice Period for Feedback

I need at least 1 week's notice to provide feedback on written work of up to 5000 words.

MIBTP Project Details

Current Projects (2025-26)

Primary supervisor for:

Discovery of antimicrobial compounds associated with disease suppression in plants

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Discovery of antimicrobial compounds associated with disease suppression in plants

Secondary Supervisor(s): Professor Helen Cooper

University of Registration: University of Birmingham

BBSRC Research Themes: Understanding the Rules of Life (Microbiology, Plant Science)

Project Outline

The plant microbiome is vital for plant growth, stress tolerance and pathogen suppression. Recently, the disease-suppressive potential of plant-associated microbiota, mediated by the production of metabolites and proteins that are inhibitory to plant pathogens, has been widely reported in plants. These microbe-microbe interactions play a critical role in microbiome dynamics in the context plant health and disease but have barely been studied in tree species such as oak. Native oak trees in Britain are currently under threat from Acute Oak Decline (AOD), a complex decline disease driven by environmental stressors such as drought, bark-boring beetle activity and stem tissue necrosis caused by several bacterial species including Brenneria goodwinii and Gibbsiella quercinecans. Currently there are no available treatments for AOD, but antimicrobial compounds produced by disease-suppressive plant microbiota represent one option to manage this disease.

We have identified several bacterial species that are strongly associated with healthy oak trees, and using agar-based co-culture assays, identified >300 bacterial isolates from healthy oak trees that have suppressive activities against three bacterial species associated with necrotic lesion tissue formation in AOD (B. goodwinii, G. quercinecans, Rahnella victoriana).

The aim of this project is to identify and characterise the antimicrobial compounds responsible for the disease suppressive phenotypes observed in these bacteria. The project will provide important insights into the role of antimicrobial compounds in disease suppressive microbiomes and develop potential treatments for AOD.

The candidate will utilise a range of methods in microbiology and mass spectrometry including liquid and agar-based bacterial co-culture assays, genome analysis, gene knock-out experiments and mass spectrometry approaches to address the following research objectives:

1. Use bacterial co-culture assays to identify and measure the effects of antimicrobial compounds produced by oak microbiota on the inhibition of bacteria causing AOD.

2. Use mass spectrometry approaches to identify the compound(s) responsible for disease suppression.

3. Validate the antimicrobial activity of identified compounds.

The University of Birmingham (UoB) is a top 100 global university (QS World University Rankings, 2024). The successful candidate will join a dynamic and multidisciplinary research team with access to excellent academic expertise and facilities, a vibrant and diverse community of researchers, professional development opportunities, seminars and workshops. The studentship will provide a broad intellectual training in microbiology, mass spectrometry and plant health, opportunities to develop new skills and techniques, but importantly, will embolden the candidate to contribute their own ideas and expertise. Our team occupies newly refurbished laboratories within the School of Biosciences (~55 group leaders) and is part of two cross-University institutes; the Institute of Microbiology and Infection (IMI, ~44 group leaders), and the Birmingham Institute of Forest Research (BIFoR). The project is supported by access to world-leading facilities, including the £2m Wolfson advanced glasshouse facility, a BBSRC-funded high-throughput microbiology platform and the Advanced Mass Spectrometry Facility in the School of Biosciences.

References

Denman S, et al. (2018) Microbiome and infectivity studies reveal complex polyspecies tree disease in Acute Oak Decline. The ISME Journal 12: 386–399. https://doi.org/10.1038%2Fismej.2017.170.

Matsumoto H, et al. (2021). Bacterial seed endophyte shapes disease resistance in rice. Nature Plants 7, 60–72 https://doi.org/10.1038/s41477-020-00826-5.

McDonald JE, et al. Application of ecological and evolutionary theory to microbiome community dynamics across systems. Proceedings of the Royal Society B: Biological Sciences 2020; 287: 20202886. https://doi.org/10.1098%2Frspb.202.

Previous Projects (2024-25)

Primary supervisor for:

Synthetic microbial communities for anaerobic digestion of waste to biogas

Co-supervisor on a project with Dr Lucy Crouch.

Previous Projects (2023-24)

Primary supervisor for:

Establishing universal principles for invasion of the microbiome in the context of disease