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Thesis (Ph. D.)--University of Texas at Austin, 2004. / Supervisor: Philip C. Bennett. Vita. Includes bibliographical references. Also available from UMI.

Thesis (Ph. D.)--University of Texas at Austin, 2004. / Available also in an electronic version.

Thesis (Ph. D.)--Miami University, Dept. of Geology, 2007. / Title from second page of PDF document. Includes bibliographical references (p. 192-199).

Micro-organisms are the most abundant and diverse form of life on Earth. Their ability to tolerate stress has enabled them to colonise many inhospitable environments. Microbial processes alter the chemistry of the environment which has left a lasting mark on the geological record. On the other hand, microbial life is heavily influenced by environmental conditions. Indeed, the history of the Earth is shaped by the co-evolution of microbial and geological processes. This thesis explores how micro-organisms are influenced by their environment, with particular reference to microbial rock habitats. Rock habitats are an interesting system to understand the inter-relationship between microbial life and it's environment as they are relatively simple and very common. Rock-dwelling communities are also exposed to numerous stresses such as surface UV exposure, desiccation, temperature fluctuations, low nutrient availability or toxicity from elements leached from the rocks themselves. Three specific aspects of microbial stress in rock environments are investigated here: 1) The use of rocks as a shield from surface UV radiation stress, 2) The microbial response to chemical changes during water-rock interactions, 3) The effect of simultaneous limitation of more than one nutrient. The first uses exposure facilities aboard the International Space Station to provide empirical evidence that colonisation of the early land masses by phototrophs was not inhibited by high surface UV radiation. The latter studies use quantitative proteomics to investigate the cellular response of a heterotrophic bacterium to nutrient deficiency and element leaching, two common stresses in rock habitats. Together these results further our understanding of the relationship between micro-organisms and rocks, both today and over geological time.

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Terra mine is an abandoned copper and silver mine in the Northwest Territories, Canada, from which mine tailings were deposited into Ho-Hum Lake, adjacent to the mine’s processing plant. The tailings contain elevated levels of arsenic (As), resulting in As levels exceeding Canadian sediment and water quality guidelines in the lake, and in downstream wetland water and sediment. This field and laboratory study focuses on the microbial ecology, and the reduction and oxidation of As, iron (Fe) and sulphur (S), in the wetland downstream from Ho-Hum Lake. This wetland is proposed as a passive remediation system for removal and storage of As. Using microcosm experiments, the stability of As-bearing sediments was compared in the upper, middle and lowestmost areas of the wetland over a 42-day period. Fresh sediments and sediments amended with a 10 mM acetate solution, both mixed with water, were compared. While no significant geochemical differences were found between acetate-amended and unamended microcosms, formation of inorganic As-S species was higher in amended microcosms, suggesting that micro-organisms were more active in the system because they were not carbon-limited. Formation of methylated-As species increased over time in all samples, including abiotic controls. Bacterial sulphate reduction occurred during the first 10 days of the experiment, perhaps resulting in precipitation of sulphide minerals. X-ray adsorption near edge spectroscopy was used to assess solid-state speciation of As in the sediments and indicated that pre-microcosm sediments from all sites showed high proportions of As(III)-S and As(III)-O speciation. Post-microcosm sediments revealed a 13% increase in the proportion of As(V)-O species, whereas abiotic controls showed only an 8% increase. DNA sequencing in post-microcosm sediments identified As, Fe and S reducing bacteria, and the geochemical patterns of As, Fe and S in the microcosms indicate the bacteria are likely active in the system. Microbial diversity and solid-state speciation of As in the sediments were assessed at varying depths at the microcosm sites, but correlation analysis revealed no significant relationship between As speciation and microbial diversity. A positive correlation between diversity and depth, and a negative relationship between As concentration and diversity, were found, perhaps indicating decreasing contamination with depth in the wetland. / Thesis (Master, Geological Sciences & Geological Engineering) -- Queen's University, 2011-07-03 23:27:44.373

The environmental, microbiological and technological aspects of selenium is explored with the aim of assessing and identifying microorganisms capable of interacting with Se in the environment and forming functional 'bionanomaterials'. To determine the natural microbial response to high selenium concentrations, and to understand the role soil microorganisms play in transforming Se, a field site in Co. Meath, Ireland, was identified and sampled to determine the Se contents. Detailed examination of the soil profile showed toxic levels of Se up to 156ppm. The highest Se concentrations correlated with elevated concentrations of higher plant matter, inferring a phytoconcentration mechanism for Se within a post glacial fen, and Se was identified as a reduced organic species. Microcosm experiments were established to test whether the soil microbial community displayed increased resistance to Se. These revealed the Se present in the soil was recalcitrant to microbial degradation and Se(VI) enriched experiments were noted to cause drastic alterations in community structure, indicating elevated Se resistance was not widespread throughout the community. Despite this, amended Se(VI) was rapidly reduced to Se(0), as determined by XAS. Selenium, and the group 16 element tellurium, also display physico-chemical properties that make them ideal for a range of industrial, chemical and technological applications, including sequestration of hazardous wastes and as metal chalcogenide semiconducting 'quantum dots'. Se(0) and Te(0) bionanomaterials formed by 'resting cell' cultures of the model environmental isolate Geobacter sulfurreducens, despite low MIC values, were characterised and subsequently applied to the sequestration of Hg(0)v derived from Hg historically used to preserve herbarium specimens. This showed that the Hg can be sequestered by the Se(0) bionanoparticles in the form of HgSe and demonstrated increased stability over abiotic counterparts. Finally, the bacteria G. sulfurreducens, Shewanella oneidensis and Veillonella atypica were compared for Se(IV) reducing capabilities, and V. atypica was shown to be adept at the production of significant quantities of Se(II-) utilising the electron shuttle AQDS. Biogenic Se(II-) compared favourably with abiotic Se(II-) solutions in the formation of metal selenide quantum dots, displaying increased particle growth control as shown via a novel, time resolved XAS technique. Bacterial polymeric substances are inferred in controlling Se(II-) precursor stability. This research shows that bacteria represent an alternative, facile, 'green' synthetic method for the production of next-generation technological nanomaterials.

The electron transfer mechanisms of multiheme cytochromes were examined with scanning tunneling microscopy (STM). To simulate bacterial metal reduction mediated by proteins in direct contact with mineral surfaces, monolayers of purified decaheme cytochromes from the metal-reducing bacterium Shewanella oneidensis were prepared on Au(111) surfaces. Recombinant tetracysteine sequences were added to two outermembrane decaheme cytochromes (OmcA and MtrC) from S. oneidensis MR-1 to ensure chemical immobilization on Au(111). STM images of the cytochrome monolayers showed good coverage and their shapes/sizes matched that predicted by their respective molecular masses. Current-voltage (I-V) tunneling spectroscopy revealed that OmcA and MtrC exhibit characteristic tunneling spectra. Theoretical modeling of the single-molecule tunneling spectra revealed a distinct tunneling mechanism for each cytochrome: OmcA mediates tunneling current coherently whereas MtrC temporarily traps electrons via orbital-mediated tunneling. These mechanisms suggest a superexchange electron transfer mechanism for OmcA and a redox-specific (i.e. heme-mediated) electron transfer mechanism for MtrC at mineral surfaces during bacterial metal reduction. Additionally, a novel electrochemical STM configuration was designed to measure tunneling current from multiheme cytochromes to hematite (001) surfaces in various electrolyte solutions. Current-distance (I-s) profiles on hematite (001) reveal predictable electric double layer structure that changes with ionic strength. The addition of the small tetraheme cytochrome c (STC) from S. oneidensis on insulated Au tips resulted in modified tunneling profiles that suggest STC significantly modulates the double layer. This observation is relevant to understanding metal reduction in cases where terminal metal-reducing enzymes are unable to come in direct contact with reducible mineral surfaces. Electronic coupling to the mineral surface might therefore be mediated by a localized ion swarm specific to the mineral surface. / Ph. D.