Project Highlights

  • Forests are critical for carbon sequestration but threatened by climate change
  • You will study the response of trees and associated microorganisms to a rise in atmospheric CO2
  • Access a unique research infrastructure and become part of a multidisciplinary project

Climate change is arguably the biggest threat to our forest ecosystems. It is critically important that we understand its impact as forests influence soil, water, temperature and light regimes as well as providing habitats for a large number of animals, birds and insects. Importantly, forests have a dramatic impact on carbon sequestration, absorbing as much as 30% of annual global anthropogenic CO2 emissions (Pan et al. 2011), approximately the same amount as the oceans. Current carbon sequestration models are controversial, either predicting that photosynthetic sequestration will match current CO2 emissions from fossil-fuel consumption/deforestation; or respiration will double current CO2 emissions (Friedlingstein et al. 2009). However, these models fail to consider the impact on forest ecosystems, the forest microbiome and consequently forest health. Elevated CO2 could modify pathogen profiles, decouple tree innate immunity and alter carbon metabolism (and hence potential nutrient resources for invading and beneficial microbes).

Currently, the best way to simulate long term elevated CO2 levels on plant ecosystems (predicted to be ~1020 ppm by 2100; C4MIP) uses Free-Air CO2 Enrichment (FACE) facilities. Most studies, primarily on crops, show that elevated CO2 levels typically result in enhanced plant growth and higher water use efficiency, but are confounded by genotype x environment interactions. Elevated CO2 can lead to a decrease in stomata density and stomatal aperture (Grimmer et al. 2012; Israelsson et al., 2006), both contributing to restricting pathogen ingress. We hypothesise that elevated CO2 will directly impact host disease susceptibility, but this needs to be validated in the context of changes in pathogen profiles, the impact on phyllosphere communities and the associated changes in the leaf metabolome.

This project will exploit unprecedented access to Birmingham University’s highly instrumented forest FACE facility – unique in the northern hemisphere - to simultaneously study the impact of elevated CO2 on the forest phyllosphere community and leaf metabolome. We will explore both temporal changes in phyllosphere communities as they adapt to elevated CO2 conditions and associated changes in the leaf metabolome, integrating a range of automatically captured biophysical data. This is only possible as we can access material prior to starting the CO2 enrichment.

BIFoR FACE facility, Staffordshire showing 
the 6 experimental rings.


The BIFoR FACE located in 150year-old Oak/Hazel woodland (Fig. 1) is globally unique and provides unprecedented opportunity to study the impact of elevated CO2 on forests and their microbial communities. It comprises nine 30 m diameter experimental plots: 3 treatment; 3 control; 3 no-infrastructure controls.

Critically, we have access to material BEFORE CO2 enhancement, and the subsequent 4 years. Samples will be collected (professionally) from canopy, south, north and sub-canopy locations three times/year (3[plots] X 4[spatial samples/plot] X 3[replicates] X 3[plots]).

Given the potential large biological variation, individual trees will be sampled in each plot but replicates will comprise pooled samples. Phyllosphere profiling and untargeted metabolite profiling will be undertaking using established methods in the Grant/Schaefer/Song groups. Control vs no-infrastructure reports inherent variation whereas comparisons with treatment plots reports how the phyllosphere communities and leaf metabolism changes both in the initial year and subsequent years after elevated CO2 treatment.

Training and Skills

This is a truly multidisciplinary project involving large data generation, visualisation and interpretation. It also requires collaborating with physical scientists and integrating diverse data sets. Full training will be provided in RNA extraction and library generation (MG); small molecule extraction and sample preparation for metabolite profiling (MG), phyllosphere data analysis (HS), metabolite data analysis (LS) and physical data integration (RMcK). In addition, the student will spend 10 days at the University of Exeter studying database integration and RNA data analysis with Assoc. Prof. David Studholme.

CENTA students are required to complete 45 days training throughout their PhD including a 10 day placement. In the first year, students will be trained as a single cohort on environmental science, research methods and core skills. Throughout the PhD, training will progress from core skills sets to master classes specific to CENTA research themes.


Year 1: Sampling and learning sample extraction methods (RNA & small molecule) on mock samples established before processing growing season 2017 & 2018 and pre-CO2 application. RNA extraction from leaves for phyllosphere will also capture the leaf transcriptome. Decisions will be made later whether this resource will be analysed. Freeze dried material extracted for metabolite analysis and a baseline oak leaf metabolome established.
Database created on existing QNAP network associated storage device. Possibly targeted metabolite analysis considered.

Year 2: Growth season 2019 sampled. Samples processed and data analysed. First opportunity to compare impact of CO2 addition to metabolome and transcriptome. First opportunity to look at impact of sampling time on phyllosphere communities.

Year 3: Growing season 2020 analysed. Intensive data analysis using pipelines established in years 1 & 2. Detailed comparisons across and between growth seasons and across leaf developmental stages during growth seasons. Integrate metabolome and phyllosphere communities to look for discriminatory signatures. Identify signatures associated with metabolites and leaf age, including how these signatures are altered by increased CO2 . Work with Birmingham to integrate physical metadata (temp, rainfall, leaf temperature, sunshine, transpiration).
Generate a model explaining impact of high CO2 on forest microbiomes. Link microbiome communities to metabolites, stomatal response and prelevance of phytopathogens,

Partners and collaboration (including CASE)

This is an unprecedented opportunity to study the impact of elevated CO2 on Northern Hemisphere temperate oak forest through collaboration the Birmingham University’s BIFoR FACE facility, which is unique in the world. This highly instrumented site will be subject to intense analysis by international experts in both the physical and biological sciences in a research programme co-ordinated by Birmingham. Our project exploits a niche not addressed by our collaborators’ expertise and hence adds value to an international effort and consequently benefits from significant added value in on-going data collection and analysis (see Year 3 work programme).

Further Details

Murray Grant (M.Grant@warwick.ac.uk) or
Hendrik Schäfer (H.Schaefer@warwick.ac.uk).

School of Life Sciences
University of Warwick, Coventry, CV4 7AL