Project highlights

  • Climate change impacts on tree health
  • Microbial community changes due to climate change
  • Links between tree metabolome, microbial communities and disease.


Trees are foundation species on earth, forming a major part of the global biomass and provides habitat, important ecosystem services (e.g. carbon sequestration and soil stability) and conservation of biodiversity in both natural and man-made landscapes. However, climate change alters the distribution of tree pathogens and can impact tree immunity, collectively increasing the likelihood of new disease outbreaks.

One predicted element of climate change is increased atmospheric CO2 concentration ([CO2]) (reaching 550 μmol mol−1 in 2050). Elevated [CO2] (e[CO2]) levels affect tree growth, susceptibility and tolerance to diseases. It increases the rate of photosynthetic carbon fixation by leaves, which will lead to a large variety of secondary effects on plant physiology, such as faster growth, with more above- and below-ground biomass. eCO2 also leads to changes in the chemical composition of plant tissues such as decreasing leaf nitrogen concentrations.

Plant ecosystems rely heavily on their microbial communities to optimise health. It is well known that microbial species composition and abundance are closely related to plant growth, function and physiology of host plants. Plant-associated microbes are critical for plant’ tolerance to diverse stresses including pathogens by boosting plant defence responses, which could benefit plant resilience. However, the relationship between the diversity of microbial community and the changes of tree response to e[CO2] is largely unexplored. With the Birmingham Institute of Forest Research (BIFoR) Free Air Carbon Dioxide (FACE) facility and our collective expertise we are in the unique position to investigate e[CO2] effects on the diversity of microbial communities (bacteria/fungi/bacteriophage) on different tree species, and how these microbes interact with tree pathogens. We hypothesise that as trees grow larger under e[CO2] there may be higher microbial abundance, but that leaf chemistry compositional changes will alter the diversity of the microbes, potentially with a resultant negative impact in ability to suppress pathogen establishment. We will examine how individuals and microbial consortia interact with key pathogens, for example a polymicrobial consortium of Gram-negative Enterobacteriaceae (e.g. Brenneria sp., Gibbsiella sp., Rahnella sp.) that cause Acute Oak Decline (AOD). This approach is essential for making accurate predictions regarding future tree health and disease man

Images depicting Longitudinal stem lesion and canopy dieback caused by AOD, Colony morphology of the four bacterial species causing AOD grown on MacConkey agar and two tables showing the Relative abundance of the top 10 class divisions for bacteria and fungi of two species of oak leaves
Figure 1. Acute Oak Decline (AOD) is a complex disease of oak trees. Longitudinal stem lesion and canopy dieback caused by AOD (top left and centre). Colony morphology of the four bacterial species causing AOD grown on MacConkey agar (top right), clockwise from top-left: Brenneria goodwinii, Gibbsiella quercinecans, Rahnella victoriana and Raoultella planticola. Relative abundance of the top 10 class divisions for bacteria (bottom left) and fungi (bottom right) of two species of oak leaves (Roy, 2019).


University of Birmingham


  • Climate and Environmental Sustainability
  • Organisms and Ecosystems


Project investigator

Prof. James McDonald, School of Biosciences, University of Birmingham ([email protected])


Dr. Mojgan Rabiey, School of Biosciences, University of Birmingham ([email protected])

Prof. Rob Jackson, School of Biosciences, University of Birmingham ([email protected])

Prof. Murray Grant, Life Sciences, University of Warwick ([email protected])

How to apply


  1. Does diversity of microbial community differ under ambient and e[CO2]? Replicated leaf/soil samples will be collected from the various tree species. 16S/ITS rRNA amplicon next generation sequencing will be undertaken to catalogue resident bacterial/fungal OTUs and communities and to identify the presence of bacterial and fungal pathogens.
  2. Do culturable microbes isolated under ambient and e[CO2] impact pathogens differently? To understand the influence of e[CO2] on the microbial communities and potential suppression of pathogens, bacteria/fungi/bacteriophages will be isolated from the samples and their antagonistic activities against pathogens will be tested individually/as consortia.
  3. How does e[CO2] alter the leaf chemistry and microbial community composition? Collected leaves will be analysed by untargeted metabolomics to first identify unique chemical signatures of different trees under the ambient and e[CO2] then using consortia generated in objectives 1&2 above, profile microbial growth on different extracts (or combinations of compound) to determine altered biological/microbiological activity.

Training and skills

Students will be awarded CENTA2 Training Credits (CTCs) for participation in CENTA2-provided and ‘free choice’ external training. One CTC equates to 1⁄2 day session and students must accrue 100 CTCs across the three years of their PhD.

The student will receive specialist training for this multidisciplinary project, encompassing fieldwork, microbiology, genomics, metabolomics, data management and statistical analysis and interpretation of large and complex data sets.

The student will be supported to develop these skills within the School of Biosciences and BIFoR (Birmingham) and at the University of Warwick (metabolomics), allowing the student to excel in all of these aspects of data acquisition, analysis and dissemination and to build important networks.

The supervisory team is multi-disciplinary and highly experienced, based in excellent, well-equipped institutions, and will provide comprehensive support for the student across all aspects of the project.

Partners and collaboration

The University of Warwick is one of the world’s leading and internationally excellent in the Research Excellent Framework. School of Life Sciences at the University of Warwick is at the forefront of interdisciplinary research and teaching. Prof Murray Grant, base at Life Sciences at Warwick, is a world leading expert in plant-microbe interactions, metagenomic and metabolomics. Prof Grant will bring expertise in metabolomics to the project, especially for untargeted metabolomic pipelines his team has developed for understanding ash dieback disease, the results in which has been published in Nature, Scientific Data and Scientific Reports.

Further details

If you wish to apply to the project, applications should include:

  • A CV with the names of at least two referees (preferably three and who can comment on your academic abilities)
  • Submit your application and complete the host institution application process via: and go to Apply Now in the PhD Bioscience (CENTA) section. Please quote CENTA23_B2 when completing the application form.

Applications to be received by the end of the day on Wednesday 11th January 2023. 

Additional information for international applicants

  • All international applicants must ensure they can fulfil the University of Birmingham’s international student entry requirements, which includes English language requirements.  For further information please visit
  • Please be aware that CENTA funding will only cover University fees at the level of support for Home-fee eligible students.  The University is only able to waive the difference on the international fee level for a maximum of two successful international applicants.

Possible timeline

Year 1

Field experimental design and field data/sample collection training undertaken. Samples will be collected from BIFoR FACE under ambient and e[CO2], 4 times during the year from different tree species present including English Oak, common Hazel and Sycamore Maple. Also, there are Ash, Elm and Elder. DNA will be extracted from samples for metagenomic sequencing to assess microbial diversity. Samples will also be propagated to isolate bacteria, fungi, bacteriophages and pathogens.

Year 2

Antagonistic activity of isolated bacteria and fungi against pathogenic bacteria will be tested. Infectivity of bacteriophages against pathogenic bacteria will be examined. Metabolomic profiling of the same leaf samples used for amplicon sequencing will be undertaken. Data will be analysed and will be linked to microbial community diversity. Where analyses predict associations between metabolomic and metagenomic signatures, samples will be further analysed; e.g. growing the isolated bacteria and fungi at different media supplemented with the tree species leaf particles and whole genome sequencing will be done.

Year 3

Metabolomic analysis will be done to identify unique chemical signatures of different trees under the ambient and e[CO2] to profile microbial growth on different extracts to determine altered biological and microbiological activity. Year 3.5: Final analysis of the data, writing up of manuscripts and thesis will be done.

Field work will be done at the BIFoR FACE facility, a unique facility located within a mature broadleaf deciduous forest, the only such facility in the northern hemisphere. BIFoR FACE employs large‐scale infrastructure, in the form of lattice towers, forming ‘arrays’ which encircle a forest plot of ~30 m diameter. BIFoR FACE consists of three treatment arrays to e[CO2] by +150 µmol mol-1.

This project has a built-in resilience in the fieldwork, covering spring/summer/autumn and winter components of data collection over one year. Genomic and microbial biodiversity assessment of tree species will include DNA metabarcoding, metagenomics and metabolomic which will be analysed using multivariate analysis tools in R and BEAR platform. Additionally, the project involves isolating bacteria and fungi for further investigation of culturable microbial community in relation to social and spatial ecology, and assessment of the role of e[CO2] on microbial diversity in trees under current climate change scenario. Uniquely, the diversity, abundance and infectivity of phages under e[CO2] will be tested in this project. Phages are the most abundant microorganism on earth. They are naturally occurring viruses that obligately kill their bacterial host in order to replicate, therefore act as an effective antimicrobial agent and can potentially be used as biocontrol of bacterial diseases. Metabolomic profiling of collected leaves will be linked to metagenomic data. All these skills and experience will allow the development of the exhibition of student individual excellence.

Further reading

  • Broberg, M., Doonan, J., Mundt, F., Denman, S., and McDonald, J. E. (2018) ‘Integrated multi-omic analysis of host-microbiota interactions in acute oak decline’, Microbiome, 6: 21. doi: 10.1186/s40168-018-0408-5.
  • Hart, K. M., Curioni, G., Blaen, P., Harper, N. J., Miles, P., Lewin, K. F., Nagy, J., Bannister, E. J., Cai, X. M., Thomas, R. M., Krause, S., Tausz, M. (2020) ‘Characteristics of free air carbon dioxide enrichment of a northern temperate mature forest’, Global Change Biology, 26: 1023–1037. doi: 10.1111/gcb.14786.
  • Jiang, M., Wang, Z., Li, X., Liu, S., Song, F., and Liu, F. (2021) ‘Relationship between endophytic microbial diversity and grain quality in wheat exposed to multi-generational CO2 elevation’, Science of The Total Environment, 776: 146029. doi: 10.1016/j.scitotenv.2021.146029.
  • Rabiey, M., Roy, S.R., Holtappels, D., Franceschetti, L., Quilty, B.J., Creeth, R., Sundin, G.W., Wagemans, J., Lavigne, R., Jackson, R.W. (2020) ‘Phage biocontrol to combat Pseudomonas syringae pathogens causing disease in cherry’, Microbial Biotechnology, 13: 1428–1445. doi: 10.1111/1751-7915.13585.
  • Roy, S.R. (2019) ‘Evaluating the impact of tree provenance, tree phenotype and emergent disease on microbial and insect populations in tree ecosystems’, PhD Thesis, University of Reading.
  • Tcherkez, G., Mariem, S.B., Larraya, L.,  García-Mina, J.M.,  Zamarreño, A.M., Paradela, A., Cui, J., Badeck, F-W., Meza, D., Rizza, F., Bunce, J., Han, X., Tausz-Posch, S., Cattivelli, L., Fangmeier, A., Aranjuelo, I. (2020) ‘Elevated CO2 has concurrent effects on leaf and grain metabolism but minimal effects on yield in wheat’, Journal of Experimental Botany, 71(19):5990-6003. doi: 10.1093/jxb/eraa330.
  • BIFoR FACE (2022) ‘Impact of climate and environmental change on woodlands’. Available at: (Accessed: 24 July 2022).
  • Forest Research (2022) ‘Acute oak decline’. Available at: (Accessed: 24 July 2022).


In case of a lockdown, bioinformatic analysis will be employed to analyse bacterial and fungal community associated with trees, including trees present at BIFoR FACE. This will include collecting all 16S and ITS rRNA from sequence data base and publications. BEAR and R will be used to collate and analyse the data. Access to online training for both statistical analysis and BEAR will be provided at Birmingham. Comparison of data from different pathosystem/ tree species/ pathogens will be performed to understand which tree has the most abundant and diverse microbial community in both healthy vs diseased tissues.