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Tree microbiomes in a changing climate

  • Full or part time
  • Application Deadline
    Monday, January 06, 2020
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Plant pathogens pose major challenges to the production of crops and in the resilience of our trees and forests. How we protect plants from their most damaging pathogens is therefore vital to a future of sustainable agriculture within a healthy ecosystem. The Kettles laboratory combines molecular biology and protein biochemistry with computational approaches to study what makes bacterial and fungal phytopathogens so adept at causing disease. We also investigate how the immune systems of both crops and trees function to repel pathogens, and how this could be improved to enhance disease resistance.

We have recently established a research program that focuses on diseases of oak trees. The two oak tree pathosystems we study are the bacterial complex associated with acute oak decline (AOD) disease and the oak powdery mildew fungus Erysiphe alphitoides. In addition, the Birmingham Institute of Forest Research (BIFoR) is host to the only Free-Air CO2 Enrichment (FACE) experiment in the northern hemisphere (Hart et al. 2019). This unique experiment immerses a native woodland, dominated by 150 yr-old oak trees, in a high-CO2 environment anticipated to exist decades from today. The BIFoR-FACE experiment provides a fantastic opportunity to ask how this futuristic atmosphere alters tree physiology and the interactions of trees and the environment.

Plant tissues are colonised by complex communities of microorganisms (microbiomes) that perform functions critical to plant health (Vorholt 2012). Colonised tissues range from the aerial leaves and stems (phyllosphere) to underground root networks (rhizosphere). Microbiome disruption can lead to the opening of niches that allow proliferation of opportunistic pathogens. This project will use a combination of culture-based techniques and high-throughput sequencing (HTS) to assess how oak tree microbiomes adapt to an atmosphere rich in CO2. Phase one of this project will involve sampling material from both above- and below-ground oak tissues inside the BIFoR-FACE experiment and analysing microbiome composition by HTS approaches. We are interested in how tree microbiomes acclimate both over a single growing season, and after exposure to several years of CO2 enrichment. Phase two of the project will examine, at the mechanistic level, how changes in microbiome composition can have direct impact on tree health. This will include investigation into nutrient acquisition by trees and in direct protection from opportunistic tree pathogens. These experiments will be performed in growth cabinets and newly-constructed glasshouses capable of replicating the high CO2 environments at BIFoR-FACE.
This project will allow the student to develop diverse expertise in the areas of microbial ecology, plant pathology, bioinformatics and the development of microbial synthetic communities. Applications are encouraged from graduates in the following disciplines: plant biology, microbiology, biochemistry and computer science.

For informal enquiries, please contact Dr Graeme Kettles (). Please state the project title on any email enquiries.

Funding Notes

This project has been shortlisted under MIBTP 2020 PhD projects. MIBTP is a BBSRC funded Doctoral Training Partnership (DTP) between the University of Warwick, the University of Birmingham, the University of Leicester, Aston University and Harper Adams University.

For more details, visit; View Website


1. Hart et al. Glob Chang Biol. 2019 Aug 3. doi: 10.1111/gcb.14786.
2. Vorholt JA. Nat Rev Microbiol. 2012 Dec;10(12):828-40. doi: 10.1038/nrmicro2910.

How good is research at University of Birmingham in Biological Sciences?

FTE Category A staff submitted: 42.80

Research output data provided by the Research Excellence Framework (REF)

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