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Microbial cycling of trace gases and pollutants

RESEARCH LEADER: Professor Hendrik Schäfer

The main focus of research in our lab are microorganisms that cycle atmospheric trace gases and pollutants relevant for climate regulation and air pollution.

Microorganisms drive major processes in the Earth system as critical components of biogeochemical cycles that effect the turnover of carbon, nitrogen, sulfur, and other elements. In doing so, microorganisms have major effects on the composition of the atmosphere, but not only on major gases such as nitrogen (N2), oxygen (O2), and carbon dioxide (CO2), bacteria also drive the production and degradation of trace gases that are present at low concentrations.

Trace gases play significant roles in the Earth system, as greenhouse gases, ozone-depleting compounds, and as aerosol precursors that affect the energy budget of the atmosphere. Many of these compounds have both natural and anthropogenic sources and understanding the processes that determine their atmospheric concentrations and how they respond to climate change is important. Some trace gases, such as carbon monoxide (CO) are also important air pollutants. Interestingly, we have shown recently that CO degrading bacteria can be found associated with trees and may be relevant in degrading this air pollutant. See a short summary of our findings on CO degrading bacteria associated with trees in the News Section of the Microbiology Society.

Microbial cycling of organic sulfur compounds

Microbial metabolism of the organic sulfur compound dimethylsulfoniopropionate (DMSP), of which large amounts are produced in the oceans and coastal marine environments, generates volatile sulfur compounds such as dimethylsulfide (DMS – often referred to as ‘the smell of the sea’) and methanethiol (MT). DMS emitted into the atmosphere reacts with other compounds to yield aerosols that contribute to the haze of the atmosphere and promote cloud formation, thus affecting the amount of solar radiation that is reflected, contributing to cooling.

Taxonomically and functionally diverse microorganisms contribute to the production and degradation of such organic sulfur compounds which has a major impact on the environmental fate and distribution of organic sulfur in the biosphere (Schäfer et al., 2010). For instance, oxidation of DMS to dimethylsulfoxide (DMSO) by the enzyme trimethylamine monooxygenase, is a co-metabolic process that is widespread in abundant marine bacteria of the Roseobacter group and SAR11 clade (Lidbury et al., 2016Link opens in a new window).

Another key step in DMS and DMSP cycling by bacteria is the degradation of methanethiol, a foul-smelling gas, which is catalysed by the enzyme methanethiol oxidase in aerobic bacteria. We showed that MT oxidase (MTO) is a member of a poorly characterised enzyme family (selenium binding protein family) and that the gene encoding MTO is found in a wide range of environments and organisms in the biosphere (Eyice et al., 2018Link opens in a new window).

Dr Alison Webb inspects an ice core obtained during the MOSAiC arctic expedition

University of Warwick Scientist Dr Alison Webb and University of Bremen PhD student Linda Thielke
categorise a sea ice core prior to sectioning.

DMS/P/O cycling in the Arctic

Due to the role of DMS in potential climate feedbacks and the prominent role of marine environments as a source of DMS, there is major interest in understanding how climate change may affect the relative fluxes of DMS into the atmosphere, particularly in the polar regions. We are contributing to the work of the international ice drift experiment MOSAiCLink opens in a new window, the largest scientific Arctic expedition to date. As part of MOSAiC, we are collaborating with colleagues from UEA in Norwich, the Netherlands, and the USA to investigate the role of sulfur cycling microorganisms in sea ice and seawater and how they affect DMS emissions in the Arctic, a region that is disproportionately affected by climate change.

Microbial degradation of air pollutants

Carbon monoxide (CO) is an example of a compound that has both natural and anthropogenic sources. As a product of the burning of biomass and fossil fuels, it significantly contributes to air pollution. CO exposure can be fatal, but even at sub-lethal levels, it can have considerable effects on human health. Specialised microorganisms, however, can degrade CO using the enzyme carbon monoxide dehydrogenase (CODH). It is well-known that CO-degrading microorganisms are present in soil and marine environments. It has been estimated that, annually, carbon monoxide degrading microorganisms are oxidising some 300 Tg and 70 Tg of CO to CO2 in soils and marine environments, respectively (King and Weber, 2007; Conte et al., 2019).

Conceptual schematic depicting the potential role of phyllosphere in mitigation of air pollutants

Microorganisms in the phyllosphere may help degrade air pollutants such as CO
(picture credit Letizia Pondini).

In studying microbial communities on the leaves of trees and their interaction with air pollution, we discovered that tree leaves are a habitat for diverse CO-oxidising bacteria. We estimate that bacteria capable of CO-oxidation may be abundant on tree leaves (~25% of total population) and that tree-associated microorganisms may potentially contribute to the mitigation of CO in polluted atmospheres (Palmer et al., 2021Link opens in a new window). Further work is ongoing to characterise how microorganisms in the phyllosphere interact with particulate matter and how air pollution affects their taxonomic and functional diversity.


CONTE, L., SZOPA, S., SEFERIAN, R. & BOPP, L. 2019. The oceanic cycle of carbon monoxide and its emissions to the atmosphere. Biogeosciences, 16, 881-902.

EYICE, Ö., MYRONOVA, N., POL, A., CARRIÓN, O., TODD, J. D., SMITH, T. J., GURMAN, S. J., CUTHBERTSON, A., MAZARD, S., MENNINK-KERSTEN, M. A. S. H., BUGG, T. D. H., ANDERSSON, K. K., JOHNSTON, A. W. B., OP DEN CAMP, H. J. M. & SCHÄFER, H. 2018. Bacterial SBP56 identified as a Cu-dependent methanethiol oxidase widely distributed in the biosphere. The ISME Journal, 12, 145.

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

LIDBURY, I., KRÖBER, E., ZHANG, Z., ZHU, Y., MURRELL, J. C., CHEN, Y. & SCHÄFER, H. 2016. A mechanism for bacterial transformations of dimethylsulfide to dimethylsulfoxide: a missing link in the marine organic sulfur cycle. Environmental Microbiology, 18, 2754-2766.

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.

SCHÄFER, H., MYRONOVA, N. & BODEN, R. 2010. Microbial degradation of dimethylsulphide and related C1-sulphur compounds: organisms and pathways controlling fluxes of sulphur in the biosphere. Journal of Experimental Botany, 61, 315-334.

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