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Understanding the languages of plant-microbe combat

Primary Supervisor: Dr Graeme Kettles, School of Biosciences

Secondary supervisor: Dr Megan McDonald (Project 1), Rob Jackson (Project 2), Dawn Arnold (Harper Adams, Project 3)

PhD project title: Understanding the languages of plant-microbe combat

University of Registration: University of Birmingham

Project outline:

Plant pathogens pose major challenges both to crop production and to the resilience of natural ecosystems. How we protect plants from their most damaging pathogens is therefore vital to a future of sustainable agriculture.

The Kettles laboratory combines molecular biology, protein biochemistry and computational approaches to study what makes fungal and bacterial phytopathogens so adept at causing disease. We investigate how the plant innate immune system functions at the molecular level and how it could be enhanced to prevent infections.

The model systems we use in the lab are the wheat-infecting fungus Zymoseptoria tritici, the oak powdery mildew fungus and the bacterial complex associated with acute oak decline (AOD) disease. Several PhD projects are currently available on the following topics;

Project 1. How do plants recognise fungal effector proteins?

Successful pathogens secrete virulence proteins (effectors) during plant colonisation. Effectors are highly diverse, often uncharacterised proteins that function to suppress immunity or disrupt plant cellular function. Previous work has revealed that effectors from the wheat pathogen Zymoseptoria tritici are differentially recognised during infection of either host (wheat) or non-host plants1. This project will investigate the extent to which effector recognition contributes to disease resistance in this pathosystem. This will be performed by investigating; (1) the functions of Z. tritici effectors during interaction with both host and non-host plants, (2) assessing effector diversity and impact on function across global Z. tritici populations, and (3) identifying effector recognition and immune signalling components in plants. This project will allow the student to gain expertise in plant biochemistry, functional genomics and plant pathology.

Project 2. Microbe-microbe warfare in the phyllosphere

Plants are colonised by complex communities of microorganisms (microbiomes) that perform functions critical to plant health2. Natural microbiomes offer protection from pathogens, whilst disruption of these communities can lead to opportunities for pathogen proliferation3. Most work to date has focussed on the roles of soil microbiomes in plant health, whilst the roles of above-ground microbiomes are comparatively understudied. This project will focus on the above-ground (phyllosphere) microbial communities that colonise plants. The overall aim is to understand the molecular language that microbes within the phyllosphere use to ensure their own survival. Using both the wheat-Z. tritici and oak-AOD pathosystems, this project will examine how bacterial and fungal phytopathogens are able to manipulate microbiomes to their advantage, and the role that secreted virulence proteins (effectors)4 play in this process.

Project 3. Tree microbiomes in a changing climate

The Birmingham Institute of Forest Research (BIFoR) is host to the only Free-Air CO2 Enrichment (FACE) experiment in the northern hemisphere. This experiment immerses 150 yr-old oak trees in a CO2-rich environment anticipated in exist decades from today. How does this futuristic, high-CO2 environment alter plant physiology, and what are the knock-on effects for the microorganisms that inhabit these trees? This project will utilise high-throughput microbiome sequencing and microbial synthetic community experiments to assess how oak tree microbiomes are acclimating to this changing atmosphere. It is anticipated this will have significant consequences for pathogen susceptibility and overall tree health.

For any informal enquiries, please contact Please state on the application form the project number for which you are applying.


  1. Kettles et al. New Phytol. 2017 213(1):338-350.
  2. Vorholt et al. Nat Rev Microbiol. 2012 10(12):828-40.
  3. Berg & Koskella. Curr Biol. 2018 28(15):2487-2492.e3.
  4. Kettles et al. New Phytol. 2018 Jan;217(1):320-331.

BBSRC Strategic Research Priority: Sustainable Agriculture and Food: Plant and Crop Science ☒

Techniques that will be undertaken during the project:

All projects listed feature both wet-lab and computational components. Students will gain extensive experience of functional genomics, molecular biology, biochemistry, fungal and bacterial pathogen handling and techniques associated with protein expression and purification. In addition, we have in place pathogen bioassays for testing virulence of all pathogens used in the lab.

Contact: Dr Graeme Kettles, University of Birmingham