The microbial ecology of spent fuel storage ponds at Sellafield, UK

  • Sharon Ruiz Lopez

Student thesis: Phd


The use of nuclear energy has been of great importance to the United Kingdom, with Sellafield being the largest nuclear site used for both power production and more recently reprocessing activities. This project, via collaboration between the Geomicrobiology Group at the University of Manchester and Sellafield Limited, aimed to investigate the microbial ecology of a spent fuel storage hyper-alkaline indoor pond (INP) in Sellafield. The main pre-reprocessing storage pond at the Sellafield site is the Indoor pond (INP), a concrete walled indoor pond filled with demineralised water, responsible for receiving, storing and mechanically processing spent nuclear fuel (SNF) from Magnox and Advanced Gas-cooled Reactor (AGR) stations from across the UK. Samples were taken from the INP at different spatial locations and depths, encompassing main ponds (MP), subponds (SP) and a feeding tank (FT). The present study intended to identify the microbial communities present in the INP and associated structures to determine if they were stable during a prolonged operational period. A more academic focus of the PhD was to understand the metabolic processes that underpin microbial colonisation and adaptation in the pond. In order to achieve these objectives, first the microbial communities from the indoor alkaline storage pond (INP) were identified to create a microbial database consisting of population density and diversity of microorganisms present. Here traditional culturing approaches were trialled but were considered ineffective for the specialised “extremophilic” organisms present in the INP. Therefore, the bulk of the microbial analyses focused on DNA sequencing, focusing initially on amplification and sequencing of two commonly used genetic marker genes, the 16S rRNA and 18S rRNA genes that can be used to identify prokaryotic (bacteria and archaea) and eukaryotic (algae and other higher organisms). Finally, a much wider range of genes were targeted to help identify key processes that support microbial colonisation, via high-throughput “metagenomic” sequencing and analyses. Overall, these findings are discussed in relation to microbial survival in hyper-alkaline, oligotrophic and radioactive extreme environments, and microbial adaptation over time observed during the thirty months of analysis. Organisms identified by 16S and 18S rRNA gene Illumina sequencing were predominantly Proteobacteria, mainly Alpha and Beta in the feeding tank (FT), main pond (MP) and Subpond (SP) sample sites. The presence of the alkali tolerant hydrogen-oxidising bacterium Hydrogenophaga sp. solely in the INP main ponds and subponds suggested the metabolism of hydrogen is occurring within the INP which could be generated by radiolysis of water. Metagenomic analysis revealed that genes related to membrane transport, oxidative and osmotic stress functions were more abundant on the FT possibly due to the presence of Na+ ions. Genes related to DNA metabolism (including DNA repair and defence systems) as well as genes related to respiration functions (hydrogenases) were more abundant on the MP and SP which reinforces the proposed microbial utilization of H2 as an energy source. In order to have a broader picture of the bacterial strategies to cope with extreme environmental conditions (hyper-alkaline, oligotrophic and radioactive background), few selected samples from an open-air pond, the First Generation Magnox Pond (FGMSP) and its auxiliary pond (Aux), were analysed and compared to the indoor system (INP). Results showed that genes associated to photosynthesis were more abundant on the open-air ponds, revealing that light exposure was a key energy source that promoted microbial colonisation. Additionally the final part of this research intended to identify virus-host interactions and its influence on key metabolic processes. Metagenomic analysis revealed the presence of phages inserted on bacteria affiliated to order Burkholderiales; surprisingly phages did n
Date of Award1 Aug 2020
Original languageEnglish
Awarding Institution
  • The University of Manchester
SupervisorJonathan Lloyd (Supervisor) & Jon Pittman (Supervisor)


  • Spent fuel ponds
  • Sellafield
  • Microbial ecology
  • Metagenomics
  • Spent nuclear fuel

Cite this