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Description
Microbial electrochemical cells (MXCs) are promising platforms for bioenergy production from renewable resources. In these systems, specialized anode-respiring bacteria (ARB) deliver electrons from oxidation of organic substrates to the anode of an MXC. While much progress has been made in understanding the microbiology, physiology, and electrochemistry of well-studied model ARB such as Geobacter and Shewanella, tremendous potential exists for MXCs as microbiological platforms for exploring novel ARB. This dissertation introduces approaches for selective enrichment and characterization of phototrophic, halophilic, and alkaliphilic ARB. An enrichment scheme based on manipulation of poised anode potential, light, and nutrient availability led to current generation that responded negatively to light. Analysis of phototrophically enriched communities suggested essential roles for green sulfur bacteria and halophilic ARB in electricity generation. Reconstruction of light-responsive current generation could be successfully achieved using cocultures of anode-respiring Geobacter and phototrophic Chlorobium isolated from the MXC enrichments. Experiments lacking exogenously supplied organic electron donors indicated that Geobacter could produce a measurable current from stored photosynthate in the dark. Community analysis of phototrophic enrichments also identified members of the novel genus Geoalkalibacter as potential ARB. Electrochemical characterization of two haloalkaliphilic, non-phototrophic Geoalkalibacter spp. showed that these bacteria were in fact capable of producing high current densities (4-8 A/m2) and using higher organic substrates under saline or alkaline conditions. The success of these selective enrichment approaches and community analyses in identifying and understanding novel ARB capabilities invites further use of MXCs as robust platforms for fundamental microbiological investigations.
ContributorsBadalamenti, Jonathan P (Author) / Krajmalnik-Brown, Rosa (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Rittmann, Bruce E. (Committee member) / Torres, César I (Committee member) / Vermaas, Willem (Committee member) / Arizona State University (Publisher)
Created2013
Description
Liquid-liquid interfaces serve as ideal 2-D templates on which solid particles can self-assemble into various structures. These self-assembly processes are important in fabrication of micron-sized devices and emulsion formulation. At oil/water interfaces, these structures can range from close-packed aggregates to ordered lattices. By incorporating an ionic liquid (IL) at the interface, new self-assembly phenomena emerge. ILs are ionic compounds that are liquid at room temperature (essentially molten salts at ambient conditions) that have remarkable properties such as negligible volatility and high chemical stability and can be optimized for nearly any application. The nature of IL-fluid interfaces has not yet been studied in depth. Consequently, the corresponding self-assembly phenomena have not yet been explored. We demonstrate how the unique molecular nature of ILs allows for new self-assembly phenomena to take place at their interfaces. These phenomena include droplet bridging (the self-assembly of both particles and emulsion droplets), spontaneous particle transport through the liquid-liquid interface, and various gelation behaviors. In droplet bridging, self-assembled monolayers of particles effectively "glue" emulsion droplets to one another, allowing the droplets to self-assembly into large networks. With particle transport, it is experimentally demonstrated the ILs overcome the strong adhesive nature of the liquid-liquid interface and extract solid particles from the bulk phase without the aid of external forces. These phenomena are quantified and corresponding mechanisms are proposed. The experimental investigations are supported by molecular dynamics (MD) simulations, which allow for a molecular view of the self-assembly process. In particular, we show that particle self-assembly depends primarily on the surface chemistry of the particles and the non-IL fluid at the interface. Free energy calculations show that the attractive forces between nanoparticles and the liquid-liquid interface are unusually long-ranged, due to capillary waves. Furthermore, IL cations can exhibit molecular ordering at the IL-oil interface, resulting in a slight residual charge at this interface. We also explore the transient IL-IL interface, revealing molecular interactions responsible for the unusually slow mixing dynamics between two ILs. This dissertation, therefore, contributes to both experimental and theoretical understanding of particle self-assembly at IL based interfaces.
ContributorsFrost, Denzil (Author) / Dai, Lenore L (Thesis advisor) / Torres, César I (Committee member) / Nielsen, David R (Committee member) / Squires, Kyle D (Committee member) / Rege, Kaushal (Committee member) / Arizona State University (Publisher)
Created2013
Description
Uranium (U) contamination has been attracting public concern, and many researchers are investigating principles and applications of U remediation. The overall goal of my research is to understand the versatile roles of sulfate-reducing bacteria (SRB) in uranium bioremediation, including direct involvement (reducing U) and indirect involvement (protecting U reoxidation). I pursue this goal by studying Desulfovibro vuglaris, a representative SRB. For direct involvement, I performed experiments on uranium bioreduction and uraninite (UO2) production in batch tests and in a H2-based membrane biofilm reactor (MBfR) inoculated with D. vuglaris. In summary, D. vuglaris was able to immobilize soluble U(VI) by enzymatically reducing it to insoluble U(IV), and the nanocrystallinte UO2 was associated with the biomass. In the MBfR system, although D. vuglaris failed to form a biofilm, other microbial groups capable of U(VI) reduction formed a biofilm, and up to 95% U removal was achieved during a long-term operation. For the indirect involvement, I studied the production and characterization of and biogenic iron sulfide (FeS) in batch tests. In summary, D. vuglaris produced nanocrystalline FeS, a potential redox buffer to protect UO2 from remobilization by O2. My results demonstrate that a variety of controllable environmental parameters, including pH, free sulfide, and types of Fe sources and electron donors, significantly determined the characteristics of both biogenic solids, and those characteristics should affect U-sequestrating performance by SRB. Overall, my results provide a baseline for exploiting effective and sustainable approaches to U bioremediation, including the application of the novel MBfR technology to U sequestration from groundwater and biogenic FeS for protecting remobilization of sequestrated U, as well as the microbe-relevant tools to optimize U sequestration applicable in reality.
ContributorsZhou, Chen (Author) / Rittmann, Bruce E. (Thesis advisor) / Krajmalnik-Brown, Rosa (Committee member) / Torres, César I (Committee member) / Arizona State University (Publisher)
Created2014
Description
With the aid of metabolic pathways engineering, microbes are finding increased use as biocatalysts to convert renewable biomass resources into fine chemicals, pharmaceuticals and other valuable compounds. These alternative, bio-based production routes offer distinct advantages over traditional synthesis methods, including lower energy requirements, rendering them as more "green" and "eco-friendly". Escherichia coli has recently been engineered to produce the aromatic chemicals (S)-styrene oxide and phenol directly from renewable glucose. Several factors, however, limit the viability of this approach, including low titers caused by product inhibition and/or low metabolic flux through the engineered pathways. This thesis focuses on addressing these concerns using magnetic mesoporous carbon powders as adsorbents for continuous, in-situ product removal as a means to alleviate such limitations. Using process engineering as a means to troubleshoot metabolic pathways by continuously removing products, increased yields are achieved from both pathways. By performing case studies in product toxicity and reaction equilibrium it was concluded that each step of a metabolic pathway can be optimized by the strategic use of in-situ adsorption as a process engineering tool.
ContributorsVasudevan, Anirudh (Author) / Nielsen, David R (Thesis advisor) / Torres, César I (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2014
Description
This dissertation provides a fundamental understanding of the properties of mesoporous carbon based materials and the utilization of those properties into different applications such as electrodes materials for super capacitors, adsorbents for water treatments and biosensors. The thickness of mesoporous carbon films on Si substrates are measured by Ellipsometry method and pore size distribution has been calculated by Kelvin equation based on toluene adsorption and desorption isotherms monitored by Ellipsometer. The addition of organometallics cobalt and vanalyl acetylacetonate in the synthesis precursor leads to the metal oxides in the carbon framework, which largely decreased the shrink of the framework during carbonization, resulting in an increase in the average pore size. In addition to the structural changes, the introduction of metal oxides into mesoporous carbon framework greatly enhances the electrochemical performance as a result of their pseudocapacitance. Also, after the addition of Co into the framework, the contraction of mesoporous powders decreased significantly and the capacitance increased prominently because of the solidification function of CoO nanoparticles. When carbon-cobalt composites are used as adsorbent, the adsorption capacity of dye pollutant in water is remarkably higher (90 mg/g) after adding Co than the mesoporous carbon powder (2 mg/g). Furthermore, the surface area and pore size of mesoporous composites can be greatly increased by addition of tetraethyl orthosilicate into the precursor with subsequent etching, which leads to a dramatic increase in the adsorption capacity from 90 mg/g up to 1151 mg/g. When used as electrode materials for amperometric biosensors, mesoporous carbons showed good sensitivity, selectivity and stability. And fluorine-free and low-cost poly (methacrylate)s have been developed as binders for screen printed biosensors. With using only 5wt% of poly (hydroxybutyl methacrylate), the glucose sensor maintained mechanical integrity and exhibited excellent sensitivity on detecting glucose level in whole rabbit blood. Furthermore, extremely high surface area mesoporous carbons have been synthesized by introducing inorganic Si precursor during self-assembly, which effectively determined norepinephrine at very low concentrations.
ContributorsDai, Mingzhi (Author) / Vogt, Bryan D (Thesis advisor) / La Belle, Jeffrey T (Committee member) / Dai, Lenore (Committee member) / Nielsen, David R (Committee member) / Torres, César I (Committee member) / Arizona State University (Publisher)
Created2012
Description
Microbial electrochemical cells (MXCs) offer an alternative to methane production in anaerobic water treatment and the recapture of energy in waste waters. MXCs use anode respiring bacteria (ARB) to oxidize organic compounds and generate electrical current. In both anaerobic digestion and MXCs, an anaerobic food web connects the metabolisms of different microorganisms, using hydrolysis, fermentation and either methanogenesis or anode respiration to break down organic compounds, convert them to acetate and hydrogen, and then convert those intermediates into either methane or current. In this dissertation, understanding and managing the interactions among fermenters, methanogens, and ARB were critical to making developments in MXCs. Deep sequencing technologies were used in order to identify key community members, understand their role in the community, and identify selective pressures that drove the structure of microbial communities. This work goes from developing ARB communities by finding and using the best partners to managing ARB communities with undesirable partners. First, the foundation of MXCs, namely the ARB they rely on, was expanded by identifying novel ARB, the genus Geoalkalibacter, and demonstrating the presence of ARB in 7 out of 13 different environmental samples. Second, a new microbial community which converted butyrate to electricity at ~70% Coulombic efficiency was assembled and demonstrated that mixed communities can be used to assemble efficient ARB communities. Third, varying the concentrations of sugars and ethanol fed to methanogenic communities showed how increasing ED concentration drove decreases in methane production and increases in both fatty acids and the propionate producing genera Bacteroides and Clostridium. Finally, methanogenic batch cultures, fed glucose and sucrose, and exposed to 0.15 – 6 g N-NH4+ L-1 showed that increased NH4+ inhibited methane production, drove fatty acid and lactate production, and enriched Lactobacillales (up to 40% abundance) above 4 g N-NH4+ L-1. Further, 4 g N-NH4+ L-1 improved Coulombic efficiencies in MXCs fed with glucose and sucrose, and showed that MXC communities, especially the biofilm, are more resilient to high NH4+ than comparable methanogenic communities. These developments offer new opportunities for MXC applications, guidance for efficient operation of MXCs, and insights into fermentative microbial communities.
ContributorsMiceli, Joseph (Author) / Torres, César I (Thesis advisor) / Krajmalnik-Brown, Rosa (Thesis advisor) / Rittmann, Bruce (Committee member) / Arizona State University (Publisher)
Created2015
Description
This research explores microbial chain elongation as a pathway for production of complex organic compounds in soils with implication for the carbon cycle. In chain elongation, simple substrates such as ethanol and short chain carboxylates such as acetate can be converted to longer carbon chain carboxylates under anaerobic conditions through cyclic, reverse β oxidation. This pathway elongates the carboxylate by two carbons. The chain elongation process is overall thermodynamically feasible, and microorganisms gain energy through this process. There have been limited insights into the versatility of chain elongating substrates, understanding the chain elongating microbial community, and its importance in sequestering carbon in the soils.
We used ethanol, methanol, butanol, and hydrogen as electron donors and acetate and propionate as electron acceptors to test the occurrence of microbial chain elongation in four soils with different physicochemical properties and microbial communities. Common chain elongation products were the even numbered chains butyrate, caproate, and butanol, the odd numbered carboxylates valerate and heptanoate, along with molecular hydrogen. At a near neutral pH and mesophilic temperature, we observed a stable and sustained production of longer fatty acids along with hydrogen. Microbial community analysis show phylotypes from families such as Clostridiaceae, Bacillaceae, and Ruminococcaceae in all tested conditions. Through chain elongation, the products formed are less biodegradable. They may undergo transformations and end up as organic carbon, decreasing the greenhouse gas emissions, thus, making this process important to study.
We used ethanol, methanol, butanol, and hydrogen as electron donors and acetate and propionate as electron acceptors to test the occurrence of microbial chain elongation in four soils with different physicochemical properties and microbial communities. Common chain elongation products were the even numbered chains butyrate, caproate, and butanol, the odd numbered carboxylates valerate and heptanoate, along with molecular hydrogen. At a near neutral pH and mesophilic temperature, we observed a stable and sustained production of longer fatty acids along with hydrogen. Microbial community analysis show phylotypes from families such as Clostridiaceae, Bacillaceae, and Ruminococcaceae in all tested conditions. Through chain elongation, the products formed are less biodegradable. They may undergo transformations and end up as organic carbon, decreasing the greenhouse gas emissions, thus, making this process important to study.
ContributorsJoshi, Sayalee (Author) / Delgado, Anca G (Thesis advisor) / Torres, César I (Committee member) / van Paassen, Leon (Committee member) / Arizona State University (Publisher)
Created2018
Description
Biological systems have long been known to utilize two processes for energy conservation: substrate-level phosphorylation and electron transport phosphorylation. Recently, a new bioenergetic process was discovered that increases ATP yields: flavin-based electron bifurcation (FBEB). This process couples an energetically favorable reaction with an energetically unfavorable one to conserve energy in the organism. Currently, the mechanisms of enzymes that perform FBEB are unknown. In this work, NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (Nfn), a FBEB enzyme, is used as a model system to study this phenomenon. Nfn is a heterodimeric enzyme that reversibly couples the exergonic reduction of NADP+ by reduced ferredoxin with the endergonic reduction of NADP+ by NADH. Protein film electrochemistry (PFE) has been utilized to characterize the catalytic properties of three ferredoxins, possible substrates for Nfn enzymes, from organisms that perform FBEB: Pyrococcus furiosus (PfFd), Thermotoga maritima (TmFd), and Caldicellulosiruptor bescii (CbFd). Additionally, PFE is utilized to characterize three Nfn enzymes from two different archaea in the family Thermococcaceae: two from P. furiosus (PfNfnI and PfXfn), and one from Thermococcus sibiricus (TsNfnABC). Key results are as follows. The reduction potentials of the [4Fe4S]2+/1+ couple for all three ferredoxins are pH independent and modestly temperature dependent, and the Marcus reorganization energies of PfFd and TmFd are relatively small, suggesting optimized electron transfer. Electrocatalytic experiments show that PfNfnI is tuned for NADP+ reduction by both fast rates and a low binding constant for NADP+. A PfNfnI variant engineered to have only cysteines as coordinating ligands for its [FeS] clusters has significantly altered rates of electrocatalysis, substrate binding, and FBEB activity. This suggests that the heteroligands in the primary coordination sphere of the [FeS] clusters play a role in controlling catalysis by Nfn. Furthermore, a variant of PfNfnI lacking its small subunit, designed to probe allosteric effects at the bifurcating site, has altered substrate binding at the NADP(H) binding site, i.e. the bifurcation site. PfXfn and TsNfnABC, representing different types of Nfn enzymes, have different electrocatalytic properties than PfNfnI, including slower rates of FBEB. This suggests that Nfn enzymes vary significantly over phylogenetically similar organisms despite relatively high primary sequence homology.
ContributorsJennings, David Peter (Author) / Jones, Anne K (Thesis advisor) / Redding, Kevin E (Committee member) / Torres, César I (Committee member) / Arizona State University (Publisher)
Created2018
Description
Microbial electrochemical cells (MxCs) are a novel technology that use anode-respiring bacteria (ARB) to bioremediate wastewaters and respire an electrical current, which can then be used directly to produce value-added products like hydrogen peroxide (H2O2). Ninety-five percent of the world’s H2O2 is currently produced using the anthraquinone process, whose production requires expensive and potentially carcinogenic catalysts and high amounts of electricity. However, the amount of H2O2 that can be produced from these microbial peroxide-producing cells (MPPCs) has not been thoroughly investigated. Predicting potential H2O2 production in MxCs is further complicated by a lack of mathematical models to predict performance utilizing complex waste streams like primary sludge (PS).
A reactor design methodology was developed for MPPCs to systematically optimize H2O2 production with minimal energy consumption. H2O2 stability was evaluated with different catholytes, membranes, and catalysts materials, and the findings used to design and operate long-term a dual-chamber, flat-plate MPPC using different catholytes, ferrochelating stabilizers, and hydraulic retention times (HRT). Up to 3.1 ± 0.37 g H2O2 L-1 was produced at a 4-h HRT in an MPPC with as little as 1.13 W-h g-1 H2O2 power input using NaCl catholytes. Attempts to improve H2O2 production by using weak acid buffers as catholytes or ferrochelating stabilizers failed for different reasons.
A non-steady-state mathematical model, MYAnode, was developed combinging existing wastewater treatment, anode biofilm, and chemical speciation models to predict MxC performance utilizing complex substrates. The model simulated the large-scale trends observed when operating an MPPC with PS substrate. At HRTs ≥ 12-d, the model demonstrated up to 20% Coulombic recovery. At these conditions, ARB required additional alkalinity production by ≥ 100 mgVSS/L of acetoclastic methanogens to prevent pH inhibition when little influent alkalinity is available. At lower HRTs, methanogens are unable to produce the alkalinity required to prevent ARB inhibition due to washout and rapid acidification of the system during fermentation. At ≥ 100 mgVSS/L of methanogens, increasing the diffusion layer thickness from 500 to 1000 μm improved Coulombic efficiency by 13.9%, while increasing particulate COD hydrolysis rates to 0.25/d only improved Coulombic efficiency by 3.9%.
A reactor design methodology was developed for MPPCs to systematically optimize H2O2 production with minimal energy consumption. H2O2 stability was evaluated with different catholytes, membranes, and catalysts materials, and the findings used to design and operate long-term a dual-chamber, flat-plate MPPC using different catholytes, ferrochelating stabilizers, and hydraulic retention times (HRT). Up to 3.1 ± 0.37 g H2O2 L-1 was produced at a 4-h HRT in an MPPC with as little as 1.13 W-h g-1 H2O2 power input using NaCl catholytes. Attempts to improve H2O2 production by using weak acid buffers as catholytes or ferrochelating stabilizers failed for different reasons.
A non-steady-state mathematical model, MYAnode, was developed combinging existing wastewater treatment, anode biofilm, and chemical speciation models to predict MxC performance utilizing complex substrates. The model simulated the large-scale trends observed when operating an MPPC with PS substrate. At HRTs ≥ 12-d, the model demonstrated up to 20% Coulombic recovery. At these conditions, ARB required additional alkalinity production by ≥ 100 mgVSS/L of acetoclastic methanogens to prevent pH inhibition when little influent alkalinity is available. At lower HRTs, methanogens are unable to produce the alkalinity required to prevent ARB inhibition due to washout and rapid acidification of the system during fermentation. At ≥ 100 mgVSS/L of methanogens, increasing the diffusion layer thickness from 500 to 1000 μm improved Coulombic efficiency by 13.9%, while increasing particulate COD hydrolysis rates to 0.25/d only improved Coulombic efficiency by 3.9%.
ContributorsYoung, Michelle Nichole (Author) / Rittmann, Bruce E. (Thesis advisor) / Torres, César I (Committee member) / Marcus, Andrew K (Committee member) / Arizona State University (Publisher)
Created2018
Description
The inherent risk in testing drugs has been hotly debated since the government first started regulating the drug industry in the early 1900s. Who can assume the risks associated with trying new pharmaceuticals is unclear when looked at through society's lens. In the mid twentieth century, the US Food and Drug Administration (FDA) published several guidance documents encouraging researchers to exclude women from early clinical drug research. The motivation to publish those documents and the subsequent guidance documents in which the FDA and other regulatory offices established their standpoints on women in drug research may have been connected to current events at the time. The problem of whether women should be involved in drug research is a question of who can assume risk and who is responsible for disseminating what specific kinds of information. The problem tends to be framed as one that juxtaposes the health of women and fetuses and sets their health as in opposition. That opposition, coupled with the inherent uncertainty in testing drugs, provides for a complex set of issues surrounding consent and access to information.
ContributorsMeek, Caroline Jane (Author) / Maienschein, Jane (Thesis director) / Brian, Jennifer (Committee member) / School of Life Sciences (Contributor) / Sanford School of Social and Family Dynamics (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05