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Important reactions in the environment often occur at the interface between a mineral surface and aqueous phase. Reactions occurring at this interface often control the uptake or release of harmful components resulting in the geochemical cycling of elements in the environment. Additionally, minerals are commonly used in the remediation of contaminated areas, where similar chemistry occurs at their interfaces. Thus, studies of the chemistry of these interfaces are essential to our understanding of complex environments. Many of these processes are controlled by electron transfer reactions between adsorbates and the mineral interface, and it is here where this research presented will concentrate. The studies in this thesis key in on redox chemistry on various environmentally relevant iron minerals, including ferrihydrite, pyrite, and amorphous iron sulfide. A large portion of this body of work is dedicated to the understanding of the surface mediated reaction between chromate (Cr(VI)) and arsenite (As(III)). Both of these species are present in the environment and are detrimental to human health. Using in- and ex-situ experiments we have monitored the coupled redox transformation of Cr(VI) and As(III) to chromite (Cr(III)) and arsenate (As(V)). Quantum mechanical modeling was used to support the experimental studies of this novel redox chemistry. The reaction was monitored in situ, using attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), on the surface of the iron oxyhydroxide, ferrihydrite, at various solution pH values by following vibrational modes unique to Cr(VI), As(III), and As(V). At pH < 9 we observed an initial growth of Cr(VI) vibrational modes due to adsorption, followed by the simultaneous decrease in Cr(VI) vibrational modes and increase in As(V) vibrational modes. Ex situ analysis of the reaction products via X-ray absorption spectroscopy (XAS) and X-ray photoelectron spectroscopy (XPS) indicated that there was an increase in the percentage of reaction products as the pH decreased. Quantum mechanical calculations were completed to model the reaction of Cr(VI) and As(III) on the ferrihydrite surface by analyzing differences in geometric and electronic structural changes and thermodynamic preferences. The results indicate that Cr(VI) and As(III) adsorbed physically separated from each other is not only thermodynamically favorable but results in changes in As(III)-Fe and Cr(VI)-Fe atomic distances, towards those characteristic of As(V)-Fe and Cr(III)-Fe. Thus a mechanism where electron transport occurs through bulk states is plausible. Additionally, natural bond order analysis reveals a redistribution of electron density away from the Cr(VI) atomic center upon adsorption, indicating probable changes in Cr(VI) reduction potential. The electrochemical reduction of Cr(VI) on three surfaces, ferrihydrite, titanium dioxide, and aluminum oxides, indicate that Cr(VI) reduction potential is surface dependent, an observation that has significance for redox chemistry in the environment. The interaction of ferric, Fe(III), with iron sulfide surfaces (during and after coal mining activities) contributes to the detrimental environmental problem known as acid mine drainage (AMD). We investigated whether Fe(III) chelating siderophores could be used to suppress the oxidation of iron sulfide surfaces and the resulting AMD chemistry. The exposure of the iron sulfide, pyrite, to the siderophore, desferrioxamine B (DFOB) at initial pH values of 3, 6, and 8 under oxic conditions showed a significant decrease in the rate of dissolution of pyrite: decreases of 43.7%, 37.5% and 78.4%, respectively. An even greater decrease in pyrite oxidation was observed when DFOB was present in anoxic conditions, specifically 56.1%, 74.4% and 91.5%, at pH 3, 6 and 8, respectively. We further compared the rate of dissolution between DFOB and another siderophore, enterobactin, which is a stronger chelator of Fe(III). The presence of enterobactin suppressed pyrite oxidation more than DFOB, consistent with the contention that inhibiting the interaction of Fe(III) with pyrite will decrease the oxidation of the mineral. We also analyzed the exposure of the pyrite surface to DFOB using ATR-FTIR, to determine if any surface chelation occurs. We found that when Fe(III) is present on the pyrite surface, DFOB adsorbs to the surface via hydroxamate groups, similar to the aqueous phase spectra of DFOB-Fe(III) complex. In contrast the spectra do not exhibit hydroxamate vibrational modes when Fe(III) was not initially present on the pyrite surface and in this circumstance the spectra resembled that of aqueous phase unchelated DFOB. Taken together the results showed that siderophore inhibited pyrite oxidation by chelating Fe(III) present on the pyrite surface and in solution. Finally, the reduction of NO(g) to NH3/NH4+ with amorphous iron sulfide (FeS) was studied. The exposure of NO gas to a suspension of FeS solid resulted in the conversion of 2.3% NO(g) to the reaction product ammonia (NH3), which was found to grow over time, while the exposure of NO(g) to water (in the absence of mineral) resulted in no NH3 formation. Additionally, we completed in situ analysis of NO exposure to FeS as a function of water concentration using ATR-FTIR. The exposure of NO to an aqueous paste of FeS or a FeS film (with adsorbed H2O), resulted in the adsorption of NO to the FeS surface and the subsequent production of NH3, as indicated by N-H vibrational modes. In contrast, the removal of all water, via thermal desorption from the film, resulted in the adsorption of NO but did not show vibrational modes consistent with the formation of NH3. We conclude that the presence of H2O, as a source of protons, and a FeS surface, as a source of electrons, results in the transformation of NO to NH3 via a heterogeneous reaction. This result has important implications towards remediation of NOx gases and mechanisms of prebiotic synthesis of NH3. In summary, the research presented expands our understanding of redox reactions at mineral interfaces in the environment. The work herein aims to inform and aid in the development of remediation methods for arsenic and chromium, the formulation of methods to inhibit the production of acid mine drainage, and develop our understanding of toxic NOx gas reduction on surfaces. / Chemistry

Las manifestaciones de cobre de la Cuenca Neuquina ubicadas en el Dorso de los Chihuidos-DCh- y la Dorsal de Huincul-DH-, corresponden a la clase de depósito de cobre tipo red-bed. Los prospectos estudiados (Grillo, Sapo Sur, Barda González y El Porvenir) están alojados en las areniscas decoloradas dentro de estratos rojos de las formaciones Huincul y Portezuelo (Grupo Neuquén). Durante la diagénesis temprana de las areniscas se formaron: coatings de hematita, caolinita (60°C), crecimientos secundarios de cuarzo (70°C) y albita (≥90°C), analcima y calcita (I) (76°-84°C). El empaquetamiento abierto de las areniscas, la significativa porosidad y la historia de soterramiento (hasta 2000m), indican que la compactación fue moderada. Durante la tectónica andina, en el Terciario, la reactivación de fallas y el desarrollo de chimeneas de gas, permitieron la conexión de reservorios profundos con los niveles someros del Grupo Neuquén, resultando en numerosos episodios de migración de hidrocarburos y salmueras. Las reacciones redox entre las areniscas rojas, las aguas de formación y los hidrocarburos generaron la disolución de clastos y cementos y la liberación de Fe2+ y S que fueron removidos o incorporados en pirita por reducción termoquímica (TSR) (δ34SV-CDT +10,2‰) o biogénica (BSR) (δ34S V-CDT -60,2‰ a +18,2‰) del sulfato, dando lugar a las areniscas blancas. La calcita (II) precipitó de un sistema heterogéneo formado por fluidos acuosos (4,18%-8,68% en peso NaCl eq.) calientes (94°-144°C) y por hidrocarburos. Este carbonato registra una fuente de δ13CV-PDB liviano (hasta -9,97‰) producto de la oxidación de los hidrocarburos. En el frente redox del sistema precipitaron montmorillonita, interestratificado clorita/esmectita ± illita/esmectita, hematita secundaria y vanadio, formando las areniscas grises y marrones. Durante un nuevo pulso de migración de fluidos, las salmueras oxidadas, que probablemente lixiviaron S y Cl de las evaporitas y Cu de las areniscas rojas y del basamento ígneo subyacentes, precipitaron los sulfuros de Cu-Fe en las areniscas blancas, en contacto con los hidrocarburos. En el DCh precipitó pirita y luego calcosina-djurleita (δ34SV-CDT -45,2‰ a -41,7‰) a temperaturas <100ºC por BSR en un sistema abierto, con una fuente ilimitada de azufre y con metano como agente reductor. En la DH, pirita fue reemplazada por bornita y calcopirita (δ34SV-CDT +12,3‰) a temperaturas >100°C consumiendo el azufre removilizado de la pirita (δ34SV-CDT +10,2‰). A temperaturas <100ºC, calcosina-espionkopita (δ34SV-CDT hasta -11,7‰) reemplazaron a pirita y bornita a partir de la mezcla del S más pesado de los sulfuros previos con un S más liviano generado por BSR y también precipitaron in situ a partir del S biogénico. Calcita tardía (III) precipitó en contacto con los sulfuros a bajas temperaturas (hasta 89°C). La composición isotópica de este carbonato (δ13CV-PDB -9‰ a -32‰) sugiere una mayor incorporación del C orgánico por oxidación de los hidrocarburos durante los procesos redox. La yacencia de la mineralización en las areniscas decoloradas y en estructuras discordantes con la roca de caja junto a la estrecha relación de la mineralización con los hidrocarburos, indican su origen epigenético. Esta mineralización, asociada a la migración de fluidos a escala regional, acentúa el rol de los hidrocarburos en las reacciones orgánicasinorgánicas desencadenantes de procesos mineralizantes. / In the Chihuidos High (DCh) and Huincul Ridge (DH), Neuquén Basin, copper mineralization belongs to red-bed type sediment-hosted copper deposits. Grillo, Sapo Sur, Barda González and El Porvenir districts occur within bleached red beds of Huincul and Portezuelo Formations (Neuquén Group). During early diagenesis the following mineral sequence precipitated: hematite coatings, kaolinite (60°C), quartz (70°C) and albite (≥90°C) overgrowths, analcite and calcite (I) (76°-84°C). Open sandstone packaging, significant porosity and burial history (up to 2000m depth) suggest moderate compaction During Andean tectonic deformation, in the Tertiary, reactivation of basement faults and development of gas chimneys, lead to the connection of deep reservoirs with the shallow stratas of the Neuquén Group, resulting in several stages of basinal brine and hydrocarbon migrations. Redox reactions developed among red stratas and related oxidizing-water formations with hydrocarbons, formed the bleached sandstones characterized by detrital and authigenic mineral dissolution, release of Fe2+ and S that were removed or precipitated as pyrite by either thermochemical (TSR) (δ34SV-CDT +10.2‰) or bacteria sulfate reduction (BSR) (δ34SV-CDT -60.2‰ and +18.2‰). Precipitation of calcite (II) from warm (94-144°C) aqueous (4.18% to 8.68% wt. NaCl eq.) fluids and hydrocarbons, record a depleted δ13CV-PDB source (up to -9.97‰) resulted by hydrocarbons oxidation. At the redox front, montmorillonite, interstratified chlorite/smectite ± illite/smectite, secondary hematite, and V precipitated, resulting in the development of the gray and brown sandstones. During a renewed stage of fluid migration, oxidized brines, charged with S and Cl from the underlying evaporites and Cu leached from the underlying red beds and igneous basement, precipitated Cu-Fe sulfides in bleached sandstones at the hydrocarbons interface. At DCh, first precipitated pyrite and then chalcocite-djurleite (δ34SV-CDT -45.2‰ to -41.7‰) at temperatures <100ºC by BSR in an open system with an unlimited source of sulfate and methane as a reductant. At DH, pyrite was replaced by chalcopyrite and bornite (δ34SV-CDT +12.3‰) at temperatures >100°C consuming the S remobilized from the former pyrite (δ34SV-CDT +10.2‰). At <100ºC chalcocite-spionkopite (δ34SV-CDT up to -11.7‰) replaced pyrite-bornite-chalcopyrite and may precipitated from heavier S of previous sulfides and lighter S generated from BSR; chalcocite-spionkopite also precipitated in situ, from the biogenic S. Calcite gangue (III) associated with sulfides formed at low temperatures (up to 89°C). The isotopic composition of this carbonate (δ13CV-PDB -9‰ a -32‰), suggest an increase of organic C related to hydrocarbon oxidation produced during redox processes. Mineralization related to bleached sandstones and hydrocarbons together with the presence of crosscutting mineralized structures, suggest an epigenetic origin for the mineralization. The mineralization, related to basin-wide fluid migration, enhance organicinorganic reactions as a plausible trigger to metals precipitation.

Understanding oxygenation throughout Earth history, particularly intervals where marine deoxygenation occurred, are crucial to investigating the changes in habitability on Earth. Marine deoxygenation events, in particular, can result in changes in the carbon, sulfur, and iron cycles on our planet. Changes in these elemental cycles lead to distinctive variation in the chemical composition of seawater that is recorded in marine sediments that are preserved into the sedimentary record. Our modern ocean is experiencing rapid deoxygenation, thus understanding the duration and extent of ancient deoxygenation events is vital to predicting future climate scenarios. Here I investigated the record of environmental change during the Early Jurassic Toarcian Oceanic Anoxic Event or T-OAE (~183 Ma). The first chapter of this dissertation investigates the record of marine anoxia across the Pliensbachian to Toarcian transition. Specifically, I investigate the temporal and geographic development of anoxia across three basins from the European Epicontinental Seaway. Through utilization of iron speciation, a local redox proxy, I identify anoxia developing before and persisting well after the negative carbon isotope excursion (NCIE) conventionally used to define the T-OAE. These data indicate an increase in the occurrence of anoxia at the Pliensbachian – Toarcian boundary, coincident with the initial phase of volcanism associated with the Karoo-Ferrar Large Igneous Province and an interval of heightened marine invertebrate extinction. Ultimately, our data support a greater temporal extent of anoxic conditions around the T-OAE, which support the greater sensitivity of marine oxygen levels to climatic change outside of the NCIE interval. The second chapter of this dissertation assesses the occurrence and extent of organic matter sulfurization (OMS), a biogeochemical feedback known to enhance the preservation and burial of OM. Because this process is accelerated when euxinic conditions develop in the water column, I investigated it as a mechanism promoting OM burial across two oceanic anoxic events of the Mesozoic. Importantly, I find that sulfurization does not occur uniformly across both events and propose a conceptual model of the depositional settings most favorable for sulfurization to occur and when throughout geologic time OMS is most likely to influence the global cycles of carbon and sulfur. / Doctor of Philosophy / Understanding past time intervals where there was widespread loss of oxygen in the oceans is crucial to understanding habitability on Earth. Since our modern oceans are experiencing a rapid loss of oxygen, understanding the duration and extent of ancient marine oxygen loss events is vital to predicting future habitability of the oceans. These ancient events can result in distinctive changes in the carbon, sulfur, and iron cycles on our planet. Variation in these elemental cycles lead to distinctive shifts in the chemical composition of seawater that is recorded in marine sediments that get preserved as rocks in the geologic record. Here, I investigated the record of environmental change during the Early Jurassic Toarcian Oceanic Anoxic Event or T-OAE (~183 Ma). The first chapter of this dissertation investigates the record of marine oxygen loss across the T-OAE. Specifically, I investigate the temporal and geographic development of oxygen loss across three ancient marine basins. Through utilization of a local tracer of water column oxygen loss (e.g. iron speciation) I identify oxygen loss developing before and persisting well after the conventional timeframe associated with the event. These data indicate oxygen loss first occurred before the T-OAE, coincident with the initial phase of volcanic eruptions from the Karoo-Ferrar Large Igneous Province and an interval of heightened marine extinction. Ultimately, these data support a longer time interval of oxygen loss around the T-OAE and the greater sensitivity of marine oxygen levels to climatic change. The second chapter of this dissertation assesses the occurrence and extent of organic matter sulfurization (OMS), a feedback known to enhance the preservation and burial of organic matter (OM). Because this process is accelerated when oxygen is lost and free sulfur builds up in the water column, I investigated its occurrence across two oceanic oxygen loss events of the Mesozoic Era. Importantly, I find that sulfurization does not occur uniformly across both events and propose a conceptual model of the settings most favorable for sulfurization to occur and also when in geologic time it is most likely to influence the global cycling of carbon and sulfur.

Methanogens are a group of microorganisms that utilize simple compounds such as H₂ + CO₂, acetate and methanol for the production of methane, an end-product of their metabolism.  These obligate anaerobes belonging to the archaeal domain inhabit diverse anoxic environments such as rice paddy fields, human guts, rumen of ruminants, and hydrothermal vents.  In these habitats, methanogens are often exposed to O₂ and previous studies have shown that many methanogens are able to tolerate O2 exposure.  Hence, methanogens must have developed survival strategies to be able to live under oxidative stress conditions.  The anaerobic species that lived on Earth during the early oxygenation event were first to face oxidative stress.  Presumably some of the strategies employed by extant methanogens for combating oxidative stress were developed on early Earth.   Our laboratory is interested in studying the mechanism underlying the oxygen tolerance and oxidative stress responses in methanogenic archaea, which are obligate anaerobe.  Our research concerns two aspects of oxidative stress.  (i) Responses toward extracellular toxic species such as SO32-, that forms as a result of reactions of O₂ with reduced compounds in the environment.  These species are mostly seen in anaerobic environments upon O₂ exposure due to the abundance of reduced components therein.  (ii) Responses toward intracellular toxic species such as superoxide and hydrogen peroxide that are generated upon entry of O₂ and subsequent reaction of O₂ with reduced component inside the cell.  Aerobic microorganisms experience the second problem.  Since a large number of microorganisms of Earth are anaerobes and the oxidative defense mechanisms of anaerobes are relatively less studied, the research in our laboratory has focused on this area.  My thesis research covers two studies that fall in the above-mentioned two focus areas. In 2005-2007 our laboratory discovered that certain methanogens use an unusual sulfite reductase, named F420-dependent sulfite reductase (Fsr), for the detoxification of SO32- that is produced outside the cell from a reaction between oxygen and sulfide.  This reaction occurred during early oxygenation of Earth and continues to occur in deep-sea hydrothermal vents.  Fsr, a flavoprotein, carries out a 6-electron reduction of SO32- to S2-.  It is a chimeric protein where N- and C-terminal halves (Fsr-N and Fsr-C) are homologs of F420H2 dehydrogenase and dissimilatory sulfite reductase (Dsr), respectively.  We hypothesized that Fsr was developed in a methanogen from pre-existing parts.  To begin testing this hypothesis we have carried out bioinformatics analyses of methanogen genomes and found that both Fsr-N homologs and Fsr-C homologs are abundant in methanogens.  We called the Fsr-C homolog dissimilatory sulfite reductase-like protein (Dsr-LP).  Thus, Fsr was likely assembled from freestanding Fsr-N homologs and Dsr-like proteins (Dsr-LP) in methanogens.  During the course of this study, we also identified two new putative F420H2-dependent enzymes, namely F420H2-dependent glutamate synthase and assimilatory sulfite reductase. Another aspect of my research concerns the reactivation of proteins that are deactivated by the entry of oxygen inside the cell.  Here I focused specifically on the role of thioredoxin (Trx) in methanogens.  Trx, a small redox regulatory protein, is ubiquitous in all living cells.  In bacteria and eukarya, Trx regulates a wide variety of cellular processes including cell divison, biosynthesis and oxidative stress response.  Though some Trxs of methanogens have been structurally and biochemically characterized, their physiological roles in these organisms are unknown.  Our bioinformatics analysis suggested that Trx is ubiquitous in methanogens and the pattern of its distribution in various phylogenetic classes paralleled the respective evolutionary histories and metabolic versatilities.  Using a proteomics approach, we have identified 155 Trx targets in a hyperthermophilic phylogenetically deeply-rooted methanogen, Methanocaldococcus jannaschii.  Our analysis of two of these targets employing biochemical assays suggested that Trx is needed for reactivation of oxidatively deactivated enzymes in M. jannaschii.  To our knowledge, this is the first report on the role of Trx in an organism from the archaeal domain. During the course of our work on methanogen Trxs, we investigated the evolutionary histories of different Trx systems that are composed of Trxs and cognate Trx reductases.  In collaboration with other laboratories, we conducted bioinformatics analysis for the distribution of one of such systems, ferredoxin-dependent thioredoxin reductase (FTR), in all organisms.  We found that FTR was most likely originated in the phylogenetically deeply-rooted microaerophilic bacteria where it regulates CO₂ fixation via the reverse citric acid cycle. / Ph. D.