Novel methods of detecting carbon cycling pathways in lakes and their impact on ecosystem change

Pete Langdon, SoGES, Dr Gordon Inglis, Dr Jessica Whiteside, Jan Janouškovec, SoBS; Celia Martin-Puertas, Royal Holloway

Freshwater lakes are a major source of atmospheric methane (CH4), a potent greenhouse gas. However, the importance of freshwater CH4 cycling in our future warm climate remains unknown. One way to better understand methane cycling in lakes is to assess changes in the past, and this project will focus on methane cycling and impacts on ecosystem community. Project aims will be to reconstruct (1) ecosystem communities through microfossil analyses (e.g. chironomids, Cladocera) from varved lake sediments; (2) methane ebullition by analyzing the stable carbon isotopic composition (δ13C) of chironomids and Cladocera; (3) methane production by analysing the abundance of archaeal lipid biomarkers; (4) methane oxidation through δ13C analysis of bacterial lipid biomarkers (e.g., hopanoids), and (5) bacterial communities that are involved in methane oxidation, via sedimentary ancient DNA (sedaDNA) analyses. This will enable the differentiation between Type I or Type II methanotrophs and will provide additional insights into methane flux (i.e., high vs low). These results can then be compared, enabling us to detect if there is a change in community structure over time (protist and/or primary consumers), and thus our interpretation of the methane cycle in the past as well as considering warmer futures. 



Sediment sampling will be done in liaison with Dr Martin-Puertas, and may involve travel to European laboratories for specific sub-sampling, and/or sample collection from the field, depending on which lakes we will focus on. The candidate and project team will have up to 8 varved lakes to consider, across European climate gradients (N/S and E/W), so different spatial and temporal scales can be considered. Initial work will focus on the microfossil analysis and ecosystem community development work from the varved lake sediments, undertaken in the microscope laboratory facilities in SoGES. The lipid biomarker work will be undertaken at SOES organic geochemical laboratories with Inglis and Whiteside, and focus on extracting the distribution and carbon isotopic composition of lipid biomarkers. The student will focus on δ13C analysis of bacterial (hopanoids) and archaeal membrane lipids (e.g., archaeol). This will provide insights into methanotrophy and methanogenesis, respectively (e.g. Inglis et al. 2022). A third strand of the work – the sedaDNA analyses will involve extractions in the SoGES specialist facility, and then sequencing likely at SOES. Data Analyses will involve comparisons of the three main datasets, and involve training in appropriate statistical techniques.  


SoGES, Southampton (Highfield)

The INSPIRE DTP programme provides comprehensive personal and professional development training alongside extensive opportunities for students to expand their multi-disciplinary outlook through interactions with a wide network of academic, research and industrial/policy partners. The student will be registered at the University of Southampton and hosted at the School of Geography and Environmental Science. Specific training will


  1. Sediment sampling and fieldwork
  2. Microfossil extraction and learning identification taxonomies.
  3. Stable carbon isotope (δ13C) analyses from microfossils.
  4. Lipid extraction and subsequent stable carbon isotope analyses.
  5. SedaDNA extraction, sequencing and bioinformatics.
  6. Statistical techniques for data analyses, which may include ordinations, isotope mixing models and data comparison techniques (spatial and temporal). This will likely include coding work.
  7. Training around paper/PhD writing.


Eligibility & Funding Details: 

Please see for details.


Background Reading: 

Grey, J. 2016. The Incredible Lightness of Being Methane-Fuelled: Stable Isotopes Reveal Alternative Energy Pathways in Aquatic Ecosystems and Beyond. Frontiers in Ecology and Evolution 4: 8.


Inglis, G.N., Bhattacharya, T., Hemingway, J.D., Hollingsworth, E.H., Feakins, S.J. and Tierney, J.E. 2022. Biomarker Approaches for Reconstructing Terrestrial Environmental Change. Annual Review of Earth and Planetary Sciences 50: 369-394.


van Hardenbroek, M., Chakraborty, A., Davies, K.L., Harding, P., Heiri, O., Henderson, A.C.G., Holmes, J.A., Lasher, G.E., Leng, M.J., Panizzo, V.N., Roberts, L., Schilder, J., Trueman, C.N. and Wooller, M.J. 2018. The stable isotope composition of organic and inorganic fossils in lake sediment records: Current understanding, challenges, and future directions. Quaternary Science Reviews 196: 154-176.