The goal of this project is to decipher the quorum sensing (cell-to-cell signaling) abilities of Shewanella oneidensis MR-1, a Gram-negative bacterium well known for its ability to use geologic substrates, such as Fe and Mn oxides, for respiratory purposes. Overall our results show that S. oneidensis cannot utilize either an acyl-homoserine lactone (AHL) or AI-2 quorum sensing signal, despite previous work that indicated that it produced an AHL that would enhance it ability to growth in certain anaerobic environments. Using a variety of quorum sensing signal sensors, no evidence could be found that S. oneidensis has a typical AHL signal. An in silco analysis of the genome also produced little evidence that S. oneidensis has the genes to accept or relay an AHL signal. S. oneidensis can produce a luminescence response in the AI-2 reporter strain, Vibrio harveyi MM32. This luminescence response is abolished upon deletion of luxS, the gene responsible for catalyzing AI-2. Deletion of luxS also affected biofilm formation. Within 16 hours of growth in a biofilm flow-through reactor, the luxS mutant had an inhibited ability to initiate biofilm formation. After 48 hours of growth, the mutant's biofilm had developed similarly to wild-type. The addition of synthetic AI-2 did not restore the mutant's ability to initiation biofilm formation, which led to the conclusion that AI-2 is not likely used as a quorum sensing signal in S. oneidensis for this phenotype. Because of the involvement of LuxS in the activated methyl cycle (AMC) in other organisms, growth on various sulfur sources was examined. A mutation in luxS produced a reduced ability to growth with methionine as the sole sulfur source. Methionine is a key metabolite used in the AMC to produce a methyl source in the cell and homocysteine. This data suggests that LuxS is important in metabolizing methionine and the AMC in S. oneidensis. / Ph. D.

Dissimilatory iron reduction (DIR) is significant to the biogeochemical cycling of iron, carbon and other elements, and may be applied to bioremediation of organic pollutants, toxic metals, and radionuclides; however, the mechanism(s) of DIR and factors controlling its kinetics are still unclear. To provide insights into these questions, the interaction between a common dissimilatory iron reducing bacterium (DIRB)was studied, Shewanella oneidensis MR-1, and ferric iron (Fe(III)) (oxy)(hydr)oxide mineral surfaces. Firstly, atomic force microscopy was used to study how S. oneidensis MR-1 dissolved Fe(III) (oxy)(hydr)oxides and compared it to two other cases where Fe(III) (oxy)(hydr)oxides were either dissolved by a chemical reductant or by a mutant with an electron shuttling compound. Without the electron shuttling compound, the mutant is unable to respire on Fe(III) (oxy)(hydr)oxides, but with the electron shuttling compound, it can. It was found that the cells of S. oneidensis MR-1 formed microcolonies on mineral surfaces and dissolved the minerals in a non-uniform way which was consistent with the shape of microcolonies, whereas Fe(III) (oxy)(hydr)oxides were uniformly dissolved in both of the other cases. Secondly, confocal microscopy was used to study the adhesion behavior of S. oneidensis MR-1 cells on Fe(III) (oxy)(hydr)oxide surfaces across a broad range of bulk cell densities. While the cells were evenly distributed under low bulk cell densities, microcolonies were observed at high bulk cell densities. This adhesion behavior was modeled by a new, two-step adhesion isotherm which fit better than a simple Langmuir or Freundlich isotherm. The results of these studies suggest that DIR is in-part transport limited and the surface cell density may control DIR.

A dissertation is presented on the bioreduction of hematite (α-Fe2O3) nanoparticles. The study shows that an alternative extracellular electron transfer mechanism other than the classical 'direct-contact' mechanism may be simultaneously employed by Shewanella oneidensis MR-1 during solid-phase metal reduction. This conclusion is supported by analysis of the bioreduction kinetics of hematite nanoparticles coupled with microscopic investigations of cell-mineral interactions. The reduction kinetics of metal-oxide nanoparticles were examined to determine how S. oneidensis utilizes these environmentally-relevant solid-phase electron acceptors. Nanoparticles involved in geochemical reactions show different properties relative to larger particles of the same phase, and their reactivity is predicted to change as a function of size. To demonstrate these size-dependent effects, the surface area normalized reduction rates of hematite nanoparticles by S. oneidensis MR-1 with lactate as the sole electron donor were measured. As evident from whole cell TEM analysis, the mode of nanoparticle adhesion to cells is different between the more aggregated, pseudo-hexagonal to irregular shaped 11 nm, 12 nm, 99 nm and the less aggregated 30 nm and 43 nm rhombohedral particles. The 11 nm, 12 nm and 99 nm particles show less cell contact and coverage than the 30 nm and 43 nm particles but still show significant rates of reduction. This leads to the provisional speculation that S. oneidensis MR-1 employs a pathway of indirect electron transfer in conjunction with the direct-contact pathway, and the relative importance of the mechanism employed depends upon aggregation level and the shape of the particles or crystal faces exposed. In accord with the proposed increase in electronic band-gap for hematite nanoparticles, the smallest particles (11 nm) exhibit one order of magnitude decrease in reduction when compared with larger (99 nm) particles, and the 12 nm rates fall in between these two. This effect may also be due to the passivation of the mineral and cell surfaces by Fe(II), or decreasing solubility due to decrease in size. / Ph. D.

The chemical and physical processes controlling contaminant fate and transport in the vadose zone limit the options for application of many remedial technologies. Foam delivery technology (FDT) has been developed as a potential solution to overcome these limitations for remediating subsurface and deep vadose zone environments using reactive amendments. Although there are many advantages to utilizing FDT for treatment in the deep vadose zone, little information is available on how the addition of these surfactants and remedial amendments affect the indigenous microbial communities in the deep vadose zone as well as the impact of biological transformations of surfactant-based foams on remediation efforts. The purpose of this study was to develop a rapid method for assessment of microbial communities in contaminated subsurface environments. This research was divided into two phases: (1) assess the toxicity of proposed FDT components on a single bacterial species, Shewanella oneidensis MR-1; and (2) determine the effects of these components on a microbial community from the vadose zone. In Phase I, S. oneidensis MR-1 was exposed to proposed FDT components to assess potential growth inhibition or stimulation caused by these chemicals. S. oneidensis MR-1 cultures were exposed to the surfactants sodium laureth sulfate (SLES), sodium dodecyl sulfate (SDS), cocamidopropyl betaine (CAPB), and NINOL 40-CO, and the remedial amendment, calcium polysulfide (CPS). Results from this phase revealed that the relative acute toxicity order for these compounds was SDS>>CPS>>NINOL40-CO>SLES≥CAPB. High concentrations of SDS were toxic to the growth of S. oneidensis MR-1 but low concentrations were stimulatory. This benchtop system provided a capability to assess adverse microbial-remediation responses and contributed to the development of in situ remedial chemistries before they are deployed in the field. For Phase II, sediments from the BC Cribs and Trenches (BCCT) area of the Hanford Site, WA, were characterized before and after exposure to potential FDT components. First, the phylogenetic and metabolic diversity of sediment from the BCCT was assessed by sequencing the microbial community and measuring the metabolic activity. The sediment was also incubated with various concentrations of SDS, CAPB, and CPS. Phylogenetic analysis detected phylotypes from the Alpha-, Beta-, Delta-, and Gammaproteobacteria, and Actinobacteria. Unlike the S. oneidensis MR-1 studies conducted in Phase I, the surfactants and CPS stimulated the metabolic activity of the native microbial communities. The observed stimulation could be caused by sorption of the chemicals to the sediment particles, or utilization of the surfactants by the microbial communities. These findings emphasize the importance of monitoring microbial activity at remediation sites in order to determine short and long term efficacy of the treatment, compliance with regulatory mandates, and act as an early warning indicator of unintended changes to the subsurface.