Healthy peat microbiota

Biogeochemical Cycles



Scottish peatlands are deep, expansive and crucial stores of carbon. They cover around 20% of the land, yet they contain over half of the total carbon stored within all Scottish soils. Damage to these fragile ecosystems, through drainage, physical disturbance or burning, upsets their ecological balance, and results in amplified release of stored carbon through greenhouse gas emissions. Careful management and restoration of these valuable natural resources is one of Scotland’s main strategies towards achieving net-zero greenhouse gas emissions by 2045. Microorganisms play a vital role in the ecology of peatlands and in the release of greenhouse gases. This project will study relationship between peat microbiota, their environment and the formation and fate of greenhouse gases in healthy, damaged and restored peat landscapes. It will address a critical gap in our current knowledge of these systems, which will better equip management and restoration strategies, enhancing the success of future Scottish peatland projects.

Deep down in waterlogged, oxygen-starved peat layers, methane (CH4), a potent greenhouse gas, is produced when organic matter is consumed by methanogenic microorganisms. Higher up, where oxygen is available, methanotrophs can convert slow moving, diffuse CH4 into the less potent but more abundant greenhouse gas, carbon dioxide (CO2; 34 times less potent), before it is released to the atmosphere. In contrast, CH4 that bubbles up to the surface by ebullition moves too fast to be oxidised by methanotrophs, and so it is released to the atmosphere unchanged. The microbial ecology of diffusion and ebullition systems has yet to be reported, and the impact of damage to them and their ability to be restored to their original microbial condition is as yet unknown.

The main objectives of this project will be to:
1) Compare the microbial composition and activity of healthy peat systems sampled from CH4 diffusion and ebullition sites.
2) Investigate the impact of peatland destruction on microbial community structure and greenhouse gas cycling activity.
3) Determine the effectiveness of peatland restoration projects on restoring the microbial composition and activity to expected former states.

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Image Captions

A peat bog below the top of Doune Hill, Luss Hills, Scotland. Image: Michal Klajban CC BY-SA 4.0 22.09.18 (Wikimedia Commons)
Methane cycling stable isotope probing microcosms. Image: Jennifer Pratscher


This project will adopt a range of multidisciplinary techniques to establish the composition, activity and drivers of greenhouse gas cycling microbiota within diffusion and ebullition CH4 release peat target sites, at damaged peat sites, and at peat restoration project sites in Scotland.

1) Greenhouse gas flux measurements:
In-situ measurements of greenhouse gas flux at a range of diffusion, ebullition, damaged and restored target sites in Scotland will be performed by constructing and deploying a network of CH4 and CO2 sensors. These will provide key information on the overall carbon budgets of each target site.

2) Greenhouse gas composition and redox potential profiles:
Gas diffusion probes and pore water sampling will be performed to determine the spatial variability of CH4 and CO2 concentrations down depth profiles and at different diffusion, ebullition, damaged and restored target sites. The redox potential of each of these sites will additionally be measured to profile the potential for biogeochemical activity.

3) Microbial composition and functional potential profiles:
Community profiles of both total and active microbiota will be profiled using rRNA gene amplicon sequencing. Profiles will be compared along depth transects and between different sites, and they will be correlated to physicochemical measurements to consider the environmental drivers of community form and function. Quantification of genes essential for methane oxidation (e.g. pmoA and mmoX) and methanogenesis (e.g. mcrA) will be profiled as indicators of the spatial variability of carbon cycling activity.

4) Link carbon cycling activity to microbiota:
To directly link microbial greenhouse gas production and cycling to individual organisms, stable isotope probing will be performed on aerobic and anaerobic microcosms using peat depth profiles from each target site. Active methanogens and methanotrophs will be isolated using 13C-labelled 13CH4 and 13CO2, and they will be profiled using 16S rRNA gene sequencing.

5) Impact analysis:
The potential impact of peatland damage to the microbial ecology of these systems will be considered though comparative statistical analyses of healthy and damaged systems. Microbial composition, abundance and activity will be considered alongside measured physicochemical conditions. The effectiveness of peatland restoration projects to restore the microbial ecology to its presumed original state will be considered and reported on through healthy, damaged and restored site comparisons.

Project Timeline

Year 1

1. Literature review
2. Site selection for healthy diffusion and ebullition systems, and for damaged and restored peatlands
3. Construction, testing and deployment of CH4 and CO2 sensors
4. Construction of redox and gas probes
5. Initial sample collection to test and optimise field and laboratory protocols

Year 2

1. Physicochemical measurements and microbial sample collection from all field sites
2. Community and functional gene profiling and abundance analysis from peat core samples
3. Stable isotope probing microcosm set-up and labelled community extraction
4. Research dissemination

Year 3

1. Sequence library production and data analysis from core samples and microcosms
2. Statistical data interpretation
3. Thesis and paper writing
4. Research dissemination

Year 3.5

1. Completion of thesis and paper writing
2. Viva preparation
3. Research dissemination

& Skills

The project provides an excellent platform to gain multidisciplinary training in an exciting, important and timely research field. It will cut across disciplines of biogeochemistry, microbiology, molecular ecology and landscape management, equipping the candidate with a wealth of skills that will be relevant to many onward career opportunities.

The candidate will work closely with all three supervisors to gain directly from their expertise. Dr Cameron will oversee the direction, development and progress of the candidate and the project, and will provide expertise in experiment design, execution and dissemination, microbial and chemical field sampling, molecular microbial ecology, ecological statistical analyses and career development. Dr Pratscher will provide expertise in field work, molecular microbial ecology, stable isotope probing and methane cycling ecology. Dr Bass will provide expertise in site selection, gas sensor construction, deployment, maintenance and data analysis, carbon flux analyses and carbon budget development. The candidate will additionally have access to extensive IAPETUS2-cohort and NERC training workshops, allowing for a wealth of broader, transferable research skills and knowledge to be gained.

The candidate will join vibrant research communities at the University of Glasgow and at Heriot Watt University, where they will be welcomed and encouraged to network with colleagues and their collaborators. The candidate will have the opportunity to present their results to at least one national and one international research conference. Furthermore, they will be encouraged to disseminate their result to the general public at school and community events, and to share their findings with other research institutes, national networks, such as Scotland’s environment and IUCN Peatlands Programme, and with members of the Scottish Parliament.

References & further reading

Gewin, V. (2020) How peat could protect the planet. Nature 578: 204-208.

Emsens, W.-J., van Diggelen, R., Aggenbach et al. (2020) Recovery of fen peatland microbiomes and predicted functional profiles after rewetting. The ISME journal 14: 1701-1712.

Scottish Parliament Information Center – Peatlands and Climate Change

Rey-Sanchez, C., Bohrer, G., Slater, J., et al. (2019) The ratio of methanogens to methanotrophs and water-level dynamics drive methane exchange velocity in a temperate kettle-hole peat bog. Biogeosciences Discuss 2019: 1-48.

Tveit, A., Schwacke, R., Svenning, M.M., and Urich, T. (2013) Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms. The ISME journal 7: 299-311.

Further Information

Application procedure: For IAPETUS2 applications to the University of Glasgow please use the dedicated application portal: Administrative details will also need to be submitted to the IAPETUS2 website (find link details here).

For further information, please contact:
Karen Cameron:
Jennifer Pratscher:
Adrian Bass:

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