Acidithiobacillus ferrooxidans is an important industrial organism used in the mining industry where it participates in passive bioleaching processes used to produce about 20% of the world’s copper supply. The bacterium thrives in strong mineral acids at ambient temperatures and derives metabolic energy from the oxidation of ferrous iron, sulfur, and reduced inorganic sulfide compounds to fix CO2 and N2. This unique metabolism provides new opportunities to engineer this organism for the production of fuels and chemicals from CO2. While A. ferrooxidans has been studied extensively for 60 years, the tools and methods necessary for a robust genetic system to manipulate and further study this bacterium are not well developed and published techniques are generally difficult to reproduce. This research focuses on developing the means to genetically modify this species to experimentally study its physiology and engineer the organism for the production of chemicals from CO2. This includes developing a robust and reproducible system to generate and select mutant strains, heterologous expression of exogenous genes, characterizing endogenous inducible promoters, and developing new plasmids to expand the repertoire of tools available for this organism.

Thesis (doctoral)--University of Helsinki, 2009. / Includes bibliographical references. Also available on the World Wide Web.

Thesis (M.S.)--Oregon State University, 2010. / Printout. Includes bibliographical references (leaves 45-52). Also available on the World Wide Web.

This work resulted in the development of multiple distinct and novel methods of cheaply producing large numbers of biologically derived, complex, 3-dimensional microstructures in a multitude of possible compositions. The biologically derived structures employed in this work were diatoms, a type of single celled algae, which grow complex silica shells in species-specific shapes. Due to the wide diversity of naturally occurring diatom shapes (on the order of 105), and the flexibility in tailoring chemical compositions using the methods developed here, real potential exists for cheaply mass-producing industrially relevant quantities of controlled shape and size 3-d particles for the first time. The central theme of this research is the use of diatoms as a transient scaffold onto which a coating is applied. After curing the coating, and in some cases firing the coating to form ceramic, the diatom can be selectively etched away leaving a free standing replica of the original structure with the salient features of the pre-form intact, but now composed of a completely different material. Using this concept, specific methods were developed to suit various precursors. Dip coating techniques were used to create epoxy diatoms, and silicon carbide diatoms. The Sol-Gel method was used to synthesize zirconia diatoms in both the tetragonal and monoclinic phases. A multi step method was developed in which previously synthesized epoxy diatoms were used as a template for deposition of a silicon carbide precursor and then heat treated to produce a silicon carbide/carbon multi-component ceramic. A hydrothermal reaction was also developed to convert Titania diatoms to barium titanate by reaction with barium hydroxide. Finally, the device potential of diatom-derived structures was conclusively demonstrated by constructing a gas sensor from a single Titania diatom. Under suitable conditions, the sensor was found to have the fastest response and recovery time of any sensor of this type reported in the literature. Furthermore, this work has laid the groundwork for the synthesis of many other tailored compositions of diatoms, and provided several compositions for device creation.

Diatoms possess characteristics such as abundance, diversity, and high reproductivity, which make their nano-structured frustules (diatom frustules) attractive for a wide range of applications. To overcome the limitation of their silica based frustule composition, diatom frustules have been converted into a variety of materials including silicon, silicon carbide, silver, gold, palladium and carbon in the present study. The compositions and the extent of shape preservation of the replicas are examined and evaluated with different characterization methods such as X-ray diffraction, SEM, TEM and FTIR analyses. These replicas still retained the complex 3D structures and nano-scaled features of the starting diatom frustules. Some properties and possible applications of converted materials are explored and the kinetics and thermodynamics related to the successful replications (conversions) are also studied and discussed.