Project highlights

  • Part of a multi-institutional experimental forest research network, offering diverse training opportunities (Birmingham Institute of Forest Research, UKCEH)
  • Provide foundational data to quantify and describe the biodiversity of the fungal endophyte community at BIFoR Free Air Carbon Enrichment Facility
  • Gain skills in Next-generation sequencing techniques and their applications in ecology and biodiversity, including MinIon long-read sequencing.
  • Interdisciplinary application of transcriptomics and cutting-edge isotope methods to understand differences in carbon and nitrogen metabolism and cycling in fungal endophyte communities under ambient and elevated C02.


As global atmospheric concentration of CO2 continues to rise, the question remains how will mature forests respond to either help or hinder carbon capture via photosynthesis and carbon sequestration subsequently. The Free Air Carbon Enrichment (FACE) experiment at the Birmingham Institute of Forest Research, seeks to answer this question by exposing a mature forest to elevated CO2 (+150 ppm above ambient levels) mimicking the atmosphere of the future (2050 and onwards). The first key results from this 10-year experiment indicates that the dominant oak trees exposed to eCO2 have a sustained elevated photosynthetic response, ~23% higher than trees in the ambient CO2 plot. Coupled with this increase in CO2 uptake rates, and fine root biomass and exudation of carbon by roots into soil have also increased. These changes in carbon allocation belowground can affect the symbiotic fungal communities associated with the dominant tree in relation to the symbiotic trade-offs between the trees and fungal communities. Trees offer organic carbon to fungi and fungi help in soil nutrient acquisition for trees. Thus with the observed changes induced by eCO2, it is very likely that the composition and activities of fungal endophytes will change. How such changes will affect fungal community size and eventually nutrient cycling? This studentship will thus evaluate changes in fungal endophytes communities composition, carbon metabolism and nutrient cycling as influenced by future climates to help support climate change mitigation policies.


This PhD project will answer these questions by identifying the number of different fungal species present in soils at the  BIFoR FACE site. This project will address three major knowledge gaps 1) What is the baseline fungal diversity in a mature Oak woodland and is this changing in response to eCO2? 2) What is the most common root endophyte associated with Oak trees? 3) Are root endophytes responding differently to eCO2 when compared to control arrays and how it affects carbon metabolism of fungi and eventually nutrient availability to trees?

Photo of Oak roots in situ with colonisation by endophytes and mycorrhizal fungi.

Figure 1: Photo of Oak roots in situ with colonisation by endophytes and mycorrhizal fungi. Photo courtesy of Claire Hewitt, Artist.

CENTA Flagship

This is a CENTA Flagship Project


University of Birmingham


  • Climate and Environmental Sustainability
  • Organisms and Ecosystems


Project investigator

Dr. Megan McDonald, University of Birmingham ([email protected])


How to apply


Fungal endophytes will be collected from leaves and roots from Oak trees both within and outside of the BIFoR FACE treatment rings. These endophytes will be cultured on selective media using established protocols. Endophyte species will be identified using ITS-sequencing. The most abundant species will be selected for whole-genome sequencing and assembly using the Oxford Nanopore Minion. Genome annotation will be performed using standard fungal gene annotation pipelines.

To study the function and contribution of these endophytes to nutrient cycling in the soil, roots will be collected from BIFoR FACE and flash froze for RNA extraction. In parallel, the availability of key macronutrients including nitrogen, phosphorus, potassium, magnesium, sulphur and calcium in soils will be quantified to fully ascertain the role of symbiotic fungi in helping trees acquire nutrients under future climate.

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.

This project will require the student to gain skills in fungal ecology, coupled with high-throughput genomics and transcriptomics. The lead Supervisor M. McDonald is an expert on fungal genome assembly, annotation and in planta transcriptomics. Therefore the student will gain skills in the molecular identification of fungal species, long-read genome sequencing and assembly. The final part of the project will link together soil nutrient cycling with transcriptomics, giving the student a cross-disciplinary skillset in both fungal genomics as well as soil science.

Partners and collaboration

This studentship benefits from access to the only global temperate forests Free Air Carbon Dioxide Enrichment (FACE) facility and infrastructure (>£20million) ( and the Forest Ecology and and UKCEH-Lancaster). This studentship will benefit from the high experimental costs of these projects and facilities, which is beyond the funding capacity of any single PhD studentship.

Further details

Megan McDonald:

Sami Ullah:

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_B4 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

  • Literature review and training in analytical instruments (chromatography, colorimetry, isotopes), transcriptomics, and experimental design at Birmingham. Introductory visits to the BIFoR-FACE in England.
  • Training in key laboratory and field research skills followed by sampling and culturing of root endophytes from BIFoR FACE.
  • Research plan finalisation including statistical design, sampling strategy and publication of a literature review paper.

Year 2

  • Culturing of pure fungal endophyte species from plant roots
  • Whole genome sequencing, assembly and annotation of most abundant fungal endophytes. Gathering of transcriptome samples and RNA extractions.
  • Nutrient availability profiles quantification.
  • Data analysis and compilation of results for publication.

Year 3

  • Analysis of RNA-sequencing data for transcriptomics analysis of fungal root endophytes
  • Continuation of nutrient mineralization, availability and root uptake preferences for different N forms.
  • Data analysis and compilation of results for publication.

Year 4:

  • Thesis write up, defence and publications.
  • Wider involvement with supervisor linked project partners offering further opportunities for pooling data within a multidisciplinary data pool potentially feeding into large synthesis papers and methodologies.

Further reading


Field work for this project will be outside at the BIFoR FACE facility in Staffordshire ( This outdoor location provides a safer and well ventilated working environment for taking samples. There is on-site office and well-being facilty at the FACE site. This facility is run and managed by the University of Birmingham. Throughout the pandemic the University has continuously managed the risks associated with the ongoing pandemic, by assessing persons limits in rooms as well as face coverings. These risk assessments will continue to be used throughout the PhD.