Doctor of Philosophy, University of Akron, 2024, Integrated Bioscience

The scientific reciprocity of environmental geomicrobiology and biotechnology harnessing microbially induced carbonate precipitation (MICP) is epitomized by cave speleothem research; delineating environmental conditions uncovers factors that inform the development of industrial bacteriogenic mineralization processes, with greater control over the end products. Reconciling bacterial metabolism and CaCO3 precipitation has the potential to recontextualize geological precipitation events as microbial byproducts, warranting interdisciplinary investigation. In Wind Cave, South Dakota, I identified a complex weave of speleoclimatic, geochemical, and microbiological dynamics that controls the materialization and polymorphism of CaCO3 secondary deposits known as frostwork. Microclimatic monitoring and analysis suggested an evaporative environment, modelled from detailed temperature, humidity and airflow data. Airflow measurements support a causal link between cave wind directionality and the occurrence of frostwork. Sequential deposition of carbonate phases characterizes bulk frostwork formations according to shifting Mg2+/Ca2+ ratios over the speleothem lifetime, yielding multiaggregate formations consisting of calcite, aragonite, hydromagnesite, dolomite, opal, and smectite. Thin sections showed diagenetic fabrics indicative of oscillating supersaturation conditions in response to surface seasonal climatic changes. Scanning electron microscopy (SEM) analyses identified frostwork's aragonite crystal topography as a microecological niche supporting filamentous Actinomyces bacteria, leaving room for a microbial component to Wind Cave frostwork development. To begin to monitor the impact of factors controlling crystal growth in vitro I developed two parallel techniques for measuring bacteriogenic carbonate precipitation in Escherichia coli cultures, using i) image analysis for agar media, and ii) inductively coupled plasma–optical emission spectroscopy (ICP-OES) ion quantifica (open full item for complete abstract)

Committee: Hazel Barton (Advisor); John Senko (Committee Member); Andreas Pflitsch (Committee Member); Bogdan Onac (Committee Member); Brian Bagatto (Committee Member) Subjects: Biology; Geobiology; Microbiology; Mineralogy

Doctor of Philosophy, University of Akron, 2024, Integrated Bioscience

Corrosion in natural gas transmission pipelines poses significant risks to infrastructure integrity, leading to environmental damage and economic loss. This dissertation investigates microbiologically influenced corrosion (MIC) mechanisms and develops detection methods using split-chamber zero-resistance ammetry (SC-ZRA). Microbial cultures were enriched from natural gas pipeline samples, focusing on fermentative and sulfur-metabolizing bacteria, and their corrosion activities were evaluated using SC-ZRA. Chapter I reviewed the threat corrosion posed to carbon steel pipelines transporting oil and natural gas, emphasizing MIC's role. It described the electrochemical nature of corrosion and explained how microorganisms like sulfate-reducing and fermentative bacteria accelerated the process through biofilm formation, production of corrosive metabolites, and disruption of electrochemical balance. The chapter also highlighted electrochemical techniques, particularly SC-ZRA, used to detect and monitor MIC. ZRA allowed real-time observation of corrosion currents and distinguished between biotic and abiotic corrosion activities. Chapter II demonstrated that organic acid production by fermentative bacteria lowered pH, accelerating corrosion through cathodic hydrogen reduction on carbon steel. When buffered with sodium bicarbonate, acidity was reduced, effectively mitigating corrosion. Chapter III explored sulfur-metabolizing bacteria's role in corrosion. Experiments with thiosulfate and thiols showed that these bacteria, particularly Desulfovibrio alaskensis, produced sulfide, promoting corrosion. SC-ZRA measurements highlighted how cysteine degradation and thiosulfate reduction drove electron transfer, leading to metal oxidation. Metagenomic analysis confirmed the presence of genes responsible for sulfate and thiosulfate reduction and hydrogenase activity, indicating that diverse metabolic pathways contributed to corrosion. Chapter IV discussed the integration of microbiol (open full item for complete abstract)

Committee: John Senko (Advisor); Nita Sahai (Committee Member); Lu-Kwang Ju (Committee Member); Susmitha Purnima Kotu (Committee Member); Teresa Cutright (Committee Member) Subjects: Chemical Engineering; Geobiology; Geochemistry; Microbiology

Doctor of Philosophy, University of Akron, 2024, Integrated Bioscience

Over 3,000 iron formation caves (IFCs) have formed in erosion-resistant Fe(III)- rich rocks throughout Brazil. These rocks include banded iron formation (BIF) and canga (BIF/goethite breccia), and serve as some of the leading global iron mining sources. Microbial Fe(III) reduction occurs in IFCs, where a microbe-rich paste (sub muros) is found behind an Fe(III)-(hydr)oxide crust in the ceilings and walls. This microbial Fe(III) reduction is thought to transform insoluble Fe(III) to soluble Fe(II), driving cave formation. Fe(III) reduction is controlled by O2 and organic carbon availability, which are linked to seasonal changes. However, it was unknown how the geochemistry in situ may affect microbial Fe(III) reduction and therefore cave formation. To address this, I conducted a series of microbial incubations and analyzed the chemical and microbial changes. This showed sub muros-associated microorganisms can reduce Fe(III) in BIF, with Acidobacteria, Alphaproteobacteria, and Firmicutes implicated as possible Fe(III) reducers. Fe(III)- and sulfate- reduction genes were detected in several Metagenome Assembled Genomes, indicating a role for sulfate reduction, which may occur concurrently with fermentation, enhancing Fe(III) reduction. Upon aeration, partial Fe(II) oxidation occurred, indicating complete oxidation may have been prevented by a chemical process that stabilized Fe(II). I analyzed the Fe(III) reducing abilities of the sub muros microbial community with a variety of substrates and the subsequent microbial community composition and found that Fe(III) reduction was enhanced with sulfate amendment, corresponding to greater relative abundance of Desulfosporosinus and Clostridium. This study also showed the sub muros microbial community reduced Fe(III) without an exogenous organic carbon source, suggesting organic carbon that percolates into IFCs from the overlying soil can support microbial Fe(III) reduction of the host rocks. These results indicate members (open full item for complete abstract)

Committee: John Senko (Advisor); Hazel Barton (Committee Member); Augusto Auler (Committee Member); Ira Sasowsky (Committee Member); Hunter King (Committee Member) Subjects: Biology; Geobiology; Geochemistry; Microbiology

Master of Science, Miami University, 2024, Geology and Environmental Earth Science

Biological nitrogen fixation (BNF), the reduction of N2 to bioavailable NH3 by diazotrophs, is essential for all life on Earth. It is accepted that diazotrophs have existed since well before the Great Oxidation Event (GOE, 2.2Ga). Diazotrophs function through synthesis of nitrogenase enzymes with one of three metal cofactors: Mo, V, or Fe; Mo being the most efficient. However, before the GOE, oceanic Mo was theoretically mainly locked within crustal rocks and mineral precipitates. Despite extremely depleted aqueous Mo, phylogenetic and geologic evidence suggest that Mo-based nitrogenases developed first. To partially solve this “Mo paradox,” Methanosarcina Acetivorans, an N2-fixing, obligately anaerobic methanogen was cultured in an aqueous Mo-depleted medium with only solid Mo sources (molybdenite and basalt). Cell growth, methane production, and nitrogen fixation abilities were monitored. Mineral-cell interactions were imaged by scanning electron microscope. Results demonstrate greater nitrogenase activity and significantly higher growth yield when cultured with solid Mo sources than cultured with no solid or aqueous Mo. Cells attached to the surface of molybdenite and basalt through production of extracellular polymeric substances (EPS). These results implicate that ancient diazotrophs adapted to aqueous Mo-depleted conditions by utilizing solid Mo sources and passed this adaptation down to modern diazotrophs.

Committee: Hailiang Dong (Advisor); Claire McLeod (Committee Member); Jason Rech (Committee Member) Subjects: Agriculture; Biogeochemistry; Geobiology; Geology; Microbiology

PHD, Kent State University, 2023, College of Arts and Sciences / Department of Biological Sciences

Climate change is exerting profound and far-reaching impacts on ecosystems worldwide, encompassing both aquatic and terrestrial environments. The evolving precipitation patterns and shifting temperature regimes impact fluctuations in hydrology, resulting in shifts in redox conditions which can impact the availability of nutrients like phosphorus (P). Phosphate, the bioavailable form of P, is only present in small amounts within soils, making the biological demand greater than soil phosphate availability. The majority of soil P is present in non-labile forms including organic P and phosphate sorbed to metal oxides like iron (Fe). Microorganisms must content with geochemical and other abiotic factors to access phosphate from these non-labile sources through the use of various strategies including the secretion of enzymes, the production of phosphate solubilizing acids, as well as indirect mechanisms associated with the reduction of Fe oxides. The primary goal of this dissertation was to advance our understanding of how microorganisms access both labile and non-labile forms of P in the presence of changing hydrologic and redox conditions which impact the speciation of Fe that is present, altering phosphate availability. Specifically, I investigated 1) how phosphate availability changes across a permafrost thaw gradient (palsa, bog, and fen) in the presence of iron oxides, 2) how microorganisms access and mobilize chemically diverse phosphorus sources under contrasting redox conditions, and 3) how changes in hydrology, redox, iron mineralogy, and phosphate availability drive shifts in microbial community composition, specifically iron oxidizers, reducers, and phosphate solubilizers. In our first study assessing microbial phosphate accessibility across a permafrost thaw gradient, we found that near surface redox conditions changed as a function of permafrost thaw which impacted phosphate availability. Reducing conditions in the bog promoted the dissolution of Fe oxides, (open full item for complete abstract)

Committee: Lauren Kinsman-Costello (Advisor); Christie Bahlai (Committee Member); David Costello (Committee Member); Christopher Blackwood (Committee Member); Elizabeth Herndon (Committee Member); Timothy Gallagher (Committee Member) Subjects: Biogeochemistry; Climate Change; Ecology; Geobiology; Geochemistry; Microbiology; Mineralogy; Soil Sciences

Master of Science (MS), Ohio University, 2023, Biological Sciences (Arts and Sciences)

The Cenomanian Bahariya Formation of the Bahariya Oasis in the Egyptian Western Desert preserves one of the richest Afro-Arabian early Late Cretaceous (~98 Ma) vertebrate faunas yet discovered. This fauna includes a diversity of cartilaginous and bony fishes, plesiosaurs, squamates, turtles, crocodyliforms, and non-avian dinosaurs. The Bahariya Formation has yielded the type specimens of the non-avian theropods Spinosaurus, Carcharodontosaurus, Bahariasaurus, the titanosaurian sauropods Paralititan and Aegyptosaurus, and the crocodyliforms Libycosuchus, Stomatosuchus, and Aegyptosuchus. Regrettably, most of the Egyptian archosaur collection was destroyed during World War II in the Allied bombing of Munich in April 1944. Since then, additional paleontological efforts have endeavored to rediscover the Bahariya vertebrate fauna. Over the course of the last decade, paleontological fieldwork carried out by researchers from the Mansoura University Vertebrate Paleontology Center (MUVP) resulted in the re-identification of previously known localities and several new vertebrate fossil localities within the Bahariya Formation. New fossils recovered from this unit include those of cartilaginous and bony fishes, plesiosaurs, squamates, turtles, crocodyliforms, pterosaurs, and non-avian dinosaurs. Here we focus on the description of recently recovered fossils referable to Pterosauria and Crocodyliformes. MUVP 507, an isolated, three-dimensionally preserved left first wing phalanx (= left manual phalanx IV-1), belongs to a medium-sized pterosaur and compares favorably with the equivalent element in ornithocheirid pterosaurs in general and exhibits anhanguerid affinities specifically. The fused and ossified proximal extensor tendon process (ETP) indicates that the individual in question was osteologically mature. The ETP of the specimen is comparable in overall morphology with that in anhanguerids, including the presence of a subrectangular extensor tubercle, the position of the (open full item for complete abstract)

Committee: Patrick O'Connor (Advisor); Nancy Stevens (Committee Member); Lawrence Witmer (Committee Member) Subjects: Geobiology; Geology; Paleontology

PHD, Kent State University, 2022, College of Arts and Sciences / Department of Earth Sciences

This dissertation includes seven written chapters that each identify some uses for fossil and recent marine arthropod cuticle across studies pertaining to paleoecology, taphonomy, morphometrics, and systematic or evolutionary analyses. Chapters 1 and 2 are the dissertation Summary and Introduction, respectively. Chapter 3 describes a paleoecological study that pertained to how other organisms have interacted with arthropod cuticle. Chapter 3 focuses on the potential for modern paddle-bearing and non-paddle-bearing brachyuran crabs to remove infesting epibionts via grooming the surface cuticle of their carapaces. The modern crabs were used as proxies for several analogous fossil specimens from middle Cenozoic rocks from Oregon and Washington State to help differentiate in-vivo and post-mortem cuticle infestation by epibionts. Chapter 4 was a morphometrics study pertaining to population dynamics of the Pennsylvanian horseshoe crab Euproops danae from a new locality near Windber, Pennsylvania. By analyzing changes in surface cuticle morphology across ontogenetic stages, we can determine which cuticle characters are morphologically stable and which characters are more common across juvenile and adult members of a population. Chapter 5 describes several actualistic taphonomic experiments that were conducted to document how horseshoe crab corpse and molt cuticle break down over time when agitated in various sediment types and sizes. These experiments were performed to simulate conditions that may have led to the broken and disarticulated horseshoe crab fossil carapaces preserved in Late Jurassic lithographic limestones from Owadow-Brzezinki, Poland, to better-understand biostratinomic processes associated with horseshoe crab cuticle preservation. Chapter 6 considered the potential for marine arthropod cuticle microstructure characters to be implemented in systematic or evolutionary studies. It was the first study to create codeable cross-sectional and surfi (open full item for complete abstract)

Committee: Rodney Feldmann (Committee Chair); Loren Babcock (Committee Member); Joseph Ortiz (Committee Member); Carrie Schweitzer (Committee Co-Chair) Subjects: Geobiology; Geology; Morphology; Paleoecology; Paleontology

Master of Science (MS), Ohio University, 2022, Geological Sciences

Type Cincinnatian strata are among the best preserved Upper Ordovician deposits in the world and record a range of depositional environments as well as various biotic and abiotic changes, making them an ideal natural laboratory in which to study biotic and abiotic processes. The most substantial biotic change in the Type Cincinnatian Series is a biotic invasion known as the Richmondian Invasion. The first pulse of the Richmondian Invasion is referred to as the Clarksville Phase (Aucoin and Brett, 2016) and is the focal point of this study which quantifies the impact the Clarksville Phase had on the ecology and diversity of the fauna of the Cincinnati basin. A suite of methods were employed to quantify the invader impact including detrended correspondence analysis, cluster analysis, rarefaction, Simpson's index of dominance, guild analysis, and comparison of environmental preferences and tolerances through time. Results indicate the Clarksville Phase had numerous impacts on the fauna of the Cincinnati Sea including modification of occupied habitat, ecospace utilization, gradient structure, community structure, community composition, and biodiversity. Habitat occupation changed considerably following the introduction of the invaders with taxa shifting both their environmental tolerances and preferences. Ecospace utilization shifted as previously low diversity guilds were filled out with novel taxa. Faunal differentiation across the depth gradient increased with the introduction of the invaders. Generic richness increased within the basin, generic evenness decreased, and community composition became more complex. The results of this study contribute to our understanding of the Richmondian Invasion and our general understanding of earth history as well as provide new insights about the potential long term ecological and biodiversity impacts of biotic invasions today.

Committee: Alycia Stigall (Advisor); Gregory Springer (Committee Member); Katherine Fornash (Committee Member) Subjects: Ecology; Geobiology; Paleoecology; Paleontology

Master of Science, Miami University, 2021, Geology and Environmental Earth Science

The rate and extent of microbial reduction of Fe(III) oxides depend heavily on biochar concentration. Little is known about the impact of biochar on Fe(III) bearing clay minerals. Bioreduction experiments were conducted with lactate (electron donor), structural Fe(III) in nontronite (electron acceptor), and Shewanella putrefaciens CN32 (mediator). Increasing concentrations of wood-derived biochar enhanced the rate of Fe(III) bioreduction but the extent of reduction did not monotonically increase. High biochar concentrations (>2.5 g L-) increased the reduction extent: in contrast, lower concentrations had an inhibitory effect. When the NAu-2 was replaced with ferric citrate (aqueous Fe3+), the extent of bioreduction showed a negative correlation with biochar concentration. Further investigation revealed electron transfer was determined by the relative redox potentials of various components in the system, where the biochar served as a reductant to Fe(III) or oxidant to Fe(II) until achieving equilibrium. Biochar retains a significant proportion of electrons to maintain redox equilibrium with the Fe, explaining the inhibition. As the biochar concentration increased, stimulation from solid-solid electron shuttling outcompetes, increasing reduction rate and extent. As biochar accumulates in soils, its role as an electron shuttle and redox buffer will heavily impact Fe redox reactions, representing a vast competitive electron sink.

Committee: Hailiang Dong (Advisor); John Rakovan (Committee Member); Jason Rech (Committee Member) Subjects: Environmental Geology; Geobiology; Geochemistry; Geology

Doctor of Philosophy, The Ohio State University, 2020, Earth Sciences

Upland catchments play an outsized role in the processing and export of water, sediments, nutrients, and organic matter, thus strongly influencing downstream water quality. In Chapter 1, an overview of biogeochemical cycling within upland fluvial sediments is presented, focusing on key regional biogeochemical cycling patterns and solute export processes. Additionally, anthropogenic influences on this environment, such as historical mining activities and climate change, are briefly reviewed in this chapter. Chapter 2 explores the relationship between spatial hydrologic heterogeneity and microbial community assembly and functional potential within the hyporheic zone. The region of groundwater and river water mixing, known as the hyporheic zone, is a hotspot of microbial activity that influences solute export and cycling in rivers. Hyporheic mixing patterns can vary over small spatial scales, leading to heterogeneity in fluid chemistry and microbial community composition and function. Here, we integrate new mass-spectrometry data, metagenomic insights, and ecological models with previous analyses of microbial community composition and dissolved organic matter (DOM) quality to understand spatial relationships between hyporheic flow and microbial community assembly, metabolism, and DOM processing at high-resolution (100 locations) along a 200 m meander of East River, Colorado (USA). Ecological modeling revealed a strong linkage between community assembly patterns and underlying hydrologic and geochemical drivers, including the impact of physical heterogeneity (riverbed grain size) on microbial community structure. Geochemical profiles associated with upwelling groundwater suggest the influence of underlying geology, specifically Mancos-derived solutes, in driving community assembly. Distinct microbial community profiles and functional potential in zones of upwelling groundwater suggest that groundwater chemistry may have a greater influence on biogeochemical cycling wi (open full item for complete abstract)

Committee: Michael Wilkins (Advisor); Steven Lower (Advisor); Audrey Sawyer (Committee Member); Elizabeth Griffith (Committee Member) Subjects: Biogeochemistry; Earth; Ecology; Environmental Geology; Environmental Science; Geobiology; Geochemistry; Geology; Hydrology; Limnology; Microbiology; Mineralogy

Master of Science, The Ohio State University, 2020, Earth Sciences

The isotopic composition and mineralogy of modern microbialites provides us with tools useful for interpreting the formation processes and environments of ancient microbialites. Growing in the hypersaline and turbid Storr's Lake on San Salvador Island in The Bahamas today are microbialites with low levels of photosynthesis and high levels of sulfate reduction-in contrast to many of their modern counterparts. Living planktonic, motile microorganisms and suspended algal and bacterial debris create the high turbidity of the shallow lake (<2 m) and rapidly attenuate sunlight in the water column. Within Storr's Lake microbial metabolisms induce precipitation of carbonate within microenvironments of the microbial mats. Both high-Mg calcite (HMC) and aragonite are found within a majority of the microbialites measured leading to the hypothesis that the organomineralization process involves a step where HMC transforms to aragonite. Mineralogy and elemental analysis of a wide sampling of microbialites was undertaken to understand the extent of aragonite within Storr's Lake microbialites. It was found that aragonite occurs at water depths greater than 40 cm within the lake and was present in all but one microbialite measured in this study. New calcium (Ca) stable isotopic analyses from the thermal ionization mass spectrometer using a 42Ca-43Ca double spike provides evidence for exploring the systems fractionating Ca within Storr's Lake water and microbialites. In contrast to geochemical data and previous Mg stable isotopic measurements on the same waters, the Ca stable isotopic value (δ44/40Ca) of water in Storr's Lake is not homogeneous. While the northern sector is primarily influenced by seawater, the southern sector δ44/40Ca is shifted away from seawater to lower values, suggesting internal variability within the lake. In both microbialites measured, δ44/40Ca is strongly correlated to mineralogy and trace elements in the carbonate. To explore the potenti (open full item for complete abstract)

Committee: Elizabeth Griffith PhD (Advisor); Matthew Saltzman PhD (Committee Member); Thomas Darrah PhD (Committee Member) Subjects: Biogeochemistry; Earth; Geobiology; Geochemistry; Geological; Geology; Morphology; Petroleum Geology

Doctor of Philosophy, The Ohio State University, 2020, Earth Sciences

Globally, gas hydrate deposits are estimated to contain 2.8 x 10^15 to 8 x 10^18 m^3 of natural gas. Though this immense volume of natural gas has the potential to be important in the global carbon budget and as an economic resource, there are still significant uncertainties regarding the genetic source and timing of methane accumulation in gas hydrate reservoirs. Natural gas can form from biogenic processes, thermogenic processes or a mixture of both. Biogenic natural gas is formed by methanogenic archaea at relatively low temperatures (less than 60oC). In comparison, thermogenic natural gas is formed by the thermocatalytic conversion of kerogen at higher temperatures (greater than 80oC). In addition to deciphering the processes responsible for natural gas formation and the source(s) of fluids, it is important to determine the relative timing of methane accumulation and associated residence times of natural gas and hydrocarbon-associated fluids in the crust. One key component of understanding gas hydrates is determining whether natural gas incorporated into the hydrate was formed in situ or if it had migrated from exogenous sources. Both hypotheses have been suggested for hydrates in various settings and the role of in situ versus exogenous sources of natural gas remains a topic of debate. During the completion of my Master's thesis in Earth Sciences, I worked on integrating hydrocarbon gas and noble gas geochemistry to determine the source(s) of natural gas in coal seams from the Illinois Basin. As part of that work, I concluded that although natural gases from the Springfield and Seelyville coal seams were dominantly biogenic, they both contained significant contributions of thermogenic natural gas derived from exogenous source rocks (the underlying New Albany Shale). During my doctoral work, I continued to advance this integrated gas geochemistry approach of determining the source(s) of natural gas in a different type of geological system. Herein, I (open full item for complete abstract)

Committee: Thomas Darrah Dr. (Advisor); Franklin Schwartz Dr. (Committee Member); Ann Cook Dr. (Committee Member); David Cole Dr. (Committee Member) Subjects: Earth; Geobiology; Geochemistry; Geology

MS, Kent State University, 2019, College of Arts and Sciences / Department of Earth Sciences

Manganese (Mn), an essential nutrient critical for photosynthesis in plants but a toxic element in excess, impacts the fate and transport of other nutrients and toxins, forest metabolism, carbon storage, and ecosystem productivity. Given the significant role Mn can play in ecosystems, it is important to understand how soil geochemistry controls Mn uptake by vegetation. The purpose of this research was to explore how Mn uptake by plants is related to Mn supply to plants through mineral dissolution. We conducted a greenhouse pot experiment to quantify Mn uptake by plants based on controlled geochemical constraints. Specifically, we investigated whether Mn uptake was limited by the supply of Mn to soil solution or by biological controls within the plants. Greenhouse soil pots (quartz sand + peat) that were non-vegetated or vegetated with red maple saplings were supplied with either no added Mn, dissolved Mn, Mn oxides, or crushed shale containing Mn-bearing pyrite. We analyzed the chemical composition of plant tissue to quantify Mn uptake and soil leachate to quantify Mn losses. From these values, we constructed a mass balance model and calculated pseudo-first order rate constants to compare Mn mobilization between treatments. Mn uptake was higher in systems with dissolved Mn because it was not limited by mineral weathering. Mn uptake was also higher in systems supplied with fast-weathering substrates (pyrite in the shale) than slow-weathering substrates (Mn oxides). There were not significant differences in Mn leaching and total Mn loss between vegetated and non-vegetated pots in the Mn-oxide or shale treatments. We conclude that Mn uptake is controlled by dissolution rates of Mn-minerals in soil.

Committee: Elizabeth Herndon (Advisor); David Singer (Committee Member); Chris Blackwood (Committee Member) Subjects: Biogeochemistry; Environmental Geology; Environmental Science; Environmental Studies; Geobiology; Geochemistry; Geology

Doctor of Philosophy, Miami University, 2019, Geology and Environmental Earth Science

Iron and ammonium in clay minerals are accessable by bacteria and archaea to support their metabolic activities. Redox-active Fe can be present in different sites of clay minerals: structural, complexed to surface hydroxyl groups (edge sites), and ion exchangeable basal sites. Iron can be cycled between Fe(II) and Fe(III) by various dissimilatory iron-reducing bacteria (DIRB) and iron oxidizers. Ammonium (NH4+) in clay interlayers can support the growth of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) by oxidizing ammonia to nitrite in the nitrification process. In both cases of Fe and NH4+, clay minerals support microbial growth via extracellular redox reactions. These electron transfer processes require the cell to transfer electrons in/out of the cell membrane, and the clay mineral to transfer electrons from/to the targeted receptor such as Fe or NH4+ in different structural sites. Several studies revealed extracellular electron transfer pathway for various dissimilatory iron-reducing bacteria (DIRB). However, the electron transfer to receptors in different sites of clay minerals is somewhat neglected. This dissertation is focused on studying the electron transfer process between clay minerals and microorganisms, with various microorganisms using elements that reside in different sites of clay minerals: The first subproject was designed to study how interfacial electron transfer (IET) between structural Fe(III) and sorbed Fe(II), and IET-induced secondary mineralization affect biologically-catalyzed nitrate-dependent Fe(II) oxidation (NDFO) in two representative clay minerals, nontronite and montmorillonite. Results indicate that IET leads to a redistribution of Fe(II) among structural, edge, and basal/interlayer sites of clay minerals and formation of various secondary minerals, which alters Fe(II) sorption capacity and clay reactivity towards the biologically mediated NDFO. The goal of the second subproject was to investigate how t (open full item for complete abstract)

Committee: Hailiang Dong (Advisor); John Rakovan (Committee Member); Mark Krekeler (Committee Member); Ravi Kukkadapu (Committee Member); Annette Bollmann (Committee Member) Subjects: Geobiology

Doctor of Philosophy, Miami University, 2019, Geology and Environmental Earth Science

All organisms require trace elements as cofactors that provide unique catalytic properties to proteins. These proteins, known as metalloproteins, are involved in important biogeochemical processes such as nitrogen, carbon, and sulfur cycling. Extreme environments, such as terrestrial hot springs, have unique physicochemical conditions that may affect trace metal bioavailability and thus, microbial taxonomic and metabolic diversity. This dissertation first investigates the abundance and taxonomic affiliation of Mo transport and utilization genes, with a special emphasis on Mo-nitrogenase protein nifD, in the Tengchong hot springs, with a wide range of pH (2.3 to 9) and temperature (43.1°C to 84.8°C) conditions. Within each spring, a combination of metagenomic and geochemical approach was employed. Mo-based microbial community composition was similar to overall 16S rRNA gene based composition, with Crenarchaeota and Thaumarchaeota dominating the high temperature sites (>74°C). All sites contained xanthine dehydrogenase, formate dehydrogenase, carbon-monoxide dehydrogenase, and nitrate reductase despite different community compositions. Major Mo related metabolic functions, such as nitrogen metabolism, sulfur metabolism, and glycolysis/ gluconeogenesis, were detected at all sites, demonstrating the importance of Mo. However, the rates of these processes are sensitive to physicochemical conditions of the springs. Cu is another bio-essential trace metal. In this study, the effect of Tengchong hot spring geochemistry on the distribution and functional affiliations of Cu binding proteins was investigated. Dissolved Cu and Cu-binding domains were detected across all temperature and pH gradients, with Cu-binding domains of cytochrome c oxidase subunits, heavy-metal associated domain and nitrous oxide reductase detected at all sites. Metagenomic analysis also showed that the type of cytochrome c oxidase pathway employed by microbes is affected by the physicochemical c (open full item for complete abstract)

Committee: Hailiang Dong (Advisor) Subjects: Geobiology; Geology

Doctor of Philosophy, The Ohio State University, 2019, Microbiology

The Arctic system has been undergoing a rampant change during the Anthropocene. This anthropogenic change has allowed for additional physical and biological positive feedback processes that in turn accelerate warming in the arctic and subarctic systems. Microbial community/functional dynamics are both (i) dramatically impacted by these rapid changes and (ii) key players in the biological positive feedback process that accelerates the change. Recent technological, analytical, and computational advances have allowed us to ask systems-level questions that encompass microbial and viral community dynamics (along with their potential functional dynamics) and high-resolution environmental measurements. This research took a systems-level approach to look for the first time at (i) the characteristics of Arctic marine viruses in a global context, and (ii) microbial community gene expression in a rapidly changing permafrost thaw gradient. Additionally, novel viral sequences recovered from the marine and terrestrial ecosystems studied here were used to build new resources and tools that accelerate viral discovery in nature. First, studying marine viral macro- and microdiversity from the Arctic Ocean to the Southern Ocean, enabled by the Tara Oceans Expedition, revealed the Arctic Ocean as a hotspot of viral diversity, with ~42% of the recovered viral populations originating from the Arctic Ocean viromes. In total 195,728 viral populations >10 kb were recovered from the global ocean to constitute the Global Ocean Viromes 2.0 (GOV2.0) dataset. Viral communities assorted into five distinct global ecological zones and the arctic viral communities formed their own distinct ecological zone. Additionally, this work revealed unexpected patterns and ecological drivers of viral diversity (at the community, inter-, and intrapopulation levels), within the Arctic Ocean, across latitudes, and across the depth of the global ocean. Second, genome-resolved metaproteomic study of microbial gene (open full item for complete abstract)

Committee: Matthew Sullivan (Advisor); Virginia Rich (Advisor); Kelly Wrighton (Committee Member); Alvaro Montenegro (Committee Member) Subjects: Biogeochemistry; Bioinformatics; Biological Oceanography; Biology; Climate Change; Ecology; Environmental Science; Geobiology; Microbiology; Oceanography; Soil Sciences; Statistics; Virology

Master of Science, Miami University, 2019, Geology and Environmental Earth Science

Nitrate-dependent Fe(II) oxidation (NDFO) is important for multiple environmental processes including nitrate remediation, heavy metal mobility and transport, and nuclear waste disposal. Past research has focused on microbial oxidation of either aqueous Fe2+ or structural Fe(II) in minerals, however, the effects of organic ligands on this process are not yet well understood, though organic ligands are ubiquitous in natural environments. The aim of this research was to study the NDFO process of structural Fe(II) in reduced nontronite (rNAu-2) by lithoautotrophic Pseudogulbenkiania sp. Strain 2002 in the presence oxalate (OXA) and nitrilotriacetic acid (NTA), to determine their effects on Fe(II) oxidation and mineral transformations. Bio-oxidation experiments were conducted using microbially reduced NAu-2 and nitrate as the sole electron donor and acceptor, respectively, under bicarbonate buffered neutral pH condition. A much faster rate of Fe(II) oxidation by strain 2002 than that of chemical oxidation by nitrite suggests a dominating biological role in the NDFO process. Fe(II) oxidation rate and extent were much higher in OXA and NTA groups than in no-ligand group. The ligand-promoted dissolution of rNAu-2 and the formation of highly bio-oxidizable Fe(II)-ligand complex and reduction of Fe(III)-ligand complex back to Fe(II)-ligand complex by structural Fe(II) in rNAu-2 via a process called interfacial electron transfer are the mechanisms for the enhanced oxidation rate and extent. In all biotic treatments, nitrate was predominantly reduced to N2 with a small amount of N2O gas and a negligible amount of nitrite. The ratio of oxidized Fe(II) to reduced nitrate was non-stoichiometric, probably resulting from heterotrophic nitrate reduction by cell-stored carbon. Structural Fe in rNAu-2 was more susceptible to chelation and liberation by organic ligands compared to unreduced NAu-2, but the structure of rNAu-2 was nearly restored to unreduced NAu-2 upon microbial oxidati (open full item for complete abstract)

Committee: Hailiang Dong (Advisor); Rakovan John (Committee Member); Levy Jonathan (Committee Member) Subjects: Geobiology; Geochemistry

Doctor of Philosophy, The Ohio State University, 2019, Earth Sciences

Magnetospirillum magneticum AMB-1 is a member of a phylogenetically diverse group of bacteria characterized by their ability to biomineralize magnetic minerals known collectively as magnetotactic bacteria (MTB). MTB produce chains of membrane-bound intracellular magnetic nanocrystals, collectively known as magnetosomes. The current scientific consensus is that magnetosomes are used by MTB to orient themselves in vertically stratified water columns in order to achieve optimal oxygen concentrations in a process known as magnetoaerotaxis. Biomineralization of magnetosomes is an energy intensive process which accounts for roughly 33% of the cell's metabolic budget. This high metabolic cost seems to contradict with the amount of time MTB cells spend aligned with external magnetic fields. Due to this apparent discrepancy, I examined the potential role the magnetosome may play in bacterial metabolism. Through analysis of comparative growth on a variety of media compositions both magnetic, wild type and non-magnetic, mutant strains of AMB-1, I discovered that cells grown under stress conditions exhibit an inversion of growth dynamics which indicates some advantage for magnetic cells. Non-magnetic, mutant cells display a direct relationship between external magnetic field strength and growth, indicating magnetic field dependence. I believe that this represents a novel magnetosome-dependant mixotrophic metabolism. Due to the ubiquity of MTB and the diversity of sessile eukaryotes which either produce biogenic magnetite or exhibit magnetosensing, this system may be part of a widespread, previously unknown component of global carbon cycling.

Committee: Steven Lower (Advisor); Brian Lower (Committee Member); Ratnasingham Sooryakumar (Committee Member); Ann Cook (Committee Member) Subjects: Biogeochemistry; Geobiology; Geology; Microbiology; Mineralogy

Doctor of Philosophy, University of Akron, 2018, Integrated Bioscience

Most caves form in limestone via water-mediated dissolution and mass transport; however, increasing numbers of caves are being identified that do not fit this model, including the iron formation caves (IFCs) found in the iron mining regions of Brazil. IFCs occur predominantly at the interface of banded iron formations (BIFs; alternating hematite and silica laminae) and a cap rock composed of fragmented BIF in an amorphous Fe(III) matrix, called canga. Despite low erosional rates and insolubility of both BIF and canga, there are >3,000 IFCs in Brazil. There is currently no mechanism that adequately accounts for the growth or formation of IFCs; however, the reductive dissolution of Fe(III) by Fe(III) reducing microorganisms (FeRM) could provide a microbiological mechanism for their formation. To test this hypothesis we first evaluated the susceptibility of Fe(III) phases associated with these caves to reduction by the FeRM Shewanella oneidensis MR-1. Canga (being the least crystalline of the Fe(III) phases tested) was susceptible to reduction, and to a larger degree than the Fe(III) (predominantly hematite) associated with BIF. We then analyzed the microbial communities within the IFCs to determine if FeRM were present. While the caves were dominated by Chloroflexi, Acidobacteria and the Alpha- Beta- and Gammaproteobacteria (all containing lineages capable of FeRM activity), active Fe(III) reducing enrichment cultures from IFCs indicated the predominance of Firmicutes and Enterobacteriaceae, which coupled fermentation to Fe reduction; indicating that IFCs do contain microorganisms capable of reducing Fe(III). To test whether FeRM were actively reducing Fe(III) within the IFCs, we analyzed IFC host rock and discovered that the cave walls had undergone structural weakening. Upon further investigation, we identified an unconsolidated iron depleted (as compared to the surrounding canga) material in the walls of the IFCs. This material contained robust microbial population (open full item for complete abstract)

Committee: Hazel Barton PhD (Advisor); John Senko PhD (Committee Member); Augusto Auler PhD (Committee Member); Ira Sasowsky PhD (Committee Member); Randy Mitchell PhD (Committee Member) Subjects: Geobiology; Microbiology

Master of Science (MS), Bowling Green State University, 2018, Geology

Evapotranspiration (ET) is a hydrologically and eco-agronomically important process that can be altered by soil properties, crop type and mechanisms of photosynthesis (e.g. C3 and C4), crop status, agricultural practices (crop rotation and monoculture), and meteorology. In particular, corn monoculture, which is widely used in the U.S, may affect over agricultural fields differently than soybean and wheat deu to the different (C4) photosynthesis mechanism, and thus can have an impact on local hydrologic cycle and climate. Satellite observations are the most sophisticated technology to monitor different rates of ET at large scale. This study used data from two satellites, Landsat 8 and Sentinel 2, to examine the capability of combining those data in ET time series to explore the differences between ET rates for C3 (soybean and winter wheat) and C4 (corn) crops. ET was estimated for a study area located in the Western Lake Erie basin for 2016 and 2017 using satellite data and the Boreal Ecosystem Productivity simulator (BEPS), a process based ecosystem model, modified for the agricultural ecosystem. Satellite images (from which land cover/land use data, and leaf area index were generated), weather (Gridmet data), and soil data (SSURGO data) were main inputs to BEPS. In addition, a sensitivity analysis was conducted to estimate ET for different percent increments of the total area covered by corn to the point of becoming a monoculture using synthetically developed land covers and LAI images. For both years, corn and soybean reach the maximum ET rate in the mid-growing season as expected with the peak being somewhat later in the season for soybean. The ET relationship between two sensors was strong during the mid-season (r = 0.95 for July) when LAI was high, and at the end of the season, when many crops were harvested and soil exposed (r = 0.98 for iv October). A high correlation was also observed when data were acquired within a short period of time (open full item for complete abstract)

Committee: Anita Simic Dr. (Advisor); Peter Gorsevski Dr. (Committee Member); Ganming Liu Dr. (Committee Member) Subjects: Agriculture; Agronomy; Earth; Ecology; Environmental Geology; Geobiology; Geology; Remote Sensing