PhD Studentship: Discovery of Antimicrobial Compounds Associated with Disease Suppression in Plants

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.

Funding Details

Additional Funding Information

This project is funded by the MIBTP. For details, see: https://warwick.ac.uk/fac/cross_fac/mibtp/phd/application/

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