2025-B9 Microbial ecology of methane production in blue carbon ecosystems under changing climate

Project highlights

Blue-carbon ecosystems, including coastal wetlands, saltmarshes and peatlands, play a vital role in mitigating climate change.

Methane, a potent greenhouse gas, is predominantly produced through the breakdown of one-carbon compounds within these ecosystems.

To better understand methane production in blue-carbon ecosystems, we will study the process rates, microbial diversity and metabolic pathways using DNA- and RNA-based tools.

Overview

Blue carbon ecosystems, such as coastal wetlands, saltmarshes and peatlands, store significant amounts of carbon in their vegetation and soils through sequestration of atmospheric carbon dioxide. In fact, these ecosystems can store up to five times more carbon per hectare than tropical forests, underscoring their strong potential for climate change mitigation. However, blue carbon ecosystems are also significant sources of methane, a potent greenhouse gas with ~80 times the global warming potential of carbon dioxide over a 20-year period and rising atmospheric concentrations. Therefore, understanding the extent of methane production from these ecosystems is essential.

In coastal environments, the majority of methane is produced by microbial degradation of one-carbon compounds such as methanol, methylamines (MAs) and dimethylsulfide (DMS). This is because coastal sediments typically have high salinity, and thus high sulfate levels. In high-sulfate ecosystems, sulfate-reducing bacteria (SRB) have a thermodynamic advantage and outcompete methanogens for compounds like acetate and hydrogen. However, SRB may not outcompete methanogens for methanol, MAs and DMS. Yet, the impact of rising sea levels, which increase sulfate concentrations, on the activity of methanogens and SRB, and consequent methane production rates, remains unclear.

Research from our group and others has shown that methanogens from various genera (e.g. Methanomethylovorans, Methanolobus and Methanococcoides) can utilise one-carbon compounds to produce methane in diverse coastal sediments with varying sulfate availability such as saltmarshes and peatlands. Recent DNA-based studies have expanded our understanding of methanogens to novel phyla such as Bathyarchaeota and Methanomethyliaceae. These studies suggest that the degradation of one-carbon compounds plays a critical role in methane production in blue carbon ecosystems and that the diversity of methanogens in these settings is more widespread than previously thought. Still, there is a significant gap in our knowledge of the microbial diversity and metabolic pathways underpinning one-carbon compound degradation in coastal blue carbon sediments under changing climatic conditions (i.e. rising temperature and salinity). This project aims to fill this knowledge gap by studying the microbiology of methane production in blue carbon ecosystems and how environmental factors regulate this process.

Host

University of Birmingham

Theme

Climate and Environmental Sustainability
Organisms and Ecosystems

Supervisors

Project investigator

Ozge Eyice, University of Birmingham, [email protected]

Co-investigators

Yin Chen, University of Birmingham, [email protected]

How to apply

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Find out how to apply for this studentship.
All applications must include the CENTA application form.
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Methodology

Methane and one-carbon compound turnover in anoxic coastal sediments. We will collect seasonal sediment samples (0-20 cm depth) from selected coastal wetlands, saltmarshes and peatlands to measure the standing stock concentrations of methane and one-carbon compounds over an annual cycle. To assess the impact of temperature and salinity on methane production rates, we will set up anaerobic incubations with selected samples at two different temperatures (in situ and 4°C higher) and different salinities. We will measure the chemical concentrations using gas and ion chromatography.

Diversity and metabolism of the methanogens degrading one-carbon compounds in coastal sediments. We will employ DNA and RNA-based tools (amplicon sequencing, metagenomics and metatranscriptomics) to characterise the microbial community and metabolic pathways underlying methane production via one-carbon compound degradation in the samples. Additionally, we will use the stable isotope probing method with 13C-labelled methanol, methylamines and DMS, to identify microbes actively degrading these one-carbon compounds.

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 DR will receive comprehensive training across a range of technical skills. Initially, they will be trained in field sampling techniques, including the collection of sediment cores and the setup of microcosms for anaerobic biogeochemical and microbiological studies. Following this, they will develop analytical expertise, learning how to use gas chromatography and ion chromatography to quantify gas concentrations and other key chemicals (e.g., sulfate, trimethylamine). The training will also encompass microbial ecology and anaerobic microbiology focusing on stable-isotope probing, advanced DNA and RNA-based tools as well as the associated bioinformatics pipelines to analyse amplicon sequencing, metagenomics and metatranscriptomics data.

Further details

For any enquiries related to this project please contact Ozge Eyice, University of Birmingham, [email protected].

 To apply to this project: 

You must include a CENTA studentship application form, downloadable from: CENTA Studentship Application Form 2025.

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

Please submit your application and complete the host institution application process via: https://sits.bham.ac.uk/lpages/LES068.htm.   Please select the PhD Bioscience (CENTA) 2025/26 Apply Now button. The CENTA Studentship Application Form 2025 and CV can be uploaded to the Application Information section of the online form.  Please quote CENTA 2025-B9  when completing the application form.

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

Possible timeline

Year 1

Field sampling: Collect sediment samples from various blue carbon ecosystems, including coastal saltmarshes, peatlands, and wetlands across the UK.

Chemical analysis: Measure standing stock concentrations of methane, one-carbon compounds (methanol, methylamines, DMS), and their precursors using analytical tools.

Incubations: Set up anaerobic incubations under controlled conditions to study methane production via one-carbon compound degradation.

Microbial analysis: Extract DNA and RNA from sediment samples and incubations to investigate microbial diversity and the metabolic pathways of one-carbon compound cycling.

Year 2

Data analysis: Analyse sequencing data from sediment samples and incubations.

Stable Isotope Probing (SIP): Conduct SIP experiments with 13C-labelled methanol, methylamines, and DMS in selected coastal wetlands, saltmarshes, and peatlands.

Microbial analysis: Extract DNA and RNA from SIP fractions to identify active microorganisms underlying one-carbon compound degradation.

Year 3

Data analysis: Analyse metagenomics and metatranscriptomics data from SIP experiments.

Dissemination: Write up of manuscripts/thesis.