title: Measuring microbial metabolism in atypical environments: Bentonite in used nuclear fuel storage.
abstract: Genomics enjoys overwhelming popularity in the study of microbial ecology. However, extreme or atypical environments often limit the use of such well-established tools and consequently demand a novel approach. The bentonite clay matrix proposed for use in Deep Geological Repositories for the long-term storage of used nuclear fuel is one such challenging microbial habitat. Simple, accessible tools were developed for the study of microbial ecology and metabolic processes that occur within this habitat, since the understanding of the microbiota-niche interaction is fundamental to describing microbial impacts on engineered systems such as compacted bentonite barriers. Even when genomic tools are useful for the study of community composition, techniques to describe such microbial impacts and niche interactions should complement these. Tools optimised for assessing localised microbial activity within bentonite included: (a) the qualitative use of the resazurin-resorufin indicator system for redox localisation, (b) the use of a CaCl2 buffer for the localisation of pH, and (c) fluorometry for the localisation of precipitated sulphide. The use of the Carbon Dioxide Evolution Monitoring System was also validated for measuring microbial activity in desiccated and saturated bentonite. Finally, the buffering of highly-basic bentonite at neutral pH improved the success of isolation of microbial populations, but not DNA, from the bentonite matrix. Thus, accessible techniques were optimised for exploring microbial metabolism in the atypical environments of clay matrices and desiccated conditions. These tools have application to the applied field of used nuclear fuel management, as well as for examining the fundamental biogeochemical cycles active in sedimentary and deep geological environments.
authors.affiliation: Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada.
authors.forename: Wendy
authors.initials: W
authors.lastname: Stone
authors.affiliation: Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada.
authors.forename: Otini
authors.initials: O
authors.lastname: Kroukamp
authors.affiliation: Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada.
authors.forename: Ana
authors.initials: A
authors.lastname: Moes
authors.affiliation: Nuclear Waste Management Organization of Canada, Toronto, Ontario, Canada.
authors.forename: Jennifer
authors.initials: J
authors.lastname: McKelvie
authors.affiliation: Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
authors.forename: Darren R
authors.initials: DR
authors.lastname: Korber
authors.affiliation: Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada; Department of Microbiology, University of Stellenbosch, South Africa. Electronic address: gmw@sun.ac.za.
authors.forename: Gideon M
authors.initials: GM
authors.lastname: Wolfaardt
mesh_terms: D000538:Aluminum Silicates / Q000032:analysis / Q000737:chemistry; D001546:Bentonite / Q000032:analysis* / Q000737:chemistry; D018533:Biomass; D000077215:Clay; D004783:Environmental Microbiology; D005470:Fluorometry; D019015:Geologic Sediments / Q000382:microbiology; D006863:Hydrogen-Ion Concentration; D055442:Metabolome; D008828:Microbiological Techniques / Q000379:methods*; D009678:Nuclear Energy; D016133:Polymerase Chain Reaction; D011850:Radioactive Waste / Q000032:analysis*; D012822:Silicon Dioxide / Q000737:chemistry; D012988:Soil Microbiology; D014871:Water Microbiology
chemical_list: D000538:Aluminum Silicates; D011850:Radioactive Waste; D001546:Bentonite; D012822:Silicon Dioxide; D000077215:Clay
keywords: Bentonite; Desiccation; Low-biomass; Microbial metabolism; Tools