Mountain Scholar :: Browsing by Author "Borch, Thomas, committee member"

Browsing by Author "Borch, Thomas, committee member"

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Open Access
Advancing understanding of the formation and stability of soil organic matter in a changing environment
(Colorado State University. Libraries, 2015) Lavallee, Jocelyn M., author; Conant, Rich T., advisor; Paul, Eldor A., advisor; Cotrufo, M. Francesca, committee member; Borch, Thomas, committee member; Kelly, Eugene F., committee member
Soil is one of our most precious natural resources. It plays a key role in maintaining soil fertility and water quality, and represents a major reservoir in both the global carbon (C) and nitrogen (N) cycles. Soils contain more C and reactive N than the atmosphere and all vegetation combined, the majority of which is found in soil organic matter (SOM). Despite its considerable significance, little is known about the factors that control the formation of SOM, and its stability in the environment. Key questions pertain to whether environmental changes will increase the production of CO₂ during SOM formation and decomposition, forming a large positive feedback to climate change. Answering those questions required a better understanding of how various mechanisms that confer SOM stability are affected by environmental change. My dissertation research aimed to address some of these key questions, and to advance our overall understanding of SOM formation, SOM stability, and the response of stable SOM to changes in the environment. First, I conducted two soil incubation experiments using isotopically labeled (¹³C and ¹⁵N) plant material, which allowed me to track the incorporation of plant-derived C and N into SOM, and efflux of plant-derived C in CO₂. In one soil incubation, I tested the effects of plant litter quality and on the rate and efficiency of SOM formation (a measure of the amount of SOM formed versus the amount of CO₂ lost in the process) by comparing SOM formation from leaves versus roots. I found that plant litter chemistry (C/N ratio) was a reliable predictor of SOM formation after the initial stage of decomposition, with low C/N ratios resulting in more SOM formation and higher formation efficiencies overall. In the second soil incubation, I tested the effect of warming on the rate and efficiency of SOM formation, as well as the rate of destabilization of stable SOM. I found that warming generally led to lower formation efficiencies, causing greater CO₂ production per unit of SOM formed. Warming also led to higher rates of destabilization of stable SOM throughout the experiment. Next, I aimed to investigate the effect of warming on SOM in the field, using soils from two multi-factor climate change experiments. Results from that study suggested that while warming increased the rate of turnover of SOM in some cases, any resulting losses of SOM were offset by increased inputs of SOM, so that total SOM stocks were unchanged. Last, I investigated the persistence of pyrogenic SOM, which is thermally transformed by fire, in the face of land use change at three agricultural sites across the US. I found that pyrogenic SOM was present in all three soils, and had persisted to a greater extent than other SOM with land use change. Many studies of SOM dynamics do not account for pyrogenic SOM, and the results of my work suggest that this lack of accounting can preclude us from fully understanding the mechanisms behind SOM stability. Overall, my work advances our understanding of stable SOM in terms of how it is formed, and whether it will persist in the face of environmental change. Changes in plant litter quality and temperature may lead to changes fluxes of CO₂ to the atmosphere during SOM formation, and while some SOM (pyrogenic SOM) is highly stable in the environment, other SOM is susceptible to loss with warming and land use change. However, in the case of warming, increased plant inputs may offset increased rates of SOM decomposition.
Open Access
An investigation of the effect of surface released nitric oxide on fibrinogen adsorption
(Colorado State University. Libraries, 2014) Lantvit, Sarah Marie, author; Reynolds, Melissa, advisor; Borch, Thomas, committee member; Fisher, Ellen, committee member; Kennan, Alan, committee member; Popat, Ketul, committee member
The search for improved biomaterials is a continually ongoing effort to prevent the failure of medical devices due to blood clotting. Each group of researchers has their own set of methods to create the ideal material for biological systems. In the pursuit of materials to prevent blood clot formation, these attempts have been focused on alterations in surface properties, pre-adsorption of proteins, and release of drugs. In this work I took a high-throughput approach to the prevention of device failure by investigating a model material system. Starting with a nitric oxide (NO) releasing material, a sample preparation method was developed to ensure that surface properties could be compared to a non-NO releasing control. With this material, the effect of the NO release on fibrinogen adsorption to these surfaces could be isolated. Fibrinogen is instrumental in the formation of blood clots. Determining the effect that NO has on this protein will help determine why NO has been previously found to prevent clotting in blood-contacting systems. Once the model system was developed, further investigation into changes in the fibrinogen resulting from its interaction with the released NO could be undertaken. A full investigation was completed on control non-NO releasing, low NO flux, and high NO flux materials. A qualitative assessment of the fibrinogen adsorption shows that the high NO releasing material exhibits significantly higher fibrinogen adsorption compared to both the control and low NO flux materials. Quantitative assessment of fibrinogen adsorption was attempted through a variety of methods, which indicate that conformational changes are happening upon adsorption of fibrinogen to all materials. To this end, FTIR spectra from the adsorbed fibrinogen and native fibrinogen were compared to elucidate changes in the protein's conformation. Control and low NO flux materials had too little protein to gain insight into these changes. For the high NO flux material, the fibrinogen had a significant decrease in α-helices and an increase in random chains compared to native fibrinogen. To begin understanding the effect that these changes will have on blood clot formation, these materials were further analyzed for platelet adhesion. A comparison of the control, low NO flux, and high NO flux materials with and without fibrinogen adsorbed to the material surface shows that the fibrinogen has a distinct effect on platelet adhesion and aggregation. The high NO flux materials exhibited less aggregation and full activation of platelets when fibrinogen was adsorbed prior to incubation with platelets than if fibrinogen was not present before incubation. Overall, the effect of NO on fibrinogen adsorption can be seen through these measurements. Nitric oxide release causes an increase in fibrinogen adsorption, as well as protein reorganization. Surprisingly, we see that this adsorbed fibrinogen actually improves the viability of platelets. Further study must be done using whole blood and in vivo measurements to fully understand what effect the adsorbed fibrinogen will have on the device. Despite this we can say that the adsorption of fibrinogen onto these NO releasing materials helps to improve the biocompatibility of this biomaterial due to its bulk adsorption and conformational changes.
Open Access
Analysis and modeling of what honey bees (Apis mellifera L.) bring back to the hive and how that affects the health of the hive and humans
(Colorado State University. Libraries, 2023) Awad, Mai Mousa, author; Boone, Randall, advisor; Kato, Takamitsu, advisor; Borch, Thomas, committee member; Ode, Paul, committee member
Apis mellifera L. populations are decreasing at an alarming rate. Over the past 20 years, the number of managed honey bee colonies has declined, and this decline has become a global concern. This study focuses on chemical stressors that are found to affect the bee population. We used direct sampling to examine the variation of pesticides and heavy metals concentrations in two different landscape contexts. Subsequently, we extrapolated the risk of these toxins' residues on Apis sp. based on current literature. We found no spatial variation in metal concentrations in pollen and honey samples collected from urban and agricultural areas. Likewise, we observed no spatial variation in pesticide concentrations in pollen and honey samples collected from urban versus agricultural areas. In addition to chemical factors, we studied the nutritional factor by investigating the effect of spatial variability on the amount of stored pollen and the floral diversity of in-hive pollen. Furthermore, we estimated the most abundant botanical families that will identify honey bees' protein-source preferences. The results indicated a spatial variation in Shannon-Weaver diversity, demonstrating a higher diversity index with a wider variety of pollen taxa collected from urban sites compared to the agricultural ones with a lower diversity index with less pollen taxonomic variety. The alarming decrease in honey bees' population urges researchers to investigate the factors that enhance the deterioration of bees' population. A few models explained these factors individually. We designed a NetLogo model to assess multiple factors that would intensify the impact of the Colony Collapse Disorder phenomenon, by investigating the spatial variation of bees' exposure to a distinctive environmental toxin and the quantities of these toxins in hive products. The model indicated that there were significant spatial variation effects on the pesticides and heavy metal concentrations in the accumulated pollen and nectar inside the beehive. Pesticides and heavy metal accumulation in bees' products are mainly caused by human activities, which can affect human health by their consuming contaminated honey. Based on the results of honey analysis for pesticides and heavy metals we performed in the first study, we decided to select one pesticide and a pesticide synergist along with the most two abundant heavy metals to investigate the synergistic effect of cytotoxicity and genotoxicity that would result from the interaction of one major pesticide in honey: Imidacloprid and a pesticide synergist: Piperonyl butoxide, and two major heavy metals in honey: Lead and Selenium, at the cellular level in mammalian cells, where we found different interactional effects of these compounds on cell survival, cell apoptosis, oxidative stress, and sister chromatid induction.
Open Access
Analytical methods to enhance detection of anthropogenic radionuclides in environmental matrices
(Colorado State University. Libraries, 2016) Rosenberg, Brett L., author; Brandl, Alexander, advisor; Borch, Thomas, committee member; Henry, Charles, committee member; Pinder, John, committee member; Steinhauser, Georg, committee member
The efficacy of methods that are used to detect radionuclides is dependent on the properties of the radionuclides and the matrices being analyzed. Gamma spectroscopy is an excellent tool for detecting very low quantities of a short-lived gamma-emitting radionuclide. However, as the probability of gamma ray emission decreases and the half-life increases, greater quantities of a radionuclide are required for detection by gamma spectroscopy. Since most transuranic actinides are usually not present in such quantities or concentrations in the environment, mass spectrometry is the preferred tool. For tritium, 90Sr, and other lower-Z elements that emit no easily detectable gamma rays, liquid scintillation counting is commonly used to measure the beta particles they emit. However, this methodology requires radiochemical extraction procedures to ensure a maximized ratio between signal and background. Nondestructive gamma spectroscopy was used to evaluate radiocesium content in soil and vegetation samples collected from the Fukushima prefecture exclusion zone in 2013 and 2014. Liquid scintillation counting was used for quantifying 3H in samples collected in 2013 and 90Sr in samples collected in 2013 and 2014. The radiocesium and 90Sr activities were found to have decreased from 2013 to 2014. Although 3H activities could be quantified in most samples, a sample from Chimeiji had a specific activity that statistically exceeded background (1.2 ± 1.6 Bq mL-1); further investigation is required to ascertain if 3H is present within that sample. Reports generated by TEPCO were also evaluated; radiocesium ratios and 131I/132Te ratios calculated from the reports reveal the importance of considering counting statistics and spectroscopic interference when drawing conclusions about the presence of anthropogenic radionuclides in environmental samples. Gamma spectroscopy was then applied to explore radiochemical separation techniques that can enhance detection of anthropogenic radionuclides, especially gamma-emitting actinides like 239Np shortly after a nuclear event. Ion specific extraction chromatography was found to be effective at minimizing spectroscopic interference from fission products, and addition of stable iodide carrier and a precipitating agent facilitated decreasing radioiodine activity within environmental samples. Extraction chromatography was found to reduce 131I interference by at least one order of magnitude, making it preferred for reducing 131I activity within an environmental sample. Extraction chromatography also avoids the potential of precipitating any analyte. The separation and measurement techniques utilized herein have effectively enhanced the ability to detect low-activity anthropogenic radionuclides; supplemental measurements gathered from the exclusion zone confirm the observed trends and prove the necessity of minimizing interference.
Open Access
Atmospheric processing of chemical compounds and direct measurements of particle loss by dry and wet deposition
(Colorado State University. Libraries, 2019) Emerson, Ethan Walker, author; Farmer, Delphine, advisor; Neilson, James, advisor; Ravishankara, A. R. Ravi, committee member; Borch, Thomas, committee member; Barisas, George, committee member; Jathar, Shantanu, committee member
Anthropogenic pollutants, like NOₓ and black carbon (BC), are ubiquitous in the atmosphere and impact human health and the climate. Understanding the atmospheric fate of such pollutants is critical in understanding their impact. This work focuses on understanding the loss of two key pollutants: the chemical termination of gas phase NO and NO₂ (NOₓ) and the deposition of refractory black carbon (rBC) particles. Additionally, because the tools to analyze particle fluxes and coated rBC are lacking, this work describes the development of software to analyze particle fluxes and estimate the thickness of organic coatings on rBC. Removal of aerosols from the atmosphere occurs via wet and dry deposition. Black carbon (BC) is one form of aerosol that impacts atmospheric temperature, cloud formation and properties, the albedo of snow and ice surfaces, and the timing of snowmelt. Parameterization of BC dry deposition is particularly limited due to the lack of available instrumentation for measuring the process, and thus there is a lack of observational datasets with which to evaluate existing models. We present observations of dry and wet deposition rates of size-resolved coated rBC and total aerosol number by eddy covariance technique using a single particle soot photometer (SP2; Droplet Measurement Technologies Inc.) and ultra high sensitivity aerosol spectrometer (UHSAS; Droplet Measurement Technologies Inc.) from the remote Southern Great Plains ARM Climate Research facility in north-central Oklahoma. Using these data, we show that (1) wet deposition dominates the removal of rBC from the atmosphere, (2) dry deposition measurements agree with sophisticated deposition parameterizations, and (3) a simple parameterization adequately describes size-resolved deposition. We assess the implications of this parameterization in GEOS-Chem. Size-resolved deposition schemes, such as those used in current chemical transport models use schemes that have not been compared to recent measurements. Using aggregated deposition velocities from literature observations and those collected by our group, we show that the current scheme used in chemical transport models does not accurately describe observed deposition velocities. Highly sophisticated leaf level models can accurately describe the aggregated observations, but they are ill-suited to global chemical transport models. We present a simple scheme that reasonably describes size-resolved particle deposition in a simple sectional scheme that includes atmospheric parameters. The result of this update is substantial changes in particle concentrations across the globe and these impact cloud condensation nuclei, the direct and indirect effects, and PM2.5 concentrations. NOₓ is a key pollutant that propagates atmospheric chemistry through the coupled HOₓ-NOₓ cycle. Trace gas measurements from the 2015 spring and summer SONGNEX campaign conducted at the Boulder Atmospheric Observatory (BAO) in Northern Front Range Metropolitan Area of Colorado (NFRMA) are characteristic of environment impacted by oil and natural gas, agricultural operations, traffic, biogenic, and urban sources. Using a previously published PMF analysis of volatile organic compounds, we show the impact of a changing atmospheric composition due to emissions from anthropogenic sources on NOx sinks and the implications of HOₓ-NOₓ propagation through box modelling. These results indicate that the NFRMA is sensitive to NOₓ and VOC mixing ratios during spring, summer, and smoke-impacted periods.
Open Access
Biogeochemical characterization of a LNAPL body in support of STELA
(Colorado State University. Libraries, 2013) Irianni Renno, Maria, author; De Long, Susan K., advisor; Sale, Thomas C., advisor; Borch, Thomas, committee member; Payne, Fred, committee member
Microbially-mediated depletion of light non-aqueous phase liquids (LNAPL) has gained regulatory acceptance as a method for managing impacted sites. However, the fundamental microbiology of anaerobic hydrocarbon degradation, in source zones, remains poorly understood. Two site-specific studies (Zeman, 2012 & McCoy, 2012) performed at the Center for Contaminant Hydrology (CCH), Colorado State University (CSU) demonstrated that LNAPL biodegradation increases drastically when temperatures are maintained between 18°C and 30°C as compared to lower or higher temperatures. These results have supported the design of a Sustainable Thermally Enhanced LNAPL Attenuation (STELA) technology that is currently being tested at field scale at a former refinery in Wyoming. The focus of the present study was to perform a depth-resolved characterization of the mixed microbial communities present in LNAPL-impacted soils, as well as to characterize the site's geochemical parameters in order to establish a baseline data set to evaluate the STELA system performance. Seventeen soil cores were collected from the impacted site, frozen on dry ice and subsampled at 6-inch intervals for analysis of biogeochemical parameters. Multi-level sampling systems were installed at the core sites to monitor aqueous and gas phases. Diesel and gasoline range organics and benzene, toluene, ethylbenzene and xylenes (BTEX) present in the cores and in water samples were analyzed. Temperature, inorganic dissolved ions, pH, and oxidation reduction potential (ORP) were also measured. DNA was extracted in triplicate from each subsample corresponding to the study's center core (21 samples). Total Eubacteria and Archaea were quantified via 16S rRNA gene-targeted qPCR. Microorganisms present at selected depth intervals were identified via 454 pyrosequencing of both eubacterial and archaeal 16S rRNA genes. Results indicate that at the study site, the majority of the hydrocarbon contamination is found between 5 and 12 feet below ground surface (bgs). The average of the maximum total petroleum hydrocarbon (TPH) soil concentrations within each core was 17,800 mg/kg with a standard deviation of 8,280 mg/kg. The presence of methane in the vadose zone and depleted sulfate concentrations in water samples suggest that both methanogenesis and sulfate reduction are likely driving LNAPL depletion processes. Four distinct biogeochemical zones where identified within the surveyed aquifer region. Interestingly, the quantity of eubacterial 16S rRNA genes dominate the quantity of archaeal 16S rRNA genes at sampled depths within the aerobic aquifer region. In the strictly anaerobic aquifer regions, these quantities are approximately equal. The latter can be interpreted as evidence of syntrophism, which has been reported in other hydrocarbon biodegradation studies. Pyrosequencing results support these findings as well and contribute to further elucidating the spatial correlation between microbial communities and geochemical parameters. In-situ biodegradation rates are largely controlled by the quantity and activity of key microbes capable of mediating conversion of specific hydrocarbon constituents. Furthermore, it is anticipated that biodegradation rates are governed by complex interactions of diverse microbial communities that vary both in space and time. The overall vision of this initiative is that advancing a better understanding of processes controlling biologically mediated losses of LNAPL will support the development of more efficient treatment technologies for LNAPL releases. In particular, the site specific analysis produced through this study will support the development of STELA.
Open Access
Characterization and prediction of long-term arsenic mobility, dissolution, and kinetic behavior in arsenic contaminated floodplain deposits of Whitewood Creek and the Belle Fourche River, South Dakota
(Colorado State University. Libraries, 2021) Ji, Mu, author; Ridley, John, advisor; Stednick, John, committee member; Borch, Thomas, committee member; Gallen, Sean, committee member
From 1877 to 1977, the Homestake Mine discharged over 100 million tons of arsenic-rich mine-wastes from Lead, South Dakota into Whitewood Creek (WWC), which joins the Belle Fourche River (BFR). Arsenopyrite and other arsenic-bearing minerals were deposited in tailings (containing between 0.12% to 0.35% arsenic) and mixed with uncontaminated alluvium along the floodplains of WWC and the BFR as overbank deposits and filling abandoned meanders. Since it is not feasible to remove millions of tons of contaminated sediments from the area, an understanding of arsenic mobility on long timescales is vital. Many studies have laid the framework for factors controlling arsenic mobility appropriate to fluvial sedimentary systems; investigating mechanisms of arsenic mobilization, adsorption/desorption kinetics, and the effects of pH, changing redox conditions, etc., however, these studies were conducted on relatively short time scales and did not quantify arsenic mass-budget on field-scales. This study focuses on the long-term retention, dissolution, and kinetic behavior of arsenic from mine tailings. The uniqueness of this site enables arsenopyrite dissolution behavior to be constrained over a 135-year timespan (1877-2012). This allows for the investigation of changes in arsenic's residence sites, its rate of release into the environment, calculation of its transport mass-budget, and elucidation of how natural processes have or have not remediated arsenic contamination over a span of 35 years since the deposition of tailings have ceased (1977-2012). For this investigation, sediment, surface water, and seep water samples were collected along reaches of WWC and the BFR for analysis of arsenic and other geochemical constituents. Sequential extractions of the sediments were performed to determine the mineralogical setting of the arsenic as well as the proportion of arsenic available at different rates of release into the environment. Additionally, various historical data (discharge levels, geochemical analyses of water and sediment samples) were compiled from the United States Geological Survey database. Regressions were applied to historical data to estimate the rate of physical and chemical arsenic removal from the WWC watershed. Sediments collected along the floodplains of WWC and the BFR exhibited arsenic concentrations ranging from approximately 100 to 4,000 mg/kg. The results from the sequential extractions applied to the sediments suggest arsenic is predominantly located in residence sites that are not easily accessible, and arsenic is not readily mobilized or released into solution in large quantities under normal environmental conditions seen in WWC and the BFR. An average of 16% of the arsenic is weakly bound to readily exchangeable surface sites, water-soluble secondary minerals and available for rapid release, or is adsorbed to exchange sites that easily exchange PO43- ions for adsorbed arsenic oxyanions, is weakly bound in amorphous to poorly crystalline fine-grained metal oxides/hydroxides, reducible phases, and easily soluble carbonates. An average of 24% of the arsenic is moderately strongly bound in weakly soluble secondary minerals like clays or crystalline fine-grained metal oxides/hydroxides and will be released relatively slowly with time. The remaining 60% of arsenic is interpreted to be relatively immobile and locked in arsenopyrite in part due to the formation of metal oxyhydroxide coating, which slows down the degradation of the mineral. These interpretations are supported by the elevated but still relatively low total arsenic concentrations (EPA MCL for arsenic is 0.01 mg/L) of in-stream water in WWC (averaging 0.037 mg/L) and in the BFR (averaging 0.021 mg/L), considering that in-stream sediments carried by WWC and the BFR have high arsenic concentrations (264 to 694 mg/kg). Based on regressions applied to 30 years of historical sediment transport and arsenic concentration in solution and in sediment load (1982-2012), the average annual total arsenic load transported out of WWC during these 30 years was estimated to be between 34 to 71 megagrams (Mg) per year. At this rate, based on the 17,400 to 50,800 Mg of arsenic that remain in storage along the floodplains of WWC, complete arsenic transport out of the floodplains of WWC would range between 250 to 1,500 years. The actual rate of arsenic removal is expected to be longer because the model is based on a uniform movement of uniformly distributed sediment, and historical patterns may not be reflective of future trends, as evidenced by the decline in suspended arsenic transport rate starting in the early- to mid-1980s. The constant shifting of the stream creates abandoned meanders along WWC that can store contaminated sediment where the stream no longer has access. Conversely, as the meanders shift over time, the once-abandoned meanders could be again accessed by WWC. The majority of suspended sediment transport occurs during flood events; approximately 88% of the total arsenic load moved during the years between 1983 to 2012 occurred in only 3 of the years (1983, 1984, and 1995). Thus, the rate of arsenic transport for the next 30-year period is uncertain and could be lower if the number of flood events remains low. Although the WWC area once experienced heavy environmental degradation during the period of active mining, natural processes have allowed for relatively stable current environmental conditions. However, the physical transport of arsenic-contaminated sediment and the slow release of arsenic to the environment endures downstream to the BFR into the Cheyenne River and Lake Oahe and will continue for many generations.
Open Access
Critical state, dilatancy and particle breakage of mine waste rock
(Colorado State University. Libraries, 2011) Fox, Zachary P., author; Carraro, J. Antonio H., advisor; Shackelford, Charles D., committee member; Borch, Thomas, committee member; Overton, Daniel D., committee member
Critical state, dilatancy and particle breakage characteristics of two mine waste rock (MWR) materials were systematically studied in drained isotropic and axisymmetric compression. A specimen preparation technique that simulated material dumping in the field was adopted and the technique is shown to be suitable for reconstitution of uniform and repeatable specimens of MWR for element testing. The MWR types tested were unoxidized and oxidized sedimentary argillite taken from the Ordovician Vinini formation in northeastern Nevada. Acid-base accounting results indicate that the neutralization potential (NP) and acid-producing potential (AP) values decreased for the oxidized material. Static, monotonic, isotropically compressed drained triaxial tests were performed on 150-mm-diameter, 300-mm-tall cylindrical specimens with maximum particle size equal to 25.4 mm. Laboratory particle size distributions were modeled to be parallel to the collected field gradation in order to create specimens with appropriate maximum particle sizes for the testing apparatus. The intrinsic parameters that characterize critical-state, dilatancy and particle breakage of each MWR material tested were determined allowing analysis of constitutive behavior to be carried out using an appropriate theoretical framework for granular soils experiencing particle breakage during testing. While the critical state friction angles were very similar between the two MWR types (unoxidized = 38.3° and oxidized = 36.7°), dilatancy is much greater in the unoxidized specimens than in the oxidized specimens. Bolton's (1986) fitting parameters Q and R were determined and values agree well with those found in the literature for geomaterials with similar stress-dilatancy behavior and grain tensile strengths. Grain tensile strength was evaluated through point load strength index testing giving values for grain tensile strength for the unoxidized material that are 10 times greater than observed for the oxidized material. Particle size distributions were determined before and after testing to evaluate particle breakage due to the combined effects of isotropic and axisymmetric compression as well as evaluate the increase in surface area due to particle breakage. The fractal dimension (D) was evaluated before and after testing in order to assess the validity of the underlying assumptions of the modified work equation presented by McDowell et al. (1996). The surface energy of the materials tested was found to be in the range of 5-24 J/m2. All of these results indicate that in situ weathering may degrade the shear strength characteristics of a quarried sedimentary mine waste rockfill by weakening the intrinsic shear strength parameters of the MWR. The only rigorous way to properly assess the strength degradation of the MWR materials tested involves careful assessment of the critical state, dilatancy and particle breakage characteristics.
Open Access
Deciphering the Late Jurassic paleoenvironment through Re-Os isotope geochemistry of the Agardhfjellet Formation, Svalbard
(Colorado State University. Libraries, 2017) Connors, Marisa Leigh, author; Hannah, Judith, advisor; Stein, Holly, advisor; Borch, Thomas, committee member; Hammer, Øyvind, committee member
Accurate interpretations of environmental change throughout Earth's history rely on robust correlations of sedimentary systems. The Late Jurassic has been difficult to correlate regionally and globally due to sparse radiometric ages and lack of cosmopolitan fossils. The rhenium-osmium (Re-Os) geochronometer provides an excellent platform to approach this problem. Re-Os geochemistry provides a way to directly date organic-rich shales which can then be used to: 1) place numerical ages on boreal fossil zones and Geologic Time Scale stage boundaries, 2) correlate with regional or global units, and 3) enhance the understanding of oceanic anoxic events (OAEs) and climactic shifts when paired with additional chemical and lithological data. The Agardhfjellet Formation of Svalbard, Norway has multiple intervals of organic-rich mudrocks which are ideal for Re-Os geochemistry. Presented here are Re-Os ages which confirm placement of the Agardhfjellet Formation within the Late Jurassic to Early Cretaceous (157.9 ± 2.9 Ma to 141 ± 20 Ma). We provide an age immediately above the Kimmeridgian-Oxfordian boundary, within the Amoebocera subkitchini zone, at 153.2 ± 5.0 Ma in agreement with previous work. Furthermore we present evidence that: (1) the Agardhfjellet Formation was deposited in fluctuating anoxia conditions; (2) increasing initial 187Os/188Os (0.401±0.007 to 0.577±0.054) coupled with a decrease in δ13Corg (-25.26‰ to -29.63‰) through the Late Jurassic signifies a changing climate represented by an increase continental weathering with a warming climate and/or an increase in continental freeboard.
Open Access
Effect of matrix constituents on the determination of plutonium and americium in bone
(Colorado State University. Libraries, 2019) Nguyen, Nhung Thi Nho, author; Sudowe, Ralf, advisor; Johnson, Thomas, committee member; Borch, Thomas, committee member
There are numerous methods available in the literature for separating and analyzing radionuclides of interest from an array of environmental matrices. The quality of these methods can be affected by the stable elements that are commonly found in many of these samples. The presence of such interfering constituents can result in incomplete separation of the radioisotopes of interest as well as a reduced rate of recovery. This is especially the case when complex matrices such as samples of bone and bone ash are analyzed. Plutonium and americium tend to concentrate in bone, they are therefore often referred to as bone seekers. They accumulate in actively metabolizing portions of bones of mammals including humans. It is therefore extremely important to study and evaluate the accumulation of these radionuclides in human bone by analyzing bone samples. However, calcium, which is present in high concentrations in the hydroxyapatite that constitutes the bone, as well as sodium and potassium, have the potential to strongly affect the efficacy of radiochemical separation methods. The objective of this research is to investigate the influence of the major and minor elemental constituents present in bone on the affinity of plutonium and americium for a variety of commercial extraction chromatographic resins.
Open Access
Effects of snow persistence on soil water nitrogen across an elevation gradient
(Colorado State University. Libraries, 2019) Anenberg, Alyssa Nicole, author; Kampf, Stephanie, advisor; Baron, Jill, advisor; Borch, Thomas, committee member
In the western United States, the timing and magnitude of snowmelt is an important control on soil water and nutrient availability. Warming trends can alter the timing of snowmelt, directly impacting snow cover and soil freeze-thaw cycles, as well as available water for downstream use. While prior research relating snow to soil water nitrogen has focused on areas with persistent winter snow, the snow and soil water dynamics in lower elevation areas with intermittent snowpack are not as well documented. The broad goal of this study is to understand how the duration of snow persistence affects soil moisture and soil water nitrogen concentrations. The specific objectives are to address (1) how the duration of snow persistence affects soil moisture across an elevation gradient, from areas where the snowpack ranges from shallow and intermittent to deep and persistent throughout the winter and (2) how this gradient in snowpack affects soil water nitrogen. Three study sites that span a 1500m elevation gradient were established in the Colorado Front Range to monitor snow, soil moisture, and soil water nitrogen. The highest elevation site, Michigan River, is located in the persistent snow zone; the middle elevation site, Dry Creek, is in the transitional snow zone; and the lowest elevation site, Mill Creek, lies in the intermittent snow zone. Each site was equipped with soil moisture probes at 5 and 20cm depth, soil temperature probes, snow depth poles monitored by time-lapse cameras, and ion exchange resin probes. The Mill Creek research site also contained nine snow manipulation chambers and twenty-seven tension lysimeters to sample soil water nitrogen. Snow cover persisted for longer periods of time as elevation increased and soil temperatures decreased. Lower elevation sites were consistently warmer and drier than the higher elevation site. At the highest elevation site, soil moisture increased after a large pulse of snowmelt in the late spring, while the lower elevations experienced multiple smaller pulses of soil moisture following individual snow events. In the snow manipulation chambers, plots with increased snow depth experienced increased soil moisture, however plots with decreased snow depth did not always produce the lowest soil moisture. Additionally, soil moisture in the control snow plots and in plots with increased snow depth consistently increased throughout the melt season, whereas plots with decreased snow depth briefly increased after each snowmelt event then declined to pre-event levels. NO₃– and NH₄+ were correlated with soil moisture, and large increases in soil moisture were associated with a flushing signal of NO₃–. This suggests that soil water nitrogen is regulated by the amount of soil water available, and that nitrogen can be impacted when changes in snow alter soil moisture timing and magnitude.
Open Access
Exploring nanoaggregate structures of model asphaltenes using two dimensional infrared spectroscopy
(Colorado State University. Libraries, 2015) Cyran, Jenée D., author; Krummel, Amber T., advisor; Bernstein, Elliot, committee member; Levinger, Nancy, committee member; Borch, Thomas, committee member; Kreidenweis, Sonia, committee member
Asphaltenes have been an enigma in the scientific community; studies on the molecular masses have differed by orders of magnitude and structures have been debated between island or archipelago structures. Thus, the asphaltene community defines asphaltenes by their solubility. Asphaltenes are n-heptane-insoluble and toluene-soluble. The known nanoaggregation of asphaltenes at different timescales and concentrations causes issues to determine the molecular weight and structure of asphaltene molecules. This thesis is the first step to using two dimensional infrared (2D IR) spectroscopy to study the nanoaggregate structure of model asphaltenes. 2D IR spectroscopy is a vibrational spectroscopy that is advantageous over linear IR absorption due to the ability to spread the spectral information over two axes. The 2D IR spectra give rise to structurally sensitive cross-peaks, affording the ability to probe the structure of the nanoaggregates. The model asphaltenes used in this work are violanthrone-79 and lumogen orange, a perylene derivative. These model asphaltenes consist mostly of polycyclic aromatic hydrocarbons (PAHs), similar to asphaltenes. Violanthrone-79 and lumogen orange also have carbonyl functional groups, which provide vibrational probes. The carbonyl stretching and ring breathing vibrations are used to probe the stacked structure of the nanoaggregates. A quinone series of one, two and three ring systems was used to first study the coupling between the carbonyl stretching and ring breathing vibrational modes. The quinone series provided the foundation for the larger ring systems that emulate asphaltenes. The data from studying the stacked structure of nanoaggregate model asphaltenes can be used to reveal properties of nanoaggregate asphaltenes. This work will allow for continued study of the kinetics of nanoaggregation using 2D IR waiting time experiments for dynamic information. Thus, this work demonstrates the use of 2D IR spectroscopy, which offers femtosecond time resolution, as a viable technique for studying nanoaggregation.
Open Access
Feasibility of treating chlorinated solvents stored in low permeability zones in sandy aquifers
(Colorado State University. Libraries, 2012) Bolhari, Azadeh, author; Sale, Thomas C., advisor; Bau, Domenico A., committee member; Shackelford, Charles D., committee member; Borch, Thomas, committee member
To view the abstract, please see the full text of the document.
Open Access
Investigation of the bioavailability of radiocesium in the Fukushima exclusion zone using a sequential extraction technique
(Colorado State University. Libraries, 2019) McNabb, Ian, author; Sudowe, Ralf, advisor; Johnson, Thomas, committee member; Borch, Thomas, committee member
The nuclear reactor accident at the Fukushima Daiichi power plant in March of 2011, resulted in the release of large quantities of various radionuclides into the environment. The main radionuclide of concern still remaining today is cesium-137 due to its 30-year half-life. Several areas in the vicinity of the power plant are still considered an exclusion zone owing to contamination with radiocesium, and they have not been cleared for human resettlement. While these parts are not suitable for permanent habitation, they are accessible for field work. The purpose of this research was to analyze the movement and bioavailability of radiocesium in the ecosystems contaminated by fallout from the Fukushima Daiichi nuclear reactor accident. This was achieved by analyzing soil cores collected from within the exclusion zone. The core samples were run though a 5-step sequential extraction technique, which exposes the soils stepwise to an increasingly aggressive chemical treatment. Each step targets a specific soil host phase: exchangeable, carbonate bound, Fe/Mn bound, organic, and residual. The results of this extraction yielded the following distribution of Cs-137 activity (percent of total): 0% exchangeable, 1-16% carbonate bound, 0-5% Fe/Mn bound, 1-5% organic, 44-67% residual, and 25-47% non-extracted. These results show that most of the Cs-137 is irreversibly bound to clays in the soil. However there are differences between soil sampling sites in regards to the amount of Cs-137 successfully extracted in the carbonate bound, Fe/Mn bound, and Organic fraction, which provides evidence that Cs-137 mobility and bioavailability is partly dependent on local soil mineralogy and chemistry.
Open Access
LC-MS/MS determination of various drugs of abuse and metabolites in municipal wastewater effluent samples
(Colorado State University. Libraries, 2012) McPeters, Ryley Adam, author; Dooley, Gregory, advisor; Hanneman, William, advisor; Borch, Thomas, committee member
A method was developed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) for the quantification and confirmation of 8 drugs of abuse (cocaine, codeine, MDMA, methadone, methamphetamine, morphine, nicotine, and oxycodone) and their various metabolites (acetylmorphine, cotinine, EDDP, amphetamine and benzoylecgonine) in municipal wastewater effluent samples. Samples were collected once daily and drugs were extracted from the wastewater with solid phase extraction using Waters Oasis MCX cartridges. Ultra-high-pressure liquid chromatography (UPLC) and positive electrospray ionization was used along with dynamic multiple reaction monitoring (MRM) tandem mass spectrometry for identification and quantitation. The extraction method was validated with matrix matched spiked samples at the limits of quantitation (0.5 ng/mL to 30 ng/mL) for each analyte with recoveries ranging from 70%-140%. Deuterated internal standards for each analyte were used to correct for matrix effects, ion suppression, and sample preparation errors. The validated method was applied to municipal wastewater samples collected from a point source effluent into Fossil Creek, Fort Collins, CO. Eight of thirteen drugs being measured were found on a daily basis with the maximum being 307.72 mg/min of benzoylecgonine. Samples showed various spikes in drug concentration at 7 day intervals that corresponded with weekends.
Open Access
Measurements of current-use pesticides and oxidation products using chemical ionization mass spectrometry
(Colorado State University. Libraries, 2018) Murschell, Trey Daniel, author; Farmer, Delphine K., advisor; Borch, Thomas, committee member; Kennan, Alan, committee member; Collett, Jeffrey L., committee member
Pesticides are both naturally occurring compounds found within a variety of plant species and also synthetic chemicals that are used to protect vulnerable organisms against disease carriers, harmful pests, and intrusive or undesirable vegetation. Pesticide use has large agricultural, economic, and health benefits which include increased staple food production, protection of susceptible ecosystems and wetlands, increased productivity of the labor force via disease control, and the creation of a booming chemical industry. In the decades following the discovery of DDT's anti-insecticidal properties, organochlorine pesticides (OCPs) were generously applied across the globe. OCPs appeared to have low toxicity to mammals, chiefly humans, but had adverse effects to non-target species like fish and predatory birds. OCPs persisted in soil, air, and water, and were transported atmospherically, as far as the Arctic. The prohibition of OCPs by most nations spurred research into less harmful and persistent pesticides. These current-use pesticides (CUPs) have mostly replaced OCPs and are applied world-wide. However, recent studies revealed the transport of CUPs to remote areas, including isolated Pacific islands, high alpine mountain lakes, and, again, the Arctic. Once in the atmosphere, these pesticides undergo physical and chemical processes that affect atmospheric lifetimes and transport, and potentially change the toxicity of the parent pesticides, which can have unforeseen impacts on sensitive ecosystems and organisms. With pesticide use perpetually linked to negative health questions and concerns, atmospheric monitoring, understanding of chemical processes, and improving analytical methods is necessary. Presented in this dissertation is work towards understanding pesticides and their chemistry in the atmosphere using real time mass spectrometry. A new calibration and measurement method for four CUPs, atrazine, metolachlor, permethrin, and trifluralin is shown in Chapter 2. Iodide chemical ionization mass spectrometry (CIMS) offers a real-time, sensitive measurement technique for herbicides, as well as other low volatility species. Presented in Chapter 3, ambient pesticide spray volatilization and post-application volatilization of two chlorophenoxy acid herbicides, 2,4-D and MCPA, were measured using acetate CIMS. Concentrations of 2,4-D were highest during the application period, while MCPA concentrations increased with increasing ambient temperature. Henry's Law constants and vapor pressure were found to be predictors for spray volatilization and post-application volatilization, respectively. OH radical chemistry of three aromatic herbicides are presented in Chapter 4, along with proposed oxidation mechanisms and products. Experiments were performed in an Oxidative Flow Reactor (OFR) coupled to a switching reagent ion CIMS, for a non-targeted approach for pesticide oxidation product detection. Pesticide oxidation followed typical OH oxidation mechanisms (OH abstraction with subsequent peroxide formation, OH addition to aromatic systems). MCPA and Mecoprop-p reaction rate constants with OH radical were estimated and used to calculate their atmospheric lifetimes (3 and 5 days, respectively). Newly identified products from MCPA and triclopyr oxidation are potentially harmful to the environment and to humans. Lastly, Chapter 5 covers oxidation of two nitrogen containing herbicides, trifluralin and acetochlor and mechanisms with proposed products are shown. Trifluralin photolyzed to produce NOx, and both herbicides produced isocyanic acid (HNCO) upon OH oxidation, an atmospheric toxin.
Open Access
Mechanisms of interaction between bentonite and anionic polymers in enhanced geosynthetic clay liners
(Colorado State University. Libraries, 2021) Norris, Anna, author; Scalia, Joseph, advisor; Shackelford, Charles, advisor; Borch, Thomas, committee member; Benson, Craig, committee member; Bailey, Travis, committee member
Polymer enhanced bentonites (EBs) are a potential solution to the chemical incompatibility of natural bentonite in many containment applications. Relative to conventional (natural or un-enhanced) bentonites, EBs have shown improved (lower) hydraulic conductivity to high strength waste liquids, but the mechanisms underlying these improvements are not well understood. The EB geosynthetic clay liners (EB-GCLs) evaluated in this study were produced with linear anionic polymers poly(acrylic acid) (PA) and sodium carboxymethylcellulose (CMC), as well as a covalently crosslinked PA (PAx), using multiple mixing methods (dry-sprinkle, dry mix, and wet mix) and percent polymer enhancements (5-10% by mass). The results of hydraulic conductivity tests based on permeation with concentrated inorganic solutions, viz., 500 mM NaCl and 167 mM CaCl2, indicated that specific combinations of polymer type and mixing methods in the EB-GCLs produced a low hydraulic conductivity (≤ 5.0×10-11 m/s) for a given applied hydraulic gradient and permeant solution. The use of a lower hydraulic gradient (i.e., 30 vs. 300) also was shown to have the potential to yield a lower hydraulic conductivity of EB-GCLs, suggesting that EB-GCLs are sensitive to the applied hydraulic gradient in a way that conventional GCLs containing unamended sodium bentonite (NaB) are not. The reason for this difference is that there is less likelihood of any hydrogel existing within the EB-GCL being flushed from the EB-GCL at the lower hydraulic gradient. Batch adsorption tests were conducted with 16.7 and 167 mM CaCl2, 500 mM NaCl, 12.3 mM CaSO4 and 167 mM Na2SO4 solutions to compare the adsorption behavior with respect to cation and anion species and concentration. Poly (acrylic acid) adsorption onto NaB increased with increasing Ca2+ concentration (12.5 mM CaSO4 < 16.67 mM CaCl2 < 167 mM CaCl2), resulting in increasing solid (adsorbed) phase concentration of PA. Sodium bentonite tested with NaCl exhibited limited adsorption capacity for PA. Total carbon (TC) analysis was confirmed to be an accurate technique for measuring polymer loading of both as-prepared and hydrated/permeated EB-GCLs. A multiple lines of evidence approach was used to determine the mechanisms controlling the hydraulic conductivity of EB-GCLs. The results of the hydraulic conductivity testing were paired with measurements of polymer retention and qualitative measurements of hydrogel formation to understand the variables controlling polymer migration within and through the EB-GCL and the relationship between polymer retention and hydraulic conductivity. The results indicated that the low hydraulic conductivity of EB-GCLs (≤ 5.0×10-11 m/s) is controlled by a combination of pore blocking (mechanical entrapment) and adsorption of polymer hydrogel. The reduction in long-term hydraulic conductivity of EB-GCLs relative to unamended GCLs in aggressive inorganic solutions was determined to be the result of several factors, including (1) the formation of hydrogel, (2) the clogging of the largest (most conductive) pores by the hydrogel, (3) the balancing of seepage forces that are sufficient to mobilize the hydrogel into the pores but not sufficiently high to untangle and mobilize the hydrogel due to shear thinning or dislodging by inertial forces, and (4) the kinetics of hydrogel formation and adsorption of polymer to the surface of bentonite. This study illuminates the myriad of interconnected factors that can and must be optimized for EB-GCLs to provide effective long-term containment of aggressive inorganic wastes.
Open Access
Membrane behavior, diffusion, and compatibility of a polymerized bentonite for containment barrier applications
(Colorado State University. Libraries, 2012) Bohnhoff, Gretchen L., author; Shackelford, Charles D., advisor; Benson, Craig H., committee member; Borch, Thomas, committee member; Sale, Thomas C., committee member
Conventional (untreated or unmodified) bentonites are commonly used in hydraulic containment barriers to contain liquid flow and contaminant transport, because of the ability of bentonite to swell and achieve low hydraulic conductivity to water, substantial membrane behavior, and low solute diffusion coefficients. However, conventional bentonites also have been shown to be affected adversely by environmental conditions that promote multivalent-for-monovalent cation exchange. In this study, the membrane behavior and diffusive properties of a polyacrylic acid modified bentonite referred to as a bentonite polymer nanocomposite, or BPN, were determined through the simultaneous measurement of membrane efficiency coefficients, ω, and solute diffusion coefficients, D*, during combined multi-stage membrane and diffusion tests using either potassium chloride (KCl) with concentrations ranging from 4.7 mM to 54 mM or calcium chloride (CaCl2) with concentrations ranging from 5 mM to 20 mM. The BPN exhibited substantial membrane behavior when exposed to KCl with values of ω that were higher than those previously reported for conventional (unmodified) bentonite under similar testing conditions. For example, the ω value measured in this study for a BPN specimen contained within a rigid-wall cell and based on circulation of 20 mM KCl was 0.43, whereas that previously reported for a GCL specimen containing a conventional bentonite under similar testing conditions except at a lower porosity (0.74 vs. 0.92) was only 0.30. Also, in contrast to previously reported results for conventional bentonite, the membrane behavior of the BPN was sustained when exposed to 5 mM CaCl2, and values of ω for the BPN were higher than those previously reported for conventional and other modified bentonites. For example, the value of ω for the BPN tested in a rigid-wall cell with 5 mM CaCl2 was 0.95, whereas the ω values for an anionic polymer modified bentonite, known as Hyper clay, and a GCL were 0.13 and 0, respectively. However, exposure of specimens of the BPN to 10 mM CaCl2 for a test conducted in a rigid-wall cell and 20 mM CaCl2 for a test conducted in a flexible-wall cell did ultimately result in complete destruction of the membrane behavior. The destruction of the membrane behavior of the specimen in the rigid-wall test was attributed to short-circuiting along the side-walls of the rigid cell after shrinkage of the BPN specimen, whereas the destruction of the membrane behavior of the specimen in the flexible-wall test correlated with the time to reach steady-state diffusion of calcium (Ca2+). Similar to a previous study involving a conventional bentonite, the diffusive properties of the BPN also were shown to correlate well with the membrane behavior of the BPN, such that that the diffusive solute mass flux decreased as the membrane efficiency of the BPN increased. However, in contrast to previous test results, the steady-state values of D* for K+ and Ca2+ were not only not equal to but also lower than the D* value for Cl- at steady state, although the differences between the D* for K+ or Ca2+ versus that for Cl- diminished with increasing source concentration of KCl or CaCl2, respectively. This inequality between salt cation and salt anion D* values at steady state was attributed to the complicating existence of significant excess Na+ that was initially present within the specimen of BPN prior to testing and contributed to satisfying the requirement for electroneutrality, a contribution that diminished with time as the Na+ diffused out of the specimen. Finally, the use of BPN in soil-bentonite (SB) backfills of vertical cutoff walls was investigated. The hydraulic conductivity, k, to tap water, the consolidation behavior, and the chemical compatibility (Δk) based on permeation with CaCl2 solutions of SB backfills amended with BPN were evaluated and compared with those for a backfill comprised of a conventional bentonite. Although the backfills containing BPN were more sensitive to stress conditions than the backfill containing conventional bentonite, the overall hydraulic performance of a backfill containing 5 % dry BPN was better than that of the backfill containing 5 % dry conventional bentonite by approximately two orders of magnitude in terms of k. Overall, the BPN exhibited improved membrane and diffusion properties relative to conventional and other modified bentonites previously tested under similar conditions. However, the improved membrane behavior of the BPN was ultimately destroyed upon exposure to 10 mM CaCl2 in a rigid-wall cell and 20 mM CaCl2 in a flexible-wall cell. Also, despite an overall lower k of the sand-BPN backfills relative to a backfill comprised of the same sand but a conventional bentonite upon permeation with a 50 mM CaCl2 solution, the chemical resistance of the sand-BPN backfills in terms of changes in k was not any better than that for the sand-conventional bentonite backfill. Thus, the beneficial behavior of the BPN was not unlimited nor without issues, such that any perceived benefit of polymerized bentonites must first be properly characterized on a case-by-case basis prior to use.
Open Access
Metagenomic insights into microbial colonization & persistence in subsurface fractured shales
(Colorado State University. Libraries, 2023) Amundson, Kaela K., author; Wilkins, Michael J., advisor; Wrighton, Kelly C., committee member; Borch, Thomas, committee member; Ross, Matthew, committee member
Microorganisms are pervasive yet important components of hydraulically fractured shale systems. Subsurface shales harbor oil & gas and require unconventional techniques, such as hydraulic fracturing, to access these trapped hydrocarbons. Shale microbiomes are of crucial importance as they can directly impact the recovery of oil & gas and associated infrastructure. The overarching theme of this dissertation was to characterize the metabolisms and key traits that underpin the colonization and persistence of fractured shale microbiomes using a multi-omic approach to better understand the microbial impact on this important ecosystem. In Chapter 1, I first discuss the importance of subsurface shales as an important energy reserve, summarize what is known about microorganisms in these ecosystems, and highlight the strength of using a metagenomic approach to studying shale microbiomes. Subsurface shales are heterogeneous – varying in their mineral content, temperature, and other physiochemical conditions. The microbial communities that persist can have substantial impact on the fractured shale ecosystem and contribute to common challenges in hydrocarbon recovery such as corrosion, souring, and bioclogging. The literature review presented here highlights the need to study the functional potential of shale microbiomes as most studies have mostly focused solely on taxonomic composition of persisting microbial communities, and a vast majority of these studies have focused on samples from wells in the Appalachian Basin. However, functional potential of shale microbiomes across a variety of physiochemical conditions must be considered in order to gain an understanding of the role of microorganisms and what possible influences they may have on hydraulically fractured shales systems. Here, I highlight the need (1) to study the whole community at a functional scale and (2) apply a metagenomic approach to a variety of less characterized shale basins to gain a holistic understanding of shale microbiomes and the effects they may have on the broader ecosystem. In Chapter 2, I apply this metagenomic approach to study the persisting shale microbiomes of three fractured shale wells in the Anadarko Basin – a western shale basin characterized by elevated temperature and salinity. No studies using metagenomics had been applied to shale basins in the western United States prior to this research. We sampled five wells in the Anadarko basin over a timeseries >500 days and preformed NMR metabolomics and metagenomic sequencing to uncover the dominant metabolisms, community composition, and other functional traits of the Anadarko shale microbiome. This system was dominated by a fermentative microbial community and a less-abundant sub-community of inferred sulfate reducing microorganisms. Using paired NMR metabolomics and metagenomics, I demonstrated how many fermentative microorganisms have the potential to degrade common complex polymers, such as guar gum, and have potential to produce organic acids that may serve as electron donors for sulfate and thiosulfate reducing microorganisms. Thus, in this study I provided a framework for how carbon may move through the closed fractured shale ecosystem to sustain the microbial community. Finally, I investigated viral presence and diversity across all thirty-six metagenomes and found that inputs were large sources of viral diversity, but that only an extremely small proportion of viruses recovered from produced fluids were genetically similar to viruses previously reported from fractured shales. I observed that a majority of the dominant and persisting genomes encoded a CRISPR-Cas viral defense system, likely in response to the viral community. This highlights viral defense as another key trait for persisting microorganisms, as viruses are the only predators to bacteria and archaea in fractured shale ecosystems. Overall, this study expanded our knowledge of sulfate and thiosulfate reducing microorganisms in fractured shales, demonstrated the potential for common chemical inputs such as guar gum to be utilized by shale microbiomes, and highlighted how other key traits, such as CRISPR-Cas viral defense systems, may be a crucial trait for persisting shale microbiomes. Building on results from viral analyses in Chapter 2, in Chapter 3 I next sought to investigate the temporal dynamics between hosts and viruses to better understand the role of microbial defense against viruses in fractured shale ecosystems. To do this, I sampled six shale wells in the Denver-Julesburg Basin for >800 days, performed metagenomic sequencing, and identified host (bacterial & archaeal) and viral genomes from this data. I observed evidence of ongoing host defense to viral predation at both the community and genome-level through quantifying spacers from CRISPR arrays in metagenomic reads and MAGs. Through these analyses leveraging timeseries sampling and age differences between the shale wells, I provided evidence that suggested migration toward CRISPR arrays that may be more efficient at protecting the microbial host against a wider suite of viruses. Finally, I observed a temporal increase in host-viral co-existence in the closed, fractured shale ecosystem – suggesting the CRISPR defense does not entirely protect against viral predation. Chapter 4 ultimately leverages the approaches, insights, and data gained from Chapters 2 and 3 to study shale microbiomes at a cross-basin, geographic scale. Here, I collected samples from many collaborators who have previously worked in shale systems, performed metagenomic sequencing, and processed all samples in a standardized pipeline to build a comprehensive genomic shale database. In total, this database contains 978 unique MAGs and >7 million unique genes recovered from 209 metagenomic samples obtained from 36 fractured shale wells spanning eleven shale basins from North America, China, and the United Kingdom. In this chapter I analyze the functional potential of shale microbiomes at a genome-resolved level to better understand the geographic distribution of microbial metabolisms and other key traits that likely contribute to colonization and persistence of microorganisms. Here I also leveraged bioinformatic tools to build a custom annotation summary toolkit to process and analyze the large amount of sequencing data for traits of interest. The complete absence of a taxonomic core microbiome across shale basins illustrated in this chapter underscores the necessity of a genome-resolved and functional approach to studying shale microbiomes. Results from analyzing shale microbiomes at this scale could ultimately help to inform microbial management of fractured shale systems. The final chapter of this dissertation (Chapter 5) summarizes the key findings of my research into fractured shale microbiomes, and the mechanisms that may promote microbial colonization, persistence, and survival in these relatively harsh and economically relevant ecosystems. In this chapter I conclude this work by discussing future directions and lingering knowledge gaps for studying fractured shale microbiomes, as well as implications of these findings for other subsurface engineered ecosystems. Ultimately, this body of work contributes a substantial amount of new and informative insights into the functional potentials of persisting shale microbiomes across broad geographic scales.
Embargo
Multiphoton spatial frequency modulated imaging
(Colorado State University. Libraries, 2023) Wernsing, Keith, author; Bartels, Randy, advisor; Squier, Jeff, committee member; Wilson, Jesse, committee member; Borch, Thomas, committee member
Far-field optical microscopy has seen significant development in the last 20 years in its ability to resolve specimen information beyond the diffraction limit. However, nearly all of these super-resolution techniques are predicated on the use of fluorescence as the contrast mechanism in the sample. While the variety of fluorophores available for labeling a sample are a widely-utilized tool, in many instances non-fluorescent contrast mechanisms also provide valuable information. Multiphoton microscopy is one route to probing non-fluorescent contrast mechanisms. It has the benefit of sampling multiple contrast mechanisms at once, including second- and third-harmonic generation and Raman vibrational characteristics, as well as autofluorescence and labeled fluorescence. However, development of super-resolving techniques for coherent scattering processes like harmonic generation or coherent Raman excitation has lagged behind that of incoherent scattering processes like fluorescence. In this work I present the first technique to simultaneously enhance resolution in both real-state (e.g., fluorescence) and virtual-state (e.g. harmonic generation) molecular excitation mechanisms, known as multiphoton spatial-frequency modulated imaging (MP-SPIFI). Standard SPIFI works by projecting spatial cosine patterns onto the sample and gathering object spatial frequency information. Multiphoton SPIFI generates harmonics of these cosine patterns and therein gathers information beyond the frequency passband of the microscope. We demonstrate our initial results with two-photon fluorescence and SHG. An extensive model is built describing the super-resolved image formation process. We then present a method for extending the native, 1D resolution enhancement into two dimensions for an isotropic enhancement. Finally, we present development of two femtosecond, amplified pulsed laser sources tailored to boost SNR in multiphoton processes, through parabolic pulse amplification, and chirped pulse fiber broadening, in order to deliver the high average power & high peak power required by MP-SPIFI for driving nonlinear processes across a line-focus geometry.