abstract: Dissolved organic matter (DOM) is an important part of aquatic foodwebs because it contains carbon, nitrogen, and other elements required by heterotrophic organisms. It has many sources that determine its molecular composition, nutrient content, and biological lability and in turn, influence whether it is retained and processed in the stream reach or exported downstream. I examined the composition of DOM from vascular wetland plants, filamentous algae, and riparian tree leaf litter in Sonoran Desert streams and its decomposition by stream microbes. I used a combination of field observations, in-situ experiments, and a manipulative laboratory incubation to test (1) how dominant primary producers influence DOM chemical composition and ecosystem metabolism at the reach scale and (2) how DOM composition and nitrogen (N) content control microbial decomposition and stream uptake of DOM. I found that differences in streamwater DOM composition between two distinct reaches of Sycamore Creek did not affect in-situ stream respiration and gross primary production rates. Stream sediment microbial respiration rates did not differ significantly when incubated in the laboratory with DOM from wetland plants, algae, and leaf litter, thus all sources were similarly labile. However, whole-stream uptake of DOM increased from leaf to algal to wetland plant leachate. Desert streams have the potential to process DOM from leaf, wetland, and algal sources, though algal and wetland DOM, due to their more labile composition, can be more readily retained and mineralized. / Dissertation/Thesis / Masters Thesis Biology 2018

abstract: Utilizing both 16S and 18S rRNA sequencing alongside energetic calculations from geochemical measurements offers a bridged perspective of prokaryotic and eukaryotic community diversities and their relationships to geochemical diversity. Yellowstone National Park hot spring outflows from varied geochemical compositions, ranging in pH from < 2 to > 9 and in temperature from < 30°C to > 90°C, were sampled across the photosynthetic fringe, a transition in these outflows from exclusively chemosynthetic microbial communities to those that include photosynthesis. Illumina sequencing was performed to document the diversity of both prokaryotes and eukaryotes above, at, and below the photosynthetic fringe of twelve hot spring systems. Additionally, field measurements of dissolved oxygen, ferrous iron, and total sulfide were combined with laboratory analyses of sulfate, nitrate, total ammonium, dissolved inorganic carbon, dissolved methane, dissolved hydrogen, and dissolved carbon monoxide were used to calculate the available energy from 58 potential metabolisms. Results were ranked to identify those that yield the most energy according to the geochemical conditions of each system. Of the 46 samples taken across twelve systems, all showed the greatest energy yields using oxygen as the main electron acceptor, followed by nitrate. On the other hand, ammonium or ammonia, depending on pH, showed the greatest energy yields as an electron donor, followed by H2S or HS-. While some sequenced taxa reflect potential biotic participants in the sulfur cycle of these hot spring systems, many sample locations that yield the most energy from ammonium/ammonia oxidation have low relative abundances of known ammonium/ammonia oxidizers, indicating potentially untapped sources of chemotrophic energy or perhaps poorly understood metabolic capabilities of cultured chemotrophs. / Dissertation/Thesis / Masters Thesis Geological Sciences 2018

abstract: Rangelands are an extensive land cover type that cover about 40% of earth’s ice-free surface, expanding into many biomes. Moreover, managing rangelands is crucial for long-term sustainability of the vital ecosystem services they provide including carbon (C) storage via soil organic carbon (SOC) and animal agriculture. Arid rangelands are particularly susceptible to dramatic shifts in vegetation cover, physical and chemical soil properties, and erosion due to grazing pressure. Many studies have documented these effects, but studies focusing on grazing impacts on soil properties, namely SOC, are less common. Furthermore, studies testing effects of different levels of grazing intensities on SOC pools and distribution yield mixed results with little alignment. The primary objective of this thesis was to have a better understanding of the role of grazing intensity on arid rangeland soil C storage. I conducted research in long established pastures in Jornada Experimental Range (JER). I established a 1500m transect in three pastures originating at water points and analyzed vegetation cover and SOC on points along these transects to see the effect of grazing on C storage on a grazing gradient. I used the line-point intercept method to measure and categorize vegetation into grass, bare, and shrub. Since soil adjacent to each of these three cover types will likely contain differing SOC content, I then used this vegetation cover data to calculate the contribution of each cover type to SOC. I found shrub cover and total vegetation cover to decrease, while grass and bare cover increased with decreasing proximity to the water source. I found areal (g/m2) and percent (go SOC to be highest in the first 200m of the transects when accounting for the contribution of the three vegetation cover types. I concluded that SOC is being redistributed toward the water source via foraging and defecation and foraging, due to a negative trend of both total vegetation cover and percent SOC (g/g). With the decreasing trends of vegetation cover and SOC further from pasture water sources, my thesis research contributes to the understanding of storage and distribution of SOC stocks in arid rangelands. / Dissertation/Thesis / Masters Thesis Biology 2018

abstract: This research investigates the biophysical and institutional mechanisms affecting the distribution of metals in the Sonoran Desert of Arizona. To date, a long-term, interdisciplinary perspective on metal pollution in the region has been lacking. To address this gap, I integrated approaches from environmental chemistry, historical geography, and institutional economics to study the history of metal pollution in the desert. First, by analyzing the chemistry embodied in the sequentially-grown spines of long-lived cacti, I created a record of metal pollution that details biogeochemical trends in the desert since the 1980s. These data suggest that metal pollution is not simply a legacy of early industrialization. Instead, I found evidence of recent metal pollution in both the heart of the city and a remote, rural location. To understand how changing land uses may have contributed to this, I next explored the historical geography of industrialization in the desert. After identifying cities and mining districts as hot spots for airborne metals, I used a mixture of historical reports, maps, and memoirs to reconstruct the industrial history of these polluted landscapes. In the process, I identified three key transitions in the energy-metal nexus that drove the redistribution of metals from mineral deposits to urban communities. These transitions coincided with the Columbian exchange, the arrival of the railroads, and the economic restructuring that accompanied World War II. Finally, to determine how legal and political forces may be influencing the fate of metals, I studied the evolution of the rights and duties affecting metals in their various forms. This allowed me to track changes in the institutions regulating metals from the mining laws of the 19th century through their treatment as occupational and public health hazards in the 20th century. In the process, I show how Arizona’s environmental and resource institutions were often transformed by extra-territorial concerns. Ultimately, this created an institutional system that compartmentalizes metals and fails to appreciate their capacity to mobilize across legal and biophysical boundaries to accumulate in the environment. Long-term, interdisciplinary perspectives such as this are critical for untangling the complex web of elements and social relations transforming the modern world. / Dissertation/Thesis / Doctoral Dissertation Sustainability 2019

abstract: Chromatin is the dynamic structure of proteins and nucleic acids into which eukaryotic genomes are organized. For those looking to engineer mammalian genomes, chromatin is both an opportunity and an obstacle. While chromatin provides another tool with which to control gene expression, regional density can lead to variability in genome editing efficiency by CRISPR/Cas9 systems. Many groups have attempted to de-silence chromatin to regulate genes and enhance DNA's accessibility to nucleases, but inconsistent results leave outstanding questions. Here, I test different types of activators, to analyze changes in chromatin features that result for chromatin opening, and to identify the critical biochemical features that support artificially generated open, transcriptionally active chromatin. I designed, built, and tested a panel of synthetic pioneer factors (SPiFs) to open condensed, repressive chromatin with the aims of 1) activating repressed transgenes in mammalian cells and 2) reversing the inhibitory effects of closed chromatin on Cas9-endonuclease activity. Pioneer factors are unique in their ability to bind DNA in closed chromatin. In order to repurpose this natural function, I designed SPiFs from a Gal4 DNA binding domain, which has inherent pioneer functionality, fused with chromatin-modifying peptides with distinct functions. SPiFs with transcriptional activation as their primary mechanism were able to reverse this repression and induced a stably active state. My work also revealed the active site from proto-oncogene MYB as a novel transgene activator. To determine if MYB could be used generally to restore transgene expression, I fused it to a deactivated Cas9 and targeted a silenced transgene in native heterochromatin. The resulting activator was able to reverse silencing and can be chemically controlled with a small molecule drug. Other SPiFs in my panel did not increase gene expression. However, pretreatment with several of these expression-neutral SPiFs increased Cas9-mediated editing in closed chromatin, suggesting a crucial difference between chromatin that is accessible and that which contains genes being actively transcribed. Understanding this distinction will be vital to the engineering of stable transgenic cell lines for product production and disease modeling, as well as therapeutic applications such as restoring epigenetic order to misregulated disease cells. / Dissertation/Thesis / Doctoral Dissertation Biological Design 2019

Recently, biogenic carbonates have received much attention as potential proxies of environmental change; however, a major pathway of elemental incorporation is often overlooked when making interpretations or designing experiments. This research experimentally examines the influence of diet on elemental composition in juvenile shells of the bay scallop, Argopecten irradians concentricus, and the northern quahog, Mercenaria mercenaria. Exploratory trials were conducted using Argopecten irradians concentricus juveniles fed different algal diets: Isochrysis, Chaetoceros, Pavlova, Tetraselmis, or a mix of all four in a 2:1:2:2 ratio. No differences between the left and right valves were revealed, thus, subsequent analysis of the dietary influence on shell chemistry utilized both valves. Only Mg/Ca and K/Ca were significantly different between the diet groups, though different influences were determined. Experiments with juvenile Mercenaria mercenaria compared shell chemistries among clams fed unicellular diets of Isochrysis sp. (CCMP1324), Pavlova pinguis (CCMP609), Chaetoceros mulleri (CCMP1316), Isochrysis sp. (CCMP1611) culture, Pavlova sp. (CCMP1209), or Chaetoceros galvestonensis (CCMP186), a mixed diet of all species in equal ratios (Mixed), or no food (starvation control). The results indicate that diet can influence shell chemistry either directly or indirectly, with degree of influence varying by diet and mollusc species. Additional information concerning the use of alternative element ratios and changes in the shell chemistry due to starvation-induced stress are also presented. Altogether, the present research provides valuable information concerning shell dynamics and potential diet-associated fluxes, thus demonstrating the need to consider the composition of dietary inputs when assessing environmental associations with elemental shell chemistries.

In urban karst areas, such as the City of Bowling Green, Kentucky and the Tampa Bay Metropolitan Area, groundwater quality faces a variety of threats. The development of residential, commercial, and industrial landuse types allows for a wide variety of groundwater pollutants to enter the karst groundwater systems. Various different models and indices have attempted evaluative approaches to identify issues in urban karst areas, but the methods vary by location and lack a focus on urban karst groundwater quality. There also exists a lack of a data-driven approach that is able to capture short- and long-term changes in threats to groundwater quality as a result of urbanization. The overall purpose of this study was to develop a holistic, data-driven evaluation toolbox with threat, vulnerability, and monitoring assessment tools for urban karst groundwater systems to better determine the possible threats, data collection needs, monitoring parameters, and analytical approaches needed to ensure groundwater quality is maintained in urban karst regions. This study focused on: 1) determining what indicators, parameters, resolution, and data quality need to be prioritized to create an effective, holistic monitoring framework for urban karst groundwater, and 2) developing an effective assessment and evaluative tools for urban karst groundwater quality sites using historic and modern data in an urban karst setting. The outcomes include an Urban Karst Aquifer Resource Evaluation (UKARE) Toolbox with a Threat, Vulnerability, and Monitoring evaluation tools that were applied and validated through application of the Toolbox using case studies in the City of Bowling Green, Kentucky and the Tampa Bay Metropolitan Area in Florida. The results demonstrate the universal applicability of the UKARE Toolbox to different urban karst sites and its effectiveness at scoring for threats and vulnerabilities, as well as identifying potential monitoring sites through primary data collection of water quality parameters and emerging pathogens at over 150 sites between both study areas. The final results of this study are useful to develop monitoring and management plans through a standardized scoring and evaluation tool in order to influence urban karst groundwater monitoring and management.

The Wax Lake Delta (WLD) is one of the few areas of land gain in coastal Louisiana and provides an analog for a naturally developing subdelta created by a river diversion. This study examined the spatial and temporal variability of benthic respiration to broaden our current understanding of the biogeochemical functioning of diversion-created estuarine systems. Spatial and seasonal benthic respiration rates were quantified during distinct periods of discharge and water temperature conditions, which included a spring period of peak river discharge (May 2012, 2013), a summer period of low discharge and maximum seasonal water temperatures (August/Sept, 2012), and an autumn period of low discharge and intermediate water temperatures (October 2013). Benthic respiration rates for the Wax Lake Delta ranged from 4.4 – 46.8 and averaged 16.7 (± 1.5) mmol O2 m-2 d-1 . Atchafalaya Bay sites ranged from 10.3 - 26.5 and averaged 17.1 (± 1.5) mmol O2 m-2 d-1 across all sites and seasons. Benthic respiration generally increased along two spatial gradients: 1) with distance offshore from the delta into Atchafalaya Bay, and 2) toward the interior of a mouth bar island. These patterns were related to similar increases in sediment OC and N content, which were derived from a mix of terrigenous and marine sources and varied with season. Sediment organic (OC and N) content and water temperature were identified as main drivers influencing benthic respiration in the Wax Lake Delta estuary. Seasonal changes in riverine discharge and wind-driven sediment resuspension events were likely to influence the seasonal variability of benthic respiration by governing water temperature and organic matter supply to the sediments. Benthic oxygen consumption rates in the Wax Lake Delta were most sensitive to increases in water temperature during low discharge conditions (< 2,000 m3 /s) of the MI-AR system. In context of coastal restoration, results from this study suggest that opening a sediment diversion during spring peak discharge conditions will have less of an effect on benthic oxygen consumption rates than during warmer low flow conditions. / acase@tulane.edu

Iron (Fe) minerals and ferrous iron (Fe(II)) play an important role in the several natural elemental cycles, including the carbon cycle, nutrient cycles, and the cycling of metals. In this work we have characterized the reactivity structural Fe(II) in several Fe minerals and in natural soil with uranium. We have studied the reactivity of Fe(II) in solution with the Fe oxide goethite conditions relevant to many natural systems. Green rusts are widely recognized as an intermediate phase in the Fe cycle. Here we investigate the reactivity of green rusts containing different structural anions with uraniumVI (UVI). We have also investigated the effect of aqueous bicarbonate on UVI sorption and reduction by green rusts. Our findings indicate that green rusts reduce UVI to UIV, and that environmentally relevant carbonate concentrations have little effect the rate and extent on this reaction. We have also investigated UVI reduction by structural Fe(II) in magnetite. Magnetite with varying stoichiometry (x = Fe2+/Fe3+) was reacted with UVI. Results from x-ray absorption spectroscopy indicate that the redox properties of magnetite dictate whether magnetite reduces UVI. In addition, magnetite reactivity can be "recharged" by electron transfer from aqueous Fe(II). There is little evidence of the reactivity of structural Fe(II) towards UVI in natural materials. We have characterized a naturally reduced soil and found it contains structural Fe(II) in clay minerals and a possible green rust-like phase. When this soil is exposed to UVI we find that Fe(II) reduces a portion of the U added. Our work highlights the potential for abiotic reduction of UVI by Fe(II) in reduced, Fe-rich environments. We have used 57Fe Mössbauer spectroscopy to study redox reactions of Fe(II) with goethite under biogeochemical conditions relevant to natural systems. When Fe(III) in goethite is substituted with aluminum or anions such as phosphate, silicate, carbonate, and natural organic matter are sorbed onto the surface of goethite, interfacial electron transfer occurs between sorbed Fe(II) and goethite. These results indicate that electron transfer between Fe(II) and Fe oxides occurs under environmentally relevant conditions. Electron transfer was blocked by phospholipids, however, suggesting electron transfer may be inhibited under eutrophic conditions.

The global continental carbon and water cycles are intimately linked through stomatal regulation during vegetation photosynthesis and biosphere-atmosphere interactions. Therefore, to have a complete understanding of both present and future climate, these cycles must be studied as an interconnected system. This thesis presents three studies that aim to better explain these interactions and provide a direction forward for improved model projections of climate. The first study shows that biosphere-atmosphere feedbacks can contribute up to 30% of climate and weather variability in certain regions that help determine the net CO2 balance of the biosphere. It demonstrates that Earth System Models are under-estimating these contributions, mainly due to the underestimation of the biosphere response to radiation and water availability. It emphasizes the importance of correctly capturing these feedbacks in models for accurate subseasonal to seasonal climate predictions. The second demonstrates that changes in soil moisture (both short-term variability and long-term trends) strongly limit the ability of the continents to act as a carbon sink, with overall effects on the same order of magnitude as the land sink itself. Photosynthesis rates tend to be reduced when soil moisture is depleted, leading to decreased carbon uptake. Additionally, respiration rates increase due to increased temperature through land-atmosphere feedbacks. These carbon losses are not compensated for during wet anomalies due to the nonlinear response of vegetation activity (both respiration and photosynthesis) to soil moisture. This suggests that the increasing trend in carbon uptake rate may not be sustained past the middle of the century and could result in accelerated atmospheric CO2 growth. The third decouples the effects of atmospheric dryness (vapor pressure deficit) and soil dryness on vegetation activity in the largest terrestrial carbon sink: the tropics. Understanding vegetation response to environmental drivers and stressors in the tropics is essential to accurately modeling these ecosystems and predicting whether they will remain carbon sinks in the future. The study finds that in regions that are water limited, vegetation is driven by precipitation and radiation while being limited by high vapor pressure deficit. Conversely, in the wettest regions that are light limited, increases in vapor pressure deficit accompany increasing rates of photosynthesis. These three studies contribute to our understanding of land-atmosphere and biosphere-atmosphere feedbacks and the coupling of the continental carbon and water cycles. They identify model process representations, such as soil moisture and vegetation water-stress, that are hindering our ability to make accurate forecasts. By improving our knowledge of these mechanisms and evaluating the ability of models to reproduce them, we pave the way forward for improved climate and weather projections. Better predictions can be used not only to protect society in the present, but also to appropriately shape climate policy to protect society in the future.