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Application of multi-omics to identify and target microbial bloom control in legacy nuclear ponds

Department of Earth and Environmental Sciences

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Prof J Lloyd , Dr J Pittman , Prof K Morris No more applications being accepted Funded PhD Project (Students Worldwide)
Manchester United Kingdom Analytical Chemistry Biotechnology Ecology Inorganic Chemistry Microbiology Molecular Biology

About the Project

The safe operation of nuclear storage ponds is crucial to the continued provision of low carbon nuclear power to the UK, while decommissioning of legacy pond systems from historic operations remains a significant ¬£multi-billion challenge to the industry. Optimising the management and treatment of the legacy ponds on the Sellafield site is crucial to reduce the hazards, reduce the cost to the tax-payer and protect the environment. However, the impact of microorganisms on plant operations is becoming evident, as the formation of microbial blooms in legacy ponds lead to reduced visibility within these facilities and fouling of downstream water treatment systems. As a result, controlling microbial growth is of growing importance, to keep decommissioning schedules on time and to budget.  

Recent work from the Manchester Geomicrobiology group, via collaborations with Sellafield Ltd. and the National Nuclear Laboratory, have identified discrete microbiomes in a network of hydraulically-linked legacy ponds (see references above). For example, cutting edge DNA-sequencing and metabolomic profiling has identified photosynthetic algae (MeGraw et al. 2018) and cyanobacteria (Foster et al. 2020a) in outdoor ponds, adapted to high radiation levels and other extremes (e.g. high pH) associated with the ponds, and potentially playing a role in controlling the fate of priority radionuclides (MeGraw et al. 2018 and Foster et al. 2020b). In contrast the low light intensities associated with indoor ponds, has not supported the widespread growth of photosynthetic communities, resulting in unique microbiomes sustained by hydrogen (generated through radiolysis reactions; Ruiz-Lopez et al, 2020). These studies have extended our knowledge of extremophile microbiology in engineered environments, and have also helped underpin control strategies, for example through carefully controlled purging cycles (Foster et al, 2020a).   

This new study will focus on a closed-pond system, that has proved susceptible to microbial blooms, but cannot be controlled by purge systems. Recent work has resulted in the identification of a discrete microbiome in this pond, and helped fine-tune approaches for biomass control. We now wish to build on these positive initial results, via a new EPSRC CASE project which will:

1.      Use DNA-based high-throughput 16/18S rRNA gene sequencing to monitor long-term operation of the pond  and help fine-tune targeted treatments.

2.      Apply complementary multi-omics approaches to study adaptation strategies within the pond.

3.      Develop culture-based approaches to (i) confirm adaptation strategies in carefully constrained laboratory systems, (ii) quantify the impacts of microbial colonisation on radionuclide fate, and finally (iii) test additional control strategies for future use.

A cross-disciplinary approach will be adopted with training in techniques including culture-based microbiology, DNA extraction and sequencing (16S/18S rRNA and genome sequencing), bioinformatics, transcriptomic and proteomic analyses, geochemical and radiochemical profiling, and cutting-edge imaging and spectroscopy as appropriate. The student will benefit from access to our newly refurbished ¬£4M NNUF RADER laboratories ( and other facilities available through extant collaborations with Sellafield and the National Nuclear Laboratory. The student will join the largest grouping of academic researchers in the UK nuclear environmental sector, working closely with vibrant group of 40+ experimental officers, postdoctoral scientists and other PhD students. PhD students leaving the group are in high demand in both the nuclear/environmental sectors, and also by academia.  

Funding Notes

This is a 3.5 year EPSRC studentship. Funding will cover UK tuition fees/stipend only. The University of Manchester aims to support the most outstanding applicants from outside the UK. We are able to offer a limited number of full studentships to be awarded to international applicants. These full studentships will only be awarded to exceptional quality candidates, due to the competitive nature of this scheme.
We expect the programme to commence in September 2021.


1] Ruiz-Lopez, S., Foster, L., Boothman, C., Cole, N., Morris, K. and Lloyd, J.R. (2020). Identification of a Stable Hydrogen-Driven Microbiome in a Highly Radioactive Storage Facility on the Sellafield Site. Frontiers in Microbiology 11, 2915
2] Foster L, Boothman C, Ruiz-Lopez S, Boshoff, G., Jenkinson, P., Sigee, D., Pittman, J.K., Morris, K. and Lloyd, J.R (2020a). Microbial bloom formation in a high pH spent nuclear fuel pond. The Science of the Total Environment. Jun;720:137515. DOI: 10.1016/j.scitotenv.2020.137515
3] Foster L., Cleary A., Bagshaw H., Sigee D.C., Pittman J., Morris K, Zhang K, Lloyd JR (2020b) Biomineralization of Sr by the cyanobacterium Pseudanabaena catenata under alkaline conditions. Frontiers in Earth Science 8 410
4] Foster L, Muhamadali H, Boothman C, Sigee D, Pittman JK, Goodacre R, Morris K and Lloyd JR (2020c) Radiation Tolerance of Pseudanabaena catenata, a Cyanobacterium Relevant to the First Generation Magnox Storage Pond. Front. Microbiol. 11:515. doi: 10.3389/fmicb.2020.00515
5] MeGrew, V.E., Brown, A.R., Boothman, C., Goodacre, R., Morris, K., Sigee, D., Anderson, L. and Lloyd, J.R. (2018) A novel adaptation mechanism underpinning microbial colonisation of a nuclear fuel storage pond. mBio 9 (3), e02395-17
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