Lakes are dynamic methane sources where both benthic and pelagic processes shape net emissions. Sediments are the dominant methane producers, but growing evidence shows that phytoplankton can generate methane under oxic conditions, particularly under phosphorus limitation via phosphonate degradation by Bacteria. Methanotrophs mediate both sources, consuming methane at the sediment–water interface, in the oxycline, and around algal particles. Their activity is shaped by cross-feeding interactions with heterotrophs, nitrifiers, and sulfur oxidisers, yet the ecological links between benthic and planktonic methane sources and methanotroph communities remain unresolved.
This PhD will examine how methanotrophs integrate methane derived from sediments and plankton. Field surveys in the UKCEH Cumbrian Lakes (Windermere, Esthwaite, Blelham) and Lakes Tour campaigns (20 lakes across a trophic gradient) will capture seasonal shifts in phytoplankton, benthic communities, and methanotrophs, using amplicon sequencing, metatranscriptomics and metagenomics to link taxa and functional genes (pmoA, mmoX, phnJ). Depth-resolved analyses will reveal which methanotroph taxa align more strongly with sediment fluxes, phytoplankton biomass, or both. This combined with analysis of sediment derived communities will assess how present and past methanotroph taxa have changed in response to nutrient inputs into freshwater lakes and with other changing environmental conditions.
Lab experiments will move from association to mechanism. Methanotrophs will be enriched and isolated from lake water and sediment. Co-cultures will test whether phytoplankton exudates, benthic substrates, or phosphorus-limited conditions sustain methanotroph growth. Stable isotope probing with ¹³CH₄ will identify active methanotroph taxa, while ¹³CO₂ incubations with phytoplankton will test whether phytoplankton-derived methane is assimilated into methanotroph biomass. Together, these approaches will clarify how benthic and pelagic carbon pathways intersect through the methane biofilter, with implications for predicting methane emissions in a changing climate.
Figure 1: Methanotrophy within the microbial loop of Lake ecosystems (Modified from https://communities.springernature.com/posts/the-role-of-methanotrophy-in-temperate-lakes).
This project is not suitable for CASE funding
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Field sampling across Cumbrian Lakes and Lakes Tour sites will generate depth profiles of microbial communities, nutrients, and pigments. Amplicon sequencing (16S, 18S, pmoA, phnJ) and metagenomics will resolve methanotroph, phytoplankton, and benthic microbial diversity (methanogens). Co-occurrence analyses will identify links between methane producers and oxidisers. Methanotroph isolates will be obtained from both water column and sediments. Laboratory microcosms will co-culture methanotrophs with phytoplankton and with sediment-derived substrates under different nutrient regimes, particularly phosphorus limitation. Changes in response SIP experiments with ¹³CH₄ will trace active methanotrophy, while ¹³CO₂ incubations will test for phytoplankton-derived methane supporting methanotrophs. The UKCEH CORMIS facility will be used to look directly at carbon transfer between Phytoplankton and Methanotroph taxa.
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.
Training will cover limnological fieldwork, microbial isolation, cultivation, greenhouse gas measurements and co-culture, isotope probing (¹³CH₄, ¹³CO₂), and molecular microbial ecology (amplicon, metagenome, transcriptome). Skills in microbial physiology, statistical analysis (R/Python), and reproducible bioinformatics workflows will be developed. The student will also gain experience working with UKCEH long-term lake observatories and in interdisciplinary synthesis of benthic–pelagic coupling.
Joe Taylor is microbial ecologist with expertise in the environmental drivers of microbial communities in space and time. Amy Thorpe is molecular ecologist with experience in using sediment DNA to reconstruct past communities. Yin Chen is an expert on methanotrophy and microbiology in marine and freshwater ecosystems. UKCEH provides access to Cumbrian Lakes observatories, buoy monitoring data, and Lakes Tour campaigns as well as cutting edge facilities including The UK Centre for Multimodal Correlative Microscopy and Spectroscopy (CoreMiS) ; the University of Birmingham contributes expertise in microbial physiology methylotrophy and has the equipment and resources to deliver the microbiology component.
Year 1: Field campaigns (Cumbrian Lakes, Lakes Tour); amplicon sequencing of methanotrophs and phytoplankton; initial enrichments from water and sediment; bioinformatics training.
Year 2: Isolation of methanotroph taxa; laboratory co-cultures with phytoplankton and benthic substrates; stable isotope probing (¹³CH₄, ¹³CO₂).
Year 3: Integration of field and lab data; metagenomics/transcriptomics; synthesis of benthic–pelagic interactions; modelling of methanotroph niches
Bižić, M. et al. (2020) Aquatic and terrestrial cyanobacteria produce methane. Science Advances, 6, eaax5343.
Chen, Y., (2025). Beyond Meta-Omics: Functional Genomics in Future Marine Microbiome Research. Annual Review of Marine Science, 17.
McDonald, et al. (2008). Molecular ecology techniques for the study of aerobic methanotrophs. Applied and environmental microbiology, 74(5), pp.1305-1315.
Thorpe, A.C. et al. (2022). Sedimentary DNA records long‐term changes in a lake bacterial community in response to varying nutrient availability. Environmental DNA, 4(6), pp.1340-1355.
Pérez-Coronel, E. et al. (2022) Multiple sources of aerobic methane production in aquatic environments. Nature Communications, 13, 6394.
Please contact Dr Joe Taylor for further details: [email protected]
The successful applicant would be registered at the University of Birmingham.
To apply to this project:
Applications must be submitted by 23:59 GMT on Wednesday 7th January 2026.