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PhD projects

If you are interested in carrying out PhD research in my group, I would be pleased to hear from you before you submit an application.

For enquiries regarding the project, or to discuss other potential projects in my group, please feel free to email me at

Do tree microbiomes clean up urban air pollution?

Supervisors: Hendrik Schäfer, Gary Bending (School of Life Sciences) & James Covington (School of Engineering)

Carbon monoxide (CO) is a ubiquitous trace gas in the atmosphere that is produced by natural processes. It is also a significant anthropogenic air pollutant produced by combustion processes. As a toxic gas, it contributes to the high burden of premature mortality and morbidity caused by air pollution. Microorganisms play a crucial role in the removal of CO from the atmosphere and have previously been identified as abundant members of soil microbial communities (Cordero et al., 2019, King and Weber, 2007). Suprisingly, we recently found that CO-degrading bacteria are also found in the phyllosphere of trees (Palmer et al., 2021), which is defined as the above ground parts of trees and constitutes a huge microbial habitat. We showed that leaf washings from two common UK tree species, hawthorn and holly, had the potential to degrade CO, indicating the presence of CO-degrading microorganisms. We identified a wide diversity of candidate CO-oxidising bacteria in the phyllosphere community using cultivation independent approaches of microbial community analysis using 16S rRNA as a taxonomic marker and the gene encoding the large subunit of the carbon monoxide dehydrogenase (CODH, encoded by coxL) as a functional marker. Data mining of environmental phyllosphere metagenomes suggests that the bacteria containing genes for CO oxidation could constitute up to 25% of the phyllosphere microbial community. These findings suggest that phyllosphere microbiota with the potential to degrade CO could drive a significant and previously unrealised sink in the global CO cycle (Palmer et al., 2021). This project will build on those findings and aim to characterise CO degrading microorganisms more widely in above ground habitats including trees and mosses (Fig.1).

Figure 1. The principal aim of the project is to investigate if and how plant microbiomes
in the phyllosphere interact with air pollutants and may provide key ecosystem services.

You will assess the abundance and activity of CO-degrading bacteria associated with these habitats, test the potential for CO degradation and assess whether CO-degrading bacteria are active in situ. This will provide fundamental new insights into the distribution of CO-degrading bacteria in above-ground habitats and advance our understanding of the CO biogeochemical cycle. It may also lay the foundation for a mechanistic understanding of how phyllosphere microbiota may affect air quality, how air quality affects microbial activity, and it will potentially provide a basis for informed selection of tree species that could maximise microbial ecosystem services for mitigation of air pollution in urban areas.


Environmental materials (leaf and bark samples from a variety of trees, samples of mosses, soils) will be taken and analysed for their potential to degrade CO using gas chromatography (GC; equipped with methanizer and Flame Ionisation Detector).

Microbial diversity of sampled materials and of incubated materials showing CO degradation will be assessed using high throughput analysis of 16S rRNA encoding genes (taxonomic diversity), and sequencing of the genes encoding the large subunit of CODH (coxL) as described previously (Palmer et al., 2021). There is scope to attempt isolation of CO-degrading bacteria and to investigate the transcriptional activity of coxL genes using reverse transcriptase PCR to assess how environmental conditions affect activity of CO-degrading bacteria. Metagenomics approaches to further characterise uncultivated CO-degrading bacteria based on analysis of metagenome-assembled genomes will also be pursued.


COVID-19 Resilience of the Project:

The School of Life Sciences has robust risk assessment in place which should make a complete disruption of laboratory-based work unlikely. In the unlikely event that numbers of workers with simultaneous lab access will be capped again, we will be able to prioritise metagenomics work to obtain sequence data that can be analysed remotely using bioinformatics tools.


Possible timeline:

Year 1: Environmental sampling, CO degradation assays, isolation of CO-degrading bacteria (inc. genome sequencing), marker-based analysis of taxonomic and functional diversity

Year 2: Metagenomic sequencing of CO-degrading communities, transcriptional analysis of coxL in environmental samples

Year 3: Further data analysis, potential follow up work with CO degrading isolates (e.g., development of reporter strains), writing of manuscripts for publication

Further reading:

CORDERO, P. R. F., BAYLY, K., MAN LEUNG, P., HUANG, C., ISLAM, Z. F., SCHITTENHELM, R. B., KING, G. M. & GREENING, C. 2019. Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival. The ISME Journal, 13, 2868-2881.

KING, G. M. & WEBER, C. F. 2007. Distribution, diversity and ecology of aerobic CO-oxidizing bacteria. Nature Reviews Microbiology, 5, 107-118.

PALMER, J. L., HILTON, S., PICOT, E., BENDING, G. D. & SCHÄFER, H. 2021. Tree phyllospheres are a habitat for diverse populations of CO-oxidizing bacteria. Environmental Microbiology, in press.

Considering to apply?

If you consider applying or need more information, please contact me prior to submitting an application (