Project highlights

  • Microbiomes contribute significantly to plant health through provision of key nutrients and suppression of pathogens. How microbiomes ensure health of long-lived tree species is unknown.
  • This project will make use of the unique BIFoR-FACE climate change experiment to examine how oak tree microbiomes acclimate to an elevated CO2 (eCO2) world.
  • We will use synthetic microbial community experiments to assess how climate-induced changes in microbiome composition will impact future tree disease resistance.


Plant pathogens pose major challenges both to crop production and to the resilience of forest ecosystems. It is anticipated that changes in global climate will both expand the range of pathogens, and the severity of disease outbreaks. Therefore, how we protect plants from their most damaging pathogens is vital to a future of sustainable agriculture and forestry.

Plants are colonised by complex communities of microorganisms (microbiomes) that perform functions critical to plant health (Vorholt, 2012). Natural microbiomes offer protection from pathogens, whilst disruption of these communities can lead to opportunities for pathogen proliferation (Berg and Koskella, 2018).

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 a native woodland in an elevated CO2 (eCO2) atmosphere anticipated to exist decades from today. This mature, unmanaged temperate woodland consists predominantly of an upper canopy of 150 yr-old English oak (Quercus robur). It is one of only two forest FACE experiments worldwide, and the only one located in a temperate region. This facility allows us to assess the impact of eCO2 on all aspects of the forest ecosystem from carbon, nutrient and water cycling to susceptibility of trees to pests and disease. How does this futuristic, high-CO2 environment alter tree physiology? What are the knock-on effects for the microorganisms that inhabit these trees, and how does this impact forest resilience? This project will utilise high-throughput microbiome sequencing (16S/ITS) and microbial synthetic community experiments to assess how oak tree microbiomes are acclimating to the changing atmosphere in the BIFoR-FACE experiment. It is anticipated that changes in the oak microbiome will have significant consequences for pathogen susceptibility and overall tree health.

The Kettles laboratory combines molecular ecology, protein biochemistry and computational approaches to study bacterial and fungal plant pathogens. Students in our laboratory will gain from exposure to a broad range of methods used to understand plant-microbe interactions.


University of Birmingham


  • Organisms and Ecosystems


Project investigator

  •  Graeme Kettles, University of Birmingham



  •  Rob Jackson, University of Birmingham

How to apply


This project will make use of the unique resource of the BIFoR-FACE facility as a sample archive of oak tree material. Tree samples will be made both through single growing season, from bud burst in spring to leaf fall in autumn, over several years spanning the duration of the project. We will sample from three tree compartments (leaf, stem and root) and profile the microbial communities present in each tissue using 16S/ITS DNA sequencing. We will learn how microbiomes assemble in different oak tissues, both over single growing seasons, and how they change over several years. We will use culture-dependent methods to isolate specific species present in the microbiome for in-depth analysis in synthetic community type experiments. The Kettles laboratory already maintain culture collections of >400 microbial species isolated from oak and we have developed laboratory based bioassays for the study of microbe-microbe interactions.

Training and skills

The successful student will gain experience of microbial ecology through the sampling, processing and analysis of metabarcoded DNA sequence libraries. A significant component of this work will involve computational analysis of high-throughout DNA sequencing data using QIIME or other programming languages (R, Python). Some background in bioinformatics or computational biology would therefore be beneficial but not essential. The project also involves wet-lab microbiological techniques used to assess microbe-microbe interactions, plus standard molecular biology techniques such as qRT-PCR and bacterial mutagenesis.

Partners and collaboration

The student will be hosted in the Kettles laboratory in the School of Biosciences at the University of Birmingham. The student will benefit from both wet-lab and computational expertise within the group and will initially work closely with the PI (Kettles) and a PDRA (Dr Thomas Welch). Several other groups that study plant-microbe interactions (Jackson, Luna-Diez, McDonald) are active in the school, and we regularly exchange information on methods and expertise. The student will integrate into the cross-college BIFoR community of researchers, and will also benefit from cutting-edge microbiology expertise from the Institute of Microbiology & Infection (IMI).

Further details

For informal enquiries, please contact

Further information on our group’s research can be found here (

Applications need to be submitted via the University of Birmingham postgraduate portal,, by midnight 11.01.2021. Please first check whether the primary supervisor is within Geography, Earth and Environmental Sciences, or in Biosciences, and click on the corresponding PhD program on the application page.

This application should include

  • a brief cover letter, CV, and the contact details for at least two referees
  • a CENTA application form
  • the supervisor and title of the project you are applying for under the Research Information section of the application form.

Referee’s will be invited to submit their references once you submit your application, but we strongly encourage applicants to ensure referees are aware of your submission and expecting a reference request from us. Students are also encouraged to visit and explore the additional information available on the CENTA website.

Possible timeline

Year 1

Optimisation of sampling strategy and DNA extraction methods from stem, leaf and root of trees at BIFoR-FACE. Harvest and DNA extraction of sample material from spring 2022 onwards, at regular intervals for duration of project. Creation of additional culture collections from the BIFoR-FACE samples.

Year 2

Analysis of 16S/ITS DNA sequencing datasets from beginning of year 2. Depending on prior student experience, additional training will be available for this activity.

Year 3

Synthetic microbial community experiments (using culture collections) to be performed using oak seedlings grown in normal and eCO2 conditions. These will be performed using the purpose-built glasshouse complex at Elms Road, or controlled-environment rooms in Biosciences.

Further reading

Berg M, Koskella B. 2018. Nutrient- and Dose-Dependent Microbiome-Mediated Protection against a Plant Pathogen. Current Biology 28(15):2487-2492.e3.

Vorholt JA. 2012. Microbial life in the phyllosphere. Nature Reviews Microbiology 10: 828–840.


Given the woodland setting of the BIFoR-FACE experiment, social distancing is easily achieved and tree sample collection will not be impacted by COVID-19 restrictions. The remainder of the project will be conducted in the Kettles laboratory in the School of Biosciences. Since our laboratory reopened in June, we have been following strict COVID-secure operations both at the individual lab and school level. This includes limits on lab capacity, cleaning rotas and other practices to minimise contact with coworkers whilst allowing research to proceed.