Iron (Fe) scarcity limits biological productivity in high-nutrient low-chlorophyll (HNLC) ocean regions. Thus, the input, output and abundance of Fe in seawater likely played a critical role in shaping the development of modern marine ecosystems and perhaps even contributed to past changes in Earth’s climate. Three sources of Fe—wind-blown dust, hydrothermal activity, and sediment dissolution—carry distinct Fe isotopic fingerprints, and can therefore be used to track Fe source variability through time. However, establishing the timing of this source variability through Earth’s history remains challenging because the major depocenters for dissolved Fe in the ocean lack well-established chronologies. This is due to the fact that they are difficult to date with traditional techniques such as biostratigraphy and radiometric dating. Here, I develop age models for sediments collected from the International Drilling Program Expedition 329 by measuring the Os (osmium) isotopic composition of the hydrogenous portion of the clays. These extractions enable dating of the clays by aligning the Os isotope patterns observed in the clays to those in a reference curve with absolute age constraints through the Cenozoic. Our preliminary data enable future development of chronologies for three sediment cores from the high-latitude South Pacific and Southern Oceans, and demonstrate a wider utility of this method to establish age constraints on pelagic sediments worldwide. Moreover, the preliminary Os isotopic data provides a critical first step needed to examine the changes in Fe (iron) sources and cycling on millions of years timescales. Fe isotopic analysis was conducted at the same sites in the South Pacific and demonstrates that there are significant changes in the sources of Fe to the Southern Ocean over the last 90 Ma. These results lay the groundwork for the exploration of basin-scale sources to Fe source changes, which will have implications for understanding how biological productivity relates to Fe source variability over geological timescales.

Affect is a domain of psychology that includes attitudes, emotions, interests, and values. My own affect influenced the choice of topics for my dissertation. After examining asteroid interiors and the Moon’s thermal evolution, I discuss the role of affect in online science education. I begin with asteroids, which are collections of smaller objects held together by gravity and possibly cohesion. These “rubble-pile” objects may experience the Brazil Nut Effect (BNE). When a collection of particles of similar densities, but of different sizes, is shaken, smaller particles will move parallel to the local gravity vector while larger objects will do the opposite. Thus, when asteroids are shaken by impacts, they may experience the BNE as possibly evidenced by large boulders seen on their surfaces. I found while the BNE is plausible on asteroids, it is confined to only the outer layers. The Moon, which formed with a Lunar Magma Ocean (LMO), is the next topic of this work. The LMO is due to the Moon forming rapidly after a giant impact between the proto-Earth and another planetary body. The first 80% of the LMO solidified rapidly at which point a floatation crust formed and slowed solidification of the remaining LMO. Impact bombardment during this cooling process, while an important component, has not been studied in detail. Impacts considered here are from debris generated during the formation of the Moon. I developed a thermal model that incorporates impacts and find that impacts may have either expedited or delayed LMO solidification. Finally, I return to affect to consider the differences in attitudes towards science between students enrolled in fully-online degree programs and those enrolled in traditional, in-person degree programs. I analyzed pre- and post-course survey data from the online astrobiology course Habitable Worlds. Unlike their traditional program counterparts, students enrolled in online programs started the course with better attitudes towards science and also further changed towards more positive attitudes during the course. Along with important conclusions in three research fields, this work aims to demonstrate the importance of affect in both scientific research and science education.

The greatest barrier to understanding how life interacts with its environment is the complexity in which biology operates. In this work, I present experimental designs, analysis methods, and visualization techniques to overcome the challenges of deciphering complex biological datasets. First, I examine an iron limitation transcriptome of Synechocystis sp. PCC 6803 using a new methodology. Until now, iron limitation in experiments of Synechocystis sp. PCC 6803 gene expression has been achieved through media chelation. Notably, chelation also reduces the bioavailability of other metals, whereas naturally occurring low iron settings likely result from a lack of iron influx and not as a result of chelation. The overall metabolic trends of previous studies are well-characterized but within those trends is significant variability in single gene expression responses. I compare previous transcriptomics analyses with our protocol that limits the addition of bioavailable iron to growth media to identify consistent gene expression signals resulting from iron limitation. Second, I describe a novel method of improving the reliability of centroid-linkage clustering results. The size and complexity of modern sequencing datasets often prohibit constructing distance matrices, which prevents the use of many common clustering algorithms. Centroid-linkage circumvents the need for a distance matrix, but has the adverse effect of producing input-order dependent results. In this chapter, I describe a method of cluster edge counting across iterated centroid-linkage results and reconstructing aggregate clusters from a ranked edge list without a distance matrix and input-order dependence. Finally, I introduce dendritic heat maps, a new figure type that visualizes heat map responses through expanding and contracting sequence clustering specificities. Heat maps are useful for comparing data across a range of possible states. However, data binning is sensitive to clustering cutoffs which are often arbitrarily introduced by researchers and can substantially change the heat map response of any single data point. With an understanding of how the architectural elements of dendrograms and heat maps affect data visualization, I have integrated their salient features to create a figure type aimed at viewing multiple levels of clustering cutoffs, allowing researchers to better understand the effects of environment on metabolism or phylogenetic lineages.

I present a catalog of 1,794 stellar evolution models for solar-type and low-mass stars, which is intended to help characterize real host-stars of interest during the ongoing search for potentially habitable exoplanets. The main grid is composed of 904 tracks, for 0.5-1.2 M_sol at scaled metallicity values of 0.1-1.5 Z_sol and specific elemental abundance ratio values of 0.44-2.28 O/Fe_sol, 0.58-1.72 C/Fe_sol, 0.54-1.84 Mg/Fe_sol, and 0.5-2.0 Ne/Fe_sol. The catalog includes a small grid of late stage evolutionary tracks (25 models), as well as a grid of M-dwarf stars for 0.1-0.45 M_sol (856 models). The time-dependent habitable zone evolution is calculated for each track, and is strongly dependent on stellar mass, effective temperature, and luminosity parameterizations. I have also developed a subroutine for the stellar evolution code TYCHO that implements a minimalist coupled model for estimating changes in the stellar X-ray luminosity, mass loss, rotational velocity, and magnetic activity over time; to test the utility of the updated code, I created a small grid (9 models) for solar-mass stars, with variations in rotational velocity and scaled metallicity. Including this kind of information in the catalog will ultimately allow for a more robust consideration of the long-term conditions that orbiting planets may experience.

In order to gauge the true habitability potential of a given planetary system, it is extremely important to characterize the host-star's mass, specific chemical composition, and thus the timescale over which the star will evolve. It is also necessary to assess the likelihood that a planet found in the "instantaneous" habitable zone has actually had sufficient time to become "detectably" habitable. This catalog provides accurate stellar evolution predictions for a large collection of theoretical host-stars; the models are of particular utility in that they represent the real variation in stellar parameters that have been observed in nearby stars.

Many acidic hot springs in Yellowstone National Park support microbial iron oxidation, reduction, or microbial iron redox cycling (MIRC), as determined by microcosm rate experiments. Microbial dissimilatory iron reduction (DIR) was detected in numerous systems with a pH < 4. Rates of DIR are influenced by the availability of ferric minerals and organic carbon. Microbial iron oxidation (MIO) was detected from pH 2 – 5.5. In systems with abundant Fe (II), dissolved oxygen controls the presence of MIO. Rates generally increase with increased Fe(II) concentrations, but rate constants are not significantly altered by additions of Fe(II). MIRC was detected in systems with abundant ferric mineral deposition.

The rates of microbial and abiological iron oxidation were determined in a variety of cold (T= 9-12°C), circumneutral (pH = 5.5-9) environments in the Swiss Alps. Rates of MIO were measured in systems up to a pH of 7.4; only abiotic processes were detected at higher pH values. Iron oxidizing bacteria (FeOB) were responsible for 39-89% of the net oxidation rate at locations where biological iron oxidation was detected. Members of putative iron oxidizing genera, especially Gallionella, are abundant in systems where MIO was measured. Speciation calculations reveal that ferrous iron typically exists as FeCO30, FeHCO3+, FeSO40 or Fe2+ in these systems. The presence of ferrous (bi)carbonate species appear to increase abiotic iron oxidation rates relative to locations without significant concentrations. This approach, integrating geochemistry, rates, and community composition, reveals biogeochemical conditions that permit MIO, and locations where the abiotic rate is too fast for the biotic process to compete.

For a reaction to provide habitability for microbes in a given environment, it must energy yield and this energy must dissipate slowly enough to remain bioavailable. Thermodynamic boundaries exist at conditions where reactions do not yield energy, and can be quantified by calculations of chemical energy. Likewise, kinetic boundaries exist at conditions where the abiotic reaction rate is so fast that reactants are not bioavailable; this boundary can be quantified by measurements biological and abiological rates. The first habitability maps were drawn, using iron oxidation as an example, by quantifying these boundaries in geochemical space.

Marine pico-cyanobacteria of the genera Synechococcus and Prochlorococcus carry out nearly two thirds of the primary production in oligotrophic oceans. These cyanobacteria are also considered an important constituent of the biological carbon pump, the photosynthetic fixation of CO2 to dissolved and particulate organic carbon and subsequent export to the ocean’s interior. But single cells of these cyanobacteria are too small to sink, so their carbon export has to be mediated by aggregate formation and/or consumption by zooplankton that produce sinking fecal pellets. In this dissertation, I investigated for the first time the aggregation of these cyanobacteria by studying the marine Synechococcus sp. strain WH8102 as a model organism. I first found in culture experiments that Synechococcus cells aggregated and that such aggregation of cells was related to the production of transparent exopolymeric particles (TEP), known to provide the main matrix of aggregates of eukaryotic phytoplankton. I also found that despite the lowered growth rates, cells in the nitrogen or phosphorus limited cultures had a higher cell-normalized TEP production and formed a greater total volume of aggregates with higher settling velocities compared to cells in the nutrient replete cultures. I further studied the Synechococcus aggregation in roller tanks that allow the simulation of aggregates settling in the water column, and investigated the effects of the clays kaolinite and bentonite that are commonly found in the ocean. In the roller tanks, Synechococcus cells formed aggregates with diameters of up to 1.4 mm and sinking velocities of up to 440 m/d, comparable to those of larger eukaryotic phytoplankton such as diatoms. In addition, the clay minerals increased the number but reduced the size of aggregates, and their ballasting effects increased the sinking velocity and the carbon export potential of the aggregates. Lastly, I investigated the effects of heterotrophic bacteria on the Synechococcus aggregation, and found that heterotrophic bacteria generally resulted in the formation of fewer, but larger and faster sinking aggregates, and eventually led to an enhanced aggregation of cells and particles. My study contributes to the understanding of the role of marine pico-cyanobacteria in the ecology and biogeochemistry of oligotrophic oceans.

The discovery and development of novel antibacterial agents is essential to address the rising health concern over antibiotic resistant bacteria. This research investigated the antibacterial activity of a natural clay deposit near Crater Lake, Oregon, that is effective at killing antibiotic resistant human pathogens. The primary rock types in the deposit are andesitic pyroclastic materials, which have been hydrothermally altered into argillic clay zones. High-sulfidation (acidic) alteration produced clay zones with elevated pyrite (18%), illite-smectite (I-S) (70% illite), elemental sulfur, kaolinite and carbonates. Low-sulfidation alteration at neutral pH generated clay zones with lower pyrite concentrations pyrite (4-6%), the mixed-layered I-S clay rectorite (R1, I-S) and quartz.

Antibacterial susceptibility testing reveals that hydrated clays containing pyrite and I-S are effective at killing (100%) of the model pathogens tested (E. coli and S. epidermidis) when pH (< 4.2) and Eh (> 450 mV) promote pyrite oxidation and mineral dissolution, releasing > 1 mM concentrations of Fe2+, Fe3+ and Al3+. However, certain oxidized clay zones containing no pyrite still inhibited bacterial growth. These clays buffered solutions to low pH (< 4.7) and oxidizing Eh (> 400 mV) conditions, releasing lower amounts (< 1 mM) of Fe and Al. The presence of carbonate in the clays eliminated antibacterial activity due to increases in pH, which lower pyrite oxidation and mineral dissolution rates.

The antibacterial mechanism of these natural clays was explored using metal toxicity and genetic assays, along with advanced bioimaging techniques. Antibacterial clays provide a continuous reservoir of Fe2+, Fe3+ and Al3+ that synergistically attack pathogens while generating hydrogen peroxide (H2O¬2). Results show that dissolved Fe2+ and Al3+ are adsorbed to bacterial envelopes, causing protein misfolding and oxidation in the outer membrane. Only Fe2+ is taken up by the cells, generating oxidative stress that damages DNA and proteins. Excess Fe2+ oxidizes inside the cell and precipitates Fe3+-oxides, marking the sites of hydroxyl radical (•OH) generation. Recognition of this novel geochemical antibacterial process should inform designs of new mineral based antibacterial agents and could provide a new economic industry for such clays.

Natural variations in 238U/235U of marine carbonates might provide a useful way of constraining redox conditions of ancient environments. In order to evaluate the reliability of this proxy, we conducted aragonite and calcite coprecipitation experiments at pH ~7.5 and ~ 8.5 to study possible U isotope fractionation during incorporation into these minerals.

Small but significant U isotope fractionation was observed in aragonite experiments at pH ~ 8.5, with heavier U in the solid phase. 238U/235U of dissolved U in these experiments can be fit by Rayleigh fractionation curves with fractionation factors of 1.00007+0.00002/-0.00003, 1.00005 ± 0.00001, and 1.00003 ± 0.00001. In contrast, no resolvable U isotope fractionation was observed in an aragonite experiment at pH ~7.5 or in calcite experiments at either pH. Equilibrium isotope fractionation among different aqueous U species is the most likely explanation for these findings. Certain charged U species are preferentially incorporated into calcium carbonate relative to the uncharged U species Ca2UO2(CO3)3(aq), which we hypothesize has a lighter equilibrium U isotope composition than most of the charged species. According to this hypothesis, the magnitude of U isotope fractionation should scale with the fraction of dissolved U that is present as Ca2UO2(CO3)3 (aq). This expectation is confirmed by equilibrium speciation modeling of our experiments. Theoretical calculation of the U isotope fractionation factors between different U species could further test this hypothesis and our proposed fractionation mechanism.

These findings suggest that U isotope variations in ancient carbonates could be controlled by changes in the aqueous speciation of seawater U, particularly changes in seawater pH, PCO2, [Ca], or [Mg] concentrations. In general, these effects are likely to be small (<0.13 ‰), but are nevertheless potentially significant because of the small natural range of variation of 238U/235U.

Particulate trace metals can enter the atmosphere as mineral dust, sea spray, anthropogenic emissions, biomass burning, etc. Once in the atmosphere they can undergo a variety of transformations including aqueous phase (cloud) processing, photochemical reactions, interact with gases, and ultimately deposit. Metals in aerosols are of particular interest because of their natural and anthropogenic sources as well as their effects on local (human health) and global (climate change) scales. This work investigates the metal component of atmospheric particles and how it changes during physical and chemical processes at local, regional and global scales, through laboratory and field studies. In the first part of this work, the impact of local dust storms (haboobs) on ambient metal concentrations and speciation is investigated in Tempe, AZ. It was found that metal concentrations substantially increase (> 10 times) during these events before returning to pre-storm levels. In a second part of this work, the impact of fog processing on metal concentrations, solubility and speciation is examined through field observations in California’s Central Valley. The observations show that fog processing has a profound effect on local metal concentrations but the trends are not consistent between sites or even between events, indicating complex processes that need further investigation. For example, fogs have an effect on scavenging and solubility of iron in Davis, while in Fresno soluble iron content is indicative of the source of the aerosol. The last part of the thesis investigates the role of particle size on the solubilization of iron from mineral dust aerosols during global atmospheric transport through laboratory experiments. The experiments showed that mineralogy and pH have the greatest effect on iron solubility in atmospheric aerosols in general while particle size and photochemistry impact mainly the solubility of iron oxides.