Project highlights

  • Characterise bacteria degrading a key atmospheric pollutant 
  • Investigate interactions of CO-degrading bacteria in model systems 
  • Analyse the diversity and activity of plant-associated CO-degraders in natural plant communities 

Overview

Carbon monoxide (CO) is a ubiquitous atmospheric trace gas with important effects on human health produced by combustion processes and through natural pathways. Microorganisms degrading CO are widespread in the environment, including soils, seawater, and even in extreme environments such as volcanic deposits and the dry valleys of Antarctica (Greening and  Grinter, 2022). Plants and their decaying biomass have been recognised as a natural source of atmospheric CO and they are associated with CO-degrading bacteria. Although these CO-degrading bacteria have been known to be present in the rhizosphere for some time (King and  Crosby, 2002), the colonisation of the phyllosphere by CO-degraders has only been shown recently by our work (Palmer et al., 2021). CO-degrading bacteria are likely to mitigate fluxes of CO from vegetation, thus providing important ecosystem services, but the association and interactions of CO-degrading bacteria with plants, both above and below ground, is not fully understood. In nitrogen fixing plants, CO may be released by the roots and N2-fixing nodules, which is remarkable because CO is an inhibitor of nitrogenase, the key enzyme of nitrogen fixation. A potential beneficial role of CO-degrading bacteria in the phyllosphere has been speculated upon (King and  Weber, 2007), but experimental studies investigating this potentially crucial interaction have not been reported. Ongoing work in our lab suggests that the taxonomic and functional diversity of plant-associated CO–degrading bacteria may be higher than previously realised. In order to gain a more detailed understanding of the interactions of plants and associated CO-degrading bacteria, this project will build upon recent work in our lab to investigate the diversity, activity and impact of CO-degrading bacteria associated with plants, including the potential benefits for plant growth.  

A photograph of the root system of a legume with N2-fixing nodules.

Figure 1: Root system of a legume with N2-fixing nodules. 

Host

University of Warwick

Theme

  • Climate and Environmental Sustainability
  • Organisms and Ecosystems

Supervisors

Project investigator

Co-investigators

How to apply

Methodology

The project will use a combination of approaches to disentangle the interactions of CO-degrading bacteria and plants. This will include working with both model bacteria and plants, as well as characterising the taxonomic and functional diversity, and activity of plant associated bacteria using cultivation-independent methodologies. Isolation of CO-degrading organisms will also be pursued from relevant model plants. Isolates will be characterised, genome sequenced, and specific enzymes and genes induced on CO will be identified by proteomic and/or transcriptomic analyses. This will provide a basis for investigating the interactions of CO-degrading bacteria with plants and the potential role of CO-degradation in the plant-microbe system. A potential approach to assay CO oxidation in planta is the development of a fluorescent reporter strain. 

Training and skills

DRs will be awarded CENTA Training Credits (CTCs) for participation in CENTA-provided and ‘free choice’ external training. One CTC can be earned per 3 hours training, and DRs must accrue 100 CTCs across the three and a half years of their PhD.  

The supervisory team of Schäfer, Lagunas and Bending has a wide range of complementary expertise and experience in microbiology, plant biology, and environmental microbiology. The student will have the opportunity to learn new methodologies or deepen their current experience and understanding of a wide range of microbiological and environmental microbiology methods (meta-omics), bioinformatics, gas chromatography, working with plants, molecular biological methods, 16S rRNA amplicon sequencing, transcriptomics, and proteomics. 

Partners and collaboration

As a team, the supervisors have track record in all relevant aspects of the work. The School of Life Sciences has all required microbial and plant growth facilities, and internationally recognised excellence in plant and microbial sciences. All supervisors have established networks of collaborators in the UK and overseas, which may provide additional opportunities for collaboration. 

Further details

Applicants are strongly encouraged to contact Hendrik Schäfer ([email protected]) to discuss the project and ask any questions they may have. 

To apply to this project:  

  • You must include a CV with the names of at least two referees (preferably three) who can comment on your academic abilities.  

 Applications must be submitted by 23:59 GMT on Wednesday 8th January 2025.  

Possible timeline

Year 1

Characterisation of CO-degrading microorganisms from existing strain portfolio; enrichment and isolation of new CO-oxidisers; CO-uptake and release measurements with plant samples.

Year 2

Genomic, proteomics/transcriptomics analyses of isolates, experimental work with defined plant microbe systems under controlled growth conditions.

Year 3

Analysis of plant–associated CO oxidation in samples from environmental and managed ecosystems; development of fluorescent reporter strain.

Further reading

Greening, C. and Grinter, R. (2022). Microbial oxidation of atmospheric trace gases. Nat Rev Microbiol, 20, 513-528 

King, G. and Crosby, H. (2002). Impacts of plant roots on soil CO cycling and soil–atmosphere CO exchange. Global Change Biology, 8, 1085-1093 

King, G.M. and 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. and Schäfer, H. (2021). Tree phyllospheres are a habitat for diverse populations of CO-oxidizing bacteria. Environ. Microbiol., 23, 6309-6327