Microbes have shaped, and continue shaping, Earth’s atmosphere, oceans and the soil. They have oxygenated Earth’s atmosphere in the first place and currently contribute to the carbon and nitrogen cycles within the oceans, freshwater systems, and the soil.
We currently understand a lot about specific metabolic processes within individual microbes, such as photosynthesis or nitrogen fixation. In natural habitats, however, these processes occur with microbial communities that harbour many metabolic interactions. Therefore, a full understanding of stability and rates of different processes (for example rates of carbon fixation or oxygen generation via photosynthesis) requires an understanding of these processes within the context of microbial communities.
In this project, we will analyse biogeochemically relevant processes of photosynthesis and nitrogen fixation, performed by cyanobacteria, within the context of their associated heterotrophic bacteria (also known as the “cyanosphere”). We will do so by applying a two-tiered approach, consisting of: (1) monitoring cyanobacterial populations and their metabolic processes in a freshwater lake environment, and (2) monitoring the same processes, together with detailed population dynamics and microbial physiology in lab-cultivated cyanobacterial communities (i.e. laboratory cyanospheres). This work is already ongoing. In a NERC-funded pilot project, we have collected 6-month long temporal (weekly) metadata and DNA from our local freshwater lake (Draycote Reservoir). In tandem, we have established, stabilized microbial communities in the laboratory sourced from the same lake and enriched under laboratory environment, with defined media and light conditions.
The advertised PhD studentship will join our existing team to research nitrogen fixation and photosynthesis dynamics in select laboratory communities (composed of 10-20 species) and also expand on our temporal sampling in the natural lake. The proposed two-tiered approach via analysis of temporal dynamics of natural communities both in situ and through laboratory-based approaches will increase our understanding of their contribution to biogeochemical cycles and further the key strategic NERC goals of “pushing the frontiers of understanding” and enabling “environmental solutions”.
This project is not suitable for CASE funding
Each host has a slightly different application process.
Find out how to apply for this studentship.
All applications must include the CENTA application form.
Choose your application route
This work will involve studying rates of metabolic processes – photosynthesis and nitrogen fixation – and deciphering of metabolic interactions and population dynamics in laboratory adapted cyanobacterial communities on one hand, and monitoring of natural lake communities, on the other.
The former direction will involve microbial culturing, isolation, temporal metagenomics and metabolic measurements (based on gases and soluble small molecules, including targeted metabolomics). The latter direction will involve temporal metagenomics and environmental monitoring of dissolved chemicals (in particular nitrate and ammonia) and gases in the lake environment. This will be achieved by using ready-made and further engineered measurement enclosures, in collaboration with Prof. Ryan Mushinski (at Warwick).
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 objectives of the proposed project are well-defined and feasible. The student will be joining the Soyer group, supported by the PI, Orkun Soyer, an existing laboratory technician and postdoctoral research assistants in his group. This team has extensive experience with laboratory enrichment, culturing, and analysis of cyanobacterial communities. The natural sample collection will be processed using existing protocols in the Soyer, Puxty and Mushinski groups. For the computational component, the student will become part of an experienced group and will be inducted in key bioinformatics tools and methods, already utilised in the Soyer group.
Not applicable.
Year 1:
Year 2:
Year 3:
Journal:
DUXBURY, S. J. N., RAGUIDEAU, S., CREMIN, K., RICHARDS, L., MEDVECKY, M., ROSKO, J., COATES, M., RANDALL, K., CHEN, J., QUINCE, C. & SOYER, O. S. 2025. Niche formation and metabolic interactions contribute to stable diversity in a spatially structured cyanobacterial community. ISME J.
DE JESUS ASTACIOA, L. M., PRABHAKARA, K. H., LI, Z., MICKALIDE, H. & KUEHN, S. 2021. Closed microbial communities self-organize to persistently cycle carbon. Proc Natl Acad Sci U S A, 118.
GOYAL, A., FLAMHOLZ, A. I., PETROFF, A. P. & MURUGAN, A. 2023. Closed ecosystems extract energy through self-organized nutrient cycles. Proc Natl Acad Sci U S A, 120, e2309387120.
PASCAULT, N., RUE, O., LOUX, V., PEDRON, J., MARTIN, V., TAMBOSCO, J., BERNARD, C., HUMBERT, J. F. & LELOUP, J. 2021. Insights into the cyanosphere: capturing the respective metabolisms of cyanobacteria and chemotrophic bacteria in natural conditions? Environ Microbiol Rep, 13, 364-374.
For any enquiries related to this project please contact Orkun Soyer, [email protected].
To apply to this project:
Applications must be submitted by 23:59 GMT on Wednesday 7th January 2026.