Microbial diversity and function in radionuclide impacted soils and sediments

Abstract

The activity of indigenous microbial communities in a natural environment can mediate the biogeochemical cycling of key nutrients and contaminants and impose conditions (Eh and pH) that are the principal controls on metal, and radionuclide, behaviour. Contemporary molecular techniques, in particular high throughput DNA sequencing techniques and subsequent bioinformatic analysis, can be used to construct high resolution microbial taxonomic and functional profiles associated with natural environments to augment and extend our understanding of these systems, when combined with measurements of inorganic and organic geochemical profiles. Understanding the assemblages and diversity of microbial communities in natural environments can enable detailed inferences of the complexity and coupled interactions of prevailing geochemical conditions and processes of an environment to be made. This approach is particularly useful for predicting the long-term transport and fate of radionuclide contaminants, via both direct and indirect interaction with indigenous microbial communities. This project, as part of the LoRISE consortium (Long-lived Radionuclides in the Near Surface Environment) studied depth cores from a range of radionuclide-impacted sites from around the U.K. The naturally uranium (U) contaminated site (Needle’s Eye, Scotland) represented a site that exhibited a close resemblance of the classical thermodynamically-controlled vertical succession of microbial redox processes (aerobic through to anaerobic processes). Reconstructed microbial community profiles were able to anticipate the prevailing U species as a function of depth. Sellafield-impacted sites on the north west coast of England and within the Irish Sea represented more heterogeneous microbial profiles but that were still able to explain geochemical conditions observed at the sites. Further away from Sellafield, depth cores from Loch Etive (Scotland) that were anticipated to exhibit a classic redox succession profile, did not, but contained depth-related community succession focused on sulfur cycling and fermentation. The development of bioinformatics pipelines centred on the latest platforms, databases, and statistical analyses as part of this Ph.D., enabled a high level of interrogation of the DNA sequencing data that enabled specific assertions of the geochemical conditions of each site to be made based on the sequencing results, which proved to be reliable, consistent, and accurate across all sites.