Project highlights

  • Assess the distribution, activity, and microbial ecology of air pollutant degrading bacteria
  • Use metagenomics approaches to characterise environmental plant microbiomes
  • Determine the key associations between plants and bacteria, with focus on those removing carbon monoxide

Overview

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).

You will assess the abundance and activity of CO-degrading bacteria associated in 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.

Host

University of Warwick

Theme

  • Climate and Environmental Sustainability

Supervisors

Project investigator

Co-investigators

How to apply

Methodology

Environmental materials (leaf and bark samples from 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.

Training and skills

Training in GC analysis, molecular microbial ecology approaches, microbial cultivation, metagenomics, data analysis, will be provided as required.

Partners and collaboration

In addition to being an interdisciplinary, interdepartmental team at the University of Warwick (School of Life Sciences and School of Engineering) we will be actively pursuing collaboration on microbial CO cycling with colleagues elsewhere in the UK and abroad if the opportunity arises.

Further details

Please contact Hendrik Schäfer at the School of Life Sciences (University of Warwick) for more information. E-mail: [email protected]

If you would like to apply to the project please visit: https://warwick.ac.uk/fac/sci/lifesci/study/pgr/studentships/nerccenta/

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. https://doi.org/10.1038/s41396-019-0479-8

KING, G. M. & WEBER, C. F. 2007. Distribution, diversity and ecology of aerobic CO-oxidizing bacteria. Nature Reviews Microbiology, 5, 107-118. https://doi.org/10.1038/nrmicro1595

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. https://doi.org/10.1111/1462-2920.15770

COVID-19

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.