Browsing by Author "von Fischer, Joseph, committee member"
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Item Open Access A locality-aware scientific workflow engine for fast-evolving spatiotemporal sensor data(Colorado State University. Libraries, 2017) Kachikaran Arulswamy, Johnson Charles, author; Pallickara, Sangmi Lee, advisor; Pallickara, Shrideep, committee member; von Fischer, Joseph, committee memberDiscerning knowledge from voluminous data involves a series of data manipulation steps. Scientists typically compose and execute workflows for these steps using scientific workflow management systems (SWfMSs). SWfMSs have been developed for several research communities including but not limited to bioinformatics, biology, astronomy, computational science, and physics. Parallel execution of workflows has been widely employed in SWfMSs by exploiting the storage and computing resources of grid and cloud services. However, none of these systems have been tailored for the needs of spatiotemporal analytics on real-time sensor data with high arrival rates. This thesis demonstrates the development and evaluation of a target-oriented workflow model that enables a user to specify dependencies among the workflow components, including data availability. The underlying spatiotemporal data dispersion and indexing scheme provides fast data search and retrieval to plan and execute computations comprising the workflow. This work includes a scheduling algorithm that targets minimizing data movement across machines while ensuring fair and efficient resource allocation among multiple users. The study includes empirical evaluations performed on the Google cloud.Item Open Access Assessing grassland sensitivity to global change(Colorado State University. Libraries, 2015) Wilcox, Kevin Rory, author; Knapp, Alan, advisor; Kelly, Eugene, committee member; Smith, Melinda, committee member; von Fischer, Joseph, committee memberIntensification of the global hydrological cycle with atmospheric warming is expected to substantially alter precipitation regimes, and due to the tight functional relationship between precipitation and net primary productivity (NPP), these changes in climate will have large impacts on multiple NPP-linked ecosystem services such as forage production and carbon storage. At regional scales, the sensitivity of aboveground NPP (ANPP) to variation in annual precipitation increases with decreasing site-level ANPP, with this variation in sensitivity tied to turnover of plant communities over the precipitation gradient. Site-level ANPP responses are not expected to conform to regional patterns until plant communities shift, resulting in differential short- vs. long-term ANPP responses to chronically altered precipitation amounts. Although studies in grasslands have shown site-level sensitivities of ANPP to altered precipitation regimes, we lack equivalent knowledge for responses of belowground net primary productivity (BNPP) and total NPP. This will be especially important as simultaneous global change factors occur (e.g., increased fire frequency) and interact with climate change drivers to determine how the sensitivity of NPP will influence ecosystem services. My dissertation examines how plant community structure controls ecosystem sensitivity to altered precipitation amounts and patterns, and how this impacts various ecosystem services by addressing the following questions: (1) How do plant species and functional compositions control ecosystem sensitivity to altered precipitation regimes? (2) Does belowground sensitivity mirror that aboveground? And (3) What are the consequences of differential ANPP and BNPP sensitivity on biogeochemical processes in the presence of annual fire regimes? In my second chapter, I show how functional types (C₃ versus C₄ graminoids) can alter regional patterns of sensitivity to annual precipitation through differences in the timing of growth. I also show that ANPP and BNPP sensitivities can differ, but that it likely depends on vegetation and/or other attributes of an ecosystem. In chapter three, I focus on how shifts in plant species abundances, even within the same functional type, can alter sensitivity to extreme, chronic increases in precipitation. The shift in sensitivity was, again, not in agreement with regional patterns of sensitivity. Lastly, chapter four shows that the differential sensitivity of ANPP and BNPP to long term increases in precipitation can destabilize the carbon and nitrogen sequestration ability of ecosystems in the presence of extreme disturbance regimes also likely to occur in the future. Overall, my dissertation calls into question the predictive ability of regional models of NPP sensitivity under chronic shifts in precipitation amount, at least on short to moderate time scales, and I suggest that incorporation of plant community controls on above- and belowground sensitivity will be better predictors of ecosystem service responses under novel environmental conditions likely to occur in the future.Item Open Access Climate controls on ecosystem-atmosphere carbon exchange and hydrological dynamics in Rocky Mountain fens(Colorado State University. Libraries, 2015) Millar, David, author; Cooper, David, advisor; Dwire, Kate, committee member; Hubbard, Robert, committee member; Ronayne, Michael, committee member; von Fischer, Joseph, committee memberGroundwater fed peatlands known as fens are among the most important ecosystems in the Rocky Mountains of North America. These wetlands have sequestered atmospheric carbon dioxide for several millennia, provide important habitat for wildlife, and serve as refugia for regionally-rare plant species typically found in boreal regions. Perennially high water tables are critical for ecosystem functioning in fens, and provide conditions that support the development and persistence of organic soils. It is unclear how Rocky Mountain fens will respond to a changing climate, and those found at lower elevations may be particularly susceptible, where changes in hydrological cycles that control water tables are likely to be greatest. Further, it is unclear how regionally variable monsoon rainfall influences water tables and carbon dynamics, late in the growing season. In this dissertation I addressed the following questions: 1) How does ecosystem-atmosphere CO₂ exchange vary with elevation and monsoon influence in Rocky Mountain fens? 2) How do snowmelt dynamics at high and low elevations and varying monsoon influence affect groundwater dynamics in fens of the Rocky Mountains? 3) How will mountain fen hydrological dynamics potentially change under a future climate, and what will be the subsequent impact on ecosystem-atmosphere C exchange? My results show that net ecosystem production was higher for fens located at high elevations compared to those found at lower elevations. This was reflected in the negative correlation of growing season net ecosystem production with air temperature, and positive correlation with water table position, as the high elevation sites had the lowest air temperatures and highest water tables. Study fens in the San Juan Mountains of southwest Colorado received almost twice as much late summer precipitation than those in the Medicine Bow Mountains of Wyoming, causing more frequent water table rises. However, differences in net ecosystem production associated directly with varying monsoon influence were less discernable. Peak snow water equivalent was lower for fens located at low elevations, and the snow-free season occurred approximately one month earlier at these sites compared to high elevation fens. The earlier onset of snow-free conditions led to steady declines in water table position early in the growing season at the low elevation fens, driven primarily by evapotranspiration. Under two future climate modeling scenarios at a low elevation fen, warmer air temperatures increased the proportions of winter precipitation that fell as rain, and peak snow water equivalent was reduced along with the number of days which snowpack persisted. Results from a coupled carbon exchange and hydrological model showed these changes in hydrological processes led to lower water tables that persisted through the growing season, and subsequently impacted ecosystem-atmosphere C exchange. Under the future climate scenarios, the overall global warming potential of gaseous C emissions increased as a result of increased ecosystem respiration, despite decreases in methane emissions. Further, the future climate scenarios suggest that the sustainability of low-elevation fens may be in jeopardy, as losses of C exceed inputs.Item Open Access Deciphering the biological determinants on methane cycling from Gulf Coast wetlands(Colorado State University. Libraries, 2024) de Melo Ferreira, Djennyfer Karolaine, author; Wrighton, Kelly C., advisor; von Fischer, Joseph, committee member; Melzer, Suellen, committee member; Wilkins, Michael, committee memberIn Chapter 1, I introduce the importance of coastal wetlands for ecosystem services, including carbon storage, physical barrier for natural disasters, and habitat for diverse fauna and flora. Sea level rise is one of the main environmental risks affecting coastal wetlands, because of their geographic position. The effects of saltwater intrusion into freshwater wetlands can change established environmental conditions and vegetation coverage, which affects the functionality of various ecosystem functions they provide. These changes can also affect the methane emissions from coastal wetlands, which are major sources of this potent greenhouse gas. In this chapter, I evaluate the current knowledge of microbial methane production and consumption, including aspects of the ecophysiological adaptation to salinity, and the changes in the microbial ecological interactions modulated by increased salinity from marine water intrusion. In Chapter 2, I conducted a study to characterize the microbial communities and geochemistry of soil and water compartments in three coastal wetlands following a salinity gradient from Barataria Bay, Louisiana. To investigate the methane cycling microbial communities and their distribution on a freshwater flotant, Jean Lafitte swamp, and saltwater marsh wetlands, I collected soil and water samples under different vegetation coverage from each wetland. I analyzed the 16S rRNA gene sequencing and paired this data within situ methane fluxes and porewater concentrations. I also analyzed the geochemistry of the soil samples including profiling the anions, cations, pH, and redox conditions of soil and water samples across wetlands. The analysis showed that the diversity of methane cycling microbial communities decreased with increased salinity. Although the distribution and relative abundance of methanogen functional types was not impacted, with hydrogenotrophic methanogens being the most abundant across all wetlands. Looking at the methanotroph abundance and taxonomy in soil and water samples, I observed that swamp and saltwater wetlands share more methanotroph members in the water column, while the soils had more site-specific similarities. My research findings contribute to the understanding of methane cycling microbial tolerance to saltwater and may be used in future works to create more robust methane prediction models. In Chapter 3, I summarize the key aspects of microbial methane cycling in coastal wetlands and offer future directions for pairing geochemical and microbial data, including using an 'omics' approach and expanding investigation to more wetlands. We discuss the valuable findings these tools can give, contributing to a more accurate prediction of the metabolisms behind the ecophysiology and ecology of methane fluxes in coastal wetlands, and how targeting specific genes and metabolism can better help climate model efforts. In the Appendix sections, I give an expanded characterization of the wetlands site description, hydrology, vegetation and topological heterogeneity. I observed that, although relatively close in geographical position, each wetland has a different salinity range, vegetation type and microtopography that can influence the distribution of microorganisms in the soil and water. Here, we also analyzed the redox potential, dissolved oxygen, pH and geochemical compounds (bromide, nitrate, ammonium, acetate, sodium, potassium, magnesium, sulfate, chloride, and iron (II)) of these wetlands. We found no correlation between geochemistry with depth, but noticed higher salt contents in the saltwater marshes, and shared geochemistry between the swamp and freshwater flotant wetlands, as expected. Conclusively, this thesis contributes to the understanding of microbial communities to natural fluxes of methane in coastal wetlands and their interaction with the geochemistry of these ecosystems.Item Open Access Ecological effects of selenium hyperaccumulation on plant community structure and potential implications for selenium cycling(Colorado State University. Libraries, 2019) Reynolds, Ray Jason Bixler, author; Pilon-Smits, Elizabeth, advisor; Paschke, Mark, committee member; von Fischer, Joseph, committee member; Steingraeber, David, committee memberTo view the abstract, please see the full text of the document.Item Open Access Evaluating soil productivity and climate change benefits of woody biochar soil amendments for the US Interior West(Colorado State University. Libraries, 2018) Ramlow, Matthew Alan, author; Cotrufo, M. Francesca, advisor; Ogle, Stephen, committee member; Rhoades, Charles C., committee member; von Fischer, Joseph, committee memberManaging our lands to provide for today and the future requires sustainable land management practices that enhance productivity while reducing climate impacts. Proponents claim biochar soil amendments offer a comprehensive solution to enhance soil capacity to deliver water and nutrients to plants while decreasing climate impacts through reduced nitrous oxide (N2O) emissions from fertilizer use and carbon (C) sequestration. This dissertation evaluates such claims for woody biochar applications within the US Interior West; to enhance crop production and reduce N2O emissions in deficit irrigation agricultural systems, and to support forest road restoration efforts. It also employs laboratory incubations and soil biogeochemical modeling to predict and to better understand the controls on biochar's greenhouse gas mitigation potential. The field studies demonstrate that this woody biochar improved soil moisture content but its enhanced capacity to retain water did not alleviate plant water stress when water inputs were low. Similarly, in forest soils, this woody biochar amendment improved plant available N but at levels that did not impact productivity. In lab incubations this woody biochar reduced N2O emissions. While this reduction could not be explained by bulk soil mineral N transformations, the soil moisture regime did affect biochar's ability to reduce N2O emissions. Despite the observed biochar N2O emission reductions in incubated soils, under field conditions biochar effects on N2O emissions were inconclusive. When evaluating biochar's C sequestration potential, soil biogeochemical modeling revealed that 59 percent of the biochar C applied will be sequestered in soils after 100 years. Losses from biochar fragmentation and leaching may constitute a considerable proportion of the C losses. Of the applications considered, C sequestration remains the most promising use for biochar soil amendments within the US Interior West.Item Open Access From litter decomposition to soil organic matter formation: using stable isotopes to determine the fate of carbon and nitrogen(Colorado State University. Libraries, 2014) Horton, Andrew James, author; Cotrufo, M. Francesca, advisor; von Fischer, Joseph, committee member; Paschke, Mark, committee memberLitter decomposition releases the energy and nutrients fixed during photosynthesis into the atmosphere and soil. In the soil, carbon and nitrogen from the litter can be stabilized in soil organic matter pools, which globally represent large pools of both carbon (C) and nitrogen (N). Soil organic matter pools are heterogeneous, the product of different stabilization processes and will stabilize C and N for periods of time ranging from years to millennia. A thorough mechanistic understanding of the fate of above-ground litter C and N is essential to understand how climate change could affect both carbon sequestration and soil health. This research studied the fate of litter derived organic matter. Isotopically labeled litter was used in a field incubation to trace litter derived C and N into different SOM pools and soil depths over the course of 3 years. Additionally, naphthalene was used to suppress microarthropods to determine the impact of mesofauna on the fate of litter derived N. In the laboratory, soil from the field experiment was incubated for 150 to determine how different SOM pools contributed to respiration and leaching. Microarthropods do not increase overall N mineralization rates, but do influence the fate of litter derived N. When present, microarthropods increased the amount of litter derived N in the light fractions, suggesting that microarthropods increase litter fragmentation. Surprisingly, litter derived organic matter does not contribute to respiration and leaching equally, suggesting that leaching and respiration are not directly related. Litter derived OM behaves differently than older OM present in the soil, with the newer litter derived C and N being more readily lost from SOM pools. This result supports the onion layering model suggested by Sollins (Sollins et al. 2006). In order to create more accurate models, microarthropods and the onion layering model should be included in future C and N dynamic studies.Item Open Access Grassland responses to seasonal shifts in water availability(Colorado State University. Libraries, 2023) Hajek, Olivia Louise, author; Knapp, Alan K., advisor; von Fischer, Joseph, committee member; Cusack, Daniela, committee member; Schumacher, Russ, committee memberClimate change is altering seasonal dynamics across a wide range of ecosystems with consequences that include shifts in phenology, timing of nutrient availability, and changes in plant community composition. Current research has primarily focused on temperature as the key driver for these shifts because of the strong directional trend with climate warming, however, alterations in the availability of water across seasons is an unappreciated aspect of climate change that can significantly influence ecosystem functioning. While changes in the seasonal availability of water are expected to be globally pervasive, grasslands may be particularly vulnerable because these ecosystems are often water-limited and have species with distinct seasons of growth. Therefore, my dissertation examined how seasonal patterns of water availability may shift with climate change in the grasslands of the US Great Plains and the ecological consequences of these shifts. I first explored several mechanisms by which climate change is altering the seasonal water balance, using the Great Plains as a case study. Building on that, I then designed two field experiments in semi-arid grasslands that altered seasonal patterns of water availability to understand how these shifts affected ecosystem function and structure (primarily C3 vs C4 grasses). Overall, the results from both field experiments suggest that shifts in the seasonality of water availability with climate change will alter carbon cycling dynamics, shift seasonal patterns of canopy albedo, and differentially impact C3 vs. C4 species in the semi-arid grasslands of the US Great Plains. Thus, my research confirms the importance of this aspect of climate change and provides evidence that seasonal shifts in water availability can alter ecosystem processes and drive compositional changes. Since grasslands provide many economically and ecologically valuable services, understanding how climate change will impact these systems is critical for land managers and policymakers to make informed decisions.Item Open Access Interplay between selenium hyperaccumulator plants and their microbiome(Colorado State University. Libraries, 2016) Cochran, Alyssa T., author; Pilon-Smits, Elizabeth, advisor; Leach, Jan, committee member; von Fischer, Joseph, committee member; Stromberger, Mary, committee memberThe plant microbiome includes all microorganisms that occur on the plant root (rhizosphere) and shoot (phyllosphere) or inside plants (endosphere). Many of these microbes benefit their host by promoting growth, helping acquire nutrients or by alleviating biotic or abiotic stress. In addition to its intellectual merit, better knowledge of plant-microbiome interactions is important for agriculture and medicine. Microbiome studies are gaining popularity in multiple research areas, particularly due to advances in next generation sequencing, which has advantages over cultivable methods by revealing the complete microbial community. Still relatively little is known about the microbiomes of plants with extreme properties, including plants that hyperaccumulate (HA) toxic elements such as selenium (Se). Selenium HAs may contain up to 1.5% of their dry weight in Se, which can cause toxicity to herbivores and pathogens as well as neighboring plants. Many advances are yet to be made with regard to the interaction of Se and the plant microbiome: does plant Se affect microbial diversity and composition, and do plant-associated microbes affect plant Se accumulation? The first chapter of this thesis will discuss aspects of the plant microbiome as well as the discoveries to date with regard to plant-associated microbes and Se, mostly explored through culture-dependent methods. Selenium HA appear to harbor equally diverse endophytic microbial communities as non-hyperaccumulators. Thus, plant Se does not impair associations with microbes. A variety of microbes have been isolated from plants or soil in seleniferous areas, including some bacteria and fungi with extreme Se tolerance. Inoculation of plants with individual strains or consortia of microbes was able to promote plant growth, Se uptake and/or Se volatilization. Thus, microbes may facilitate their host’s fitness in seleniferous areas. Exploiting and optimizing plant-microbe associations may facilitate applications like phytoremediation (bio-based environmental cleanup) or biofortification (nutritionally fortified crops). Plant-derived microbial isolates may also be applicable without their plant host, e.g. for cleanup of wastewaters. Culture-dependent studies have dominated the plant-microbe interactions research in regards to hyperaccumulators thus far, painting an elaborate but incomplete picture. In the second chapter of this thesis, we use a mix of culture based and culture-independent methods to investigate the bacterial rhizobiome of selenium Se HAs. Using 16S rRNA Illumina sequencing, we show that the rhizobiomes of Se HAs are significantly different from non-accumulators from the same naturally seleniferous site, with a higher occurrence of Pedobacter and Deviosa surrounding HAs. In addition, we found that HAs harbor a higher species richness when compared to non-accumulators on the same seleniferous site. Thus, hyperaccumulation does not appear to negatively affect rhizobiome diversity, and may select for certain bacterial taxa in the rhizobiome. The bacterial isolates, independent from site or host plant species were in general extremely resistant to toxic concentrations of Se (up to 200mM selenate or selenite) and could reduce selenite to elemental Se. Thus, microbial Se resistance may be widespread and not be under selection by Se HAs. In future studies it will be interesting to further investigate the mechanisms by which Se HA species similarly shape their rhizobiome; this is perhaps due to Se-related root exudates. Future studies may also focus on elucidating the effects of microbes on plant Se accumulation and tolerance.Item Open Access Long duration measurements of pneumatic controller emissions on onshore natural gas gathering stations(Colorado State University. Libraries, 2019) Luck, Benjamin Kendell, author; Quinn, Jason, advisor; Zimmerle, Daniel, advisor; Marchese, Anthony, committee member; von Fischer, Joseph, committee memberOver the last 15 years, advances in hydraulic fracturing have led to a boom of natural gas production the United States and abroad. The combustion of natural gas produces less carbon dioxide (CO2) than the combustion of other fossil fuels per unit of energy released, making it an attractive option for reducing emissions from power generation and transportation industries. Uncombusted methane (CH4) has a global warming potential (GWP) of 86 times that of CO2 on 20 year time scales and a GWP of global warming potential 32 times greater than CO2 on a 100 year time scale. The increase in supply chain throughput has led to concerns regarding the greenhouse gas contributions of CH4 from accidental or operational leaks from natural gas infrastructure. Automated, pneumatic actuated valves are used to control process variables on stations in all sectors of the natural gas industry. Pneumatic valve controllers (PCs) vent natural gas to the atmosphere during their normal operation and are a significant source of fugitive emissions from the natural gas supply chain. This paper outlines the work that was done to improve the characterization of emissions from PCs using long duration measurements. This work was performed as part of the Department of Energy funded Gathering Emission Factor (GEF) study. A thermal mass flow meter based emission measurement system was developed to perform direct measurements of pneumatic controller emissions over multiday periods. This measurement system was developed based on methods used in previous studies, with design modifications made to meet site safety regulations, power supply constraints and measurement duration targets. Emissions were measured from 72 PCs at 16 gathering compressor stations between June, 2017 and May, 2018. The average emission rate of 72 PCs was 10.86 scfh [+4.31/-3.60], which is 91.2% of the EPA's current emission factor for PCs on gathering compressor stations. The mean measurement duration of these 72 samples was 76.8 hours. Due to potential biases associated with flow meter errors, updates to EPA emission factors based on these data are not proposed. However, because all previous studies to quantify PC emissions used short sampling times (typically ≤15 minutes) the long duration measurements provided insight into previously unobserved PC emissions behavior. A panel of industry experts assessed the emissions recordings and found that 30 PCs (42% of measured devices) had emissions patterns or rates that were inconsistent with their design. 73% of emissions measured during this study were attributed to these 30 PCs that were malfunctioning from an emissions perspective. It was also found that PC emission rates are more variable over time than previously thought. Due to this high temporal variability, the short duration observations currently used by leak detection programs to identify malfunctioning equipment have a low probability of providing accurate characterizations of PC emissions. Many natural gas companies are investigating ways to improve the efficiency of their operations and reduce rates of natural gas leakage in their systems. The data presented in this paper improves the characterization of emissions behavior from a significant emission source in the production, processing and transmission sectors of the natural gas supply chain and has implications for organizations with an interest in reducing emissions from PCs.Item Open Access Microbial responses to plant functional types and historical resources additions in the shortgrass steppe(Colorado State University. Libraries, 2009) Bontti, Eliana E., author; Burke, Ingrid C., advisor; Lauenroth, William K., committee member; Stromberger, Mary, committee member; von Fischer, Joseph, committee memberNutrient addition in rangelands is an appealing way to increase plant biomass and quality, but little is known about the long-term effects of these additions on soil microbial activity and nutrient cycling. In addition, microbial activity may be affected by plant functional types (PFT) through influence on the levels of inorganic nitrogen (N) and labile carbon in the rhizosphere. This is particularly important in the shortgrass steppe (SGS), where plants with the C3 or C4 photosynthetic pathway differ in phenology, which affects the timing of maximum N uptake and root exudate production. To understand the effect of PFT (C3 and C4 species) and historical nutrient additions on temporal patterns of N partitioning between microbes and plants, I estimated seasonal trends in plant biomass and N content, microbial N) and soil N availability. In addition, I evaluated monthly emissions of the greenhouse gases C02 and N20, discriminating between fungal and bacterial production through incubations of soils under the influence of different PFTs and historical N additions. Last, I tested the effect of biosolid application on C02 and N20 emissions from fungi and bacteria in SGS soils. Seasonal trends in plant and microbial N concentration indicated that the two were synchronous during most of the plant growing season and both strongly influenced by precipitation. Plant functional type did not explain differences in microbial N and available soil N, but historical N amendments increased plant N content, decreased microbial N, and had no detectable effect on soil available N. Fungi showed higher emissions of C02 and N20 compared to bacteria in the SGS, whereas there was no difference in emissions between the two groups in the historically N amended plots. There were no effects of PFT on bacterial and fungal emissions of C02 and N20 but high historical N fertilization resulted in increased C02 and N20 emissions from bacteria. Fungal emissions of C02 were higher than bacterial emissions in SGS sites compared to biosolid amended sites, but I detected no differences between microbial groups in N20 emissions. C02 and N20 emissions were higher in biosolid treated sites than non-treated SGS sites even 20 years after amendments ceased. Biosolid treated sites dominated by forbs showed higher C02 emissions compared to sites dominated by C3 grasses, while C3-dominated sites with high available inorganic N had higher N20 emissions than C4-dominated sites. In summary, historical N additions had long lasting effects on SGS by increasing plant biomass and N. Given that N additions to ecosystems are increasing worldwide, it may be important to evaluate the impacts of these changes in processes on ecosystems services that grasslands provide. My results suggest that high levels of nutrient additions have unintended consequences such us increased C02 and N20 emissions, and in particular carbon additions through biosolids increase fungal activity, which is also conducive to N20 production. These additions have a profound impact, since the elevated greenhouse gas emissions and changes in microbial communities last at least 20 years after the amendment was carried out.Item Open Access Nutrient limitation of microbial decomposition in Arctic tussock tundra soil(Colorado State University. Libraries, 2013) Melle, Caroline, author; Wallenstein, Matthew, advisor; von Fischer, Joseph, committee member; Stromberger, Mary, committee member; Steltzer, Heidi, committee memberCold, wet conditions limit microbial activity in many parts of the Arctic tundra, resulting in slow decomposition of soil organic matter, low nitrogen (N) mineralization rates and the accumulation of massive amounts of soil organic carbon (SOC). Climate change is currently reducing these physical environmental constraints, allowing for Arctic SOC to become vulnerable to decomposition. However, historically low decomposition rates due to climatic inhibition have resulted in soils with extremely poor nutrient availability in the active soil layer for much of the year further inhibiting ecosystem productivity and limiting microbial decomposition. N limitation of both primary productivity and microbial activity, in addition to extremely low soil N availability throughout much of the active season, make many Arctic tundra ecosystems among the most N limited in the world. Changing climatic conditions can potentially allow for increased annual N mineralization resulting in greater soil N availability. Enduring increases in soil N availability would alter microbial driven biogeochemical cycles with cascading long-term effects on Arctic tundra ecosystems. Despite previous experimental findings of N limitation of microbial decomposition in Arctic tundra, seasonal variability in soil N availability in conjunction with the influences of other soil factors indicate that N may not be the primary control of microbial activity in these soils during the entirety of the Arctic active season. The tight coupling of biogeochemical cycles suggests that labile carbon (C) may be co-limiting for portions of the active season when there is greater soil N available. Furthermore, most observations of N stimulation of microbial activities have originated from relatively few research sites due to the inaccessibility of much of the Arctic, but N limitation of decomposition may be site dependent and vary across small geographic areas. Questions of inter-annual and intersite variability of soil microbial activities within a singular Arctic soil type have never previously been directly addressed. I conducted laboratory soil incubations to examine intra-seasonal and annual variability of soil microbial N limitation, the potential for co-limitation of labile C and N, and the extent of intersite variability in microbial N limitation across two comparable moist acidic tundra (MAT) sites within close proximity and of similar topography, climate and vegetation. I found, contrary to previous studies and my hypotheses, that soil microbial biomass growth, C mineralization, and extracellular enzyme activities were not consistently stimulated by N additions, but rather found that N was primarily immobilized in microbial biomass. Stimulation of C mineralization by N addition was short-lived and variable across the course of a single active season. Additionally, there was significant variation in microbial responses to nutrient amendments and temperature across the two consecutive study years; differences in temperature sensitivities of C mineralization and conflicting effects of N amendment on enzyme activities were seen between study years. Intersite variability was also significant; despite the close physical proximity and similar topography, climate, and vegetation of the sample sites investigated, they differed markedly in their responses to N additions as well indications of labile C co-limitation. The uniquely uniform properties of MAT tussock soils may lead to the presumption of homogeneity of soil microbial activities. However, I found that the significance of microbial N limitation and occurrence of co-limitation by labile C were dependent on the soil sampling site even though soil properties were consistent across sites. These findings of extensive variability and labile C co-limitation within some MAT tussock soils elucidate some of the current knowledge gaps in Arctic microbial ecology and suggest that the current paradigm of Arctic N limitation as one of the primary active season controls on ecosystem activity needs to be expanded and further refined to better predict the fate of the large amounts of C currently sequestered in Arctic tundra soils.Item Open Access On the use of locality aware distributed hash tables for homology searches over voluminous biological sequence data(Colorado State University. Libraries, 2015) Tolooee, Cameron, author; Pallickara, Sangmi, advisor; Ben-Hur, Asa, committee member; von Fischer, Joseph, committee memberRapid advances in genomic sequencing technology have resulted in a data deluge in biology and bioinformatics. This increase in data volumes has introduced computational challenges for frequently performed sequence analytics routines such as DNA and protein homology searches; these must also preferably be done in real-time. This thesis proposes a scalable and similarity-aware distributed storage framework, Mendel, that enables retrieval of biologically significant DNA and protein alignments against a voluminous genomic sequence database. Mendel fragments the sequence data and generates an inverted-index, which is then dispersed over a distributed collection of machines using a locality aware distributed hash table. A novel distributed nearest neighbor search algorithm identifies sequence segments with high similarity and splices them together to form an alignment. This paper includes an empirical evaluation of the performance, sensitivity, and scalability of the proposed system over the NCBI's non-redundant protein dataset. In these benchmarks, Mendel demonstrates higher sensitivity and faster query evaluations when compared to other modern frameworks.Item Open Access Restoring carbon accumulating processes in a degraded wet meadow(Colorado State University. Libraries, 2018) Baldwin, Lydia, author; Cooper, David, advisor; Steingraeber, David, committee member; von Fischer, Joseph, committee memberWet meadows throughout the Sierra Nevada range of western North America were historically disturbed and are thought to be losing soil water holding capacity and the ability to store carbon (C). I tested whether herbivore exclosures and the reestablishment of a sedge-dominated community at Tuolumne Meadows, a high elevation wet meadow in Yosemite National Park, can restore the C accumulating function of this ecosystem. In 2016, 20,000 Carex scopulorum (mountain sedge) were planted into the meadow. An empirical model of growing season carbon dynamics was created to determine if these treatments increase the meadow's C storage compared to controls. The second summer after planting, there was no difference in C storage capacity between treatment types and controls, and model estimates indicate that Tuolumne Meadows is a net source of carbon dioxide (CO2) to the atmosphere. Significant relationships between net ecosystem exchange (NEE) and percent vascular cover indicate that increasing vegetation cover could revert the ecosystem to carbon storing. However, future warmer, drier climatic conditions could maintain the system's current state as a C source.Item Open Access Sedimentology, facies architecture and sequence stratigraphy of a Mississippian age, black mudstone succession -- the upper member of the Bakken Formation, North Dakota, U.S.A.(Colorado State University. Libraries, 2013) Borcovsky, Damien A., author; Egenhoff, Sven, advisor; Harry, Dennis, committee member; von Fischer, Joseph, committee member; Fishman, Neil, committee memberThe early Mississippian age, upper member of the Bakken Formation in the North Dakota portion of the Williston Basin consists of a succession of organic-rich, black siliciclastic mudstones deposited offshore on a low-gradient ramp or shelf. Based on ichnological and sedimentological characteristics twelve fine-grained facies are recognized within the succession and these are grouped into five reoccurring facies associations. Very fine-grained, massive to faintly laminated mudstone (FA1) records deposition in the deepest, calmest parts of the offshore environment, whereas well laminated mudstones (FA2a), well laminated clay clast-bearing mudstones (FA2b), burrow-mottled mudstone with shells (FA3), and interlaminated siltstone and mudstone (FA4) contain sedimentological evidence that argues for deposition in the shallower, less calm, and generally more proximal parts of the offshore environment. These proximal-offshore mudstones (FA2a, FA2b, FA3, and FA4) reflect (1) variation in overall bottom water oxygen levels from dysoxic to possibly as high as oxic, and (2) lateral variation in the input of silt and clay clasts along the basin margin. Ubiquitous Phycosiphon incertum fecal strings throughout the succession along with patches of small shells and centimeter-scale burrows, and rare agglutinated foraminifera indicate that the upper Bakken member was likely deposited primarily in dysoxic to suboxic basinal conditions, and not within a persistently stratified, anoxic environment. In all facies associations, storm event laminae deposited by bedload processes range from sparse to ubiquitous. Repeated stacking of facies associations, which reflect different offshore energy regimes define up to ten coarsening-upward parasequences mostly 0.15-0.60 m thick. These are bounded by flooding surfaces that can be correlated laterally for at least 300 km through the basin, delimiting individual parasequences. Distinct formation-scale facies changes indicate that the lower half of the succession, herein termed Interval 1, represents the distal expression of a transgressive systems tract and was characterized by high radiolaria productivity with minor silt input during higher order sea level lowstands. The upper half of the succession, herein termed Interval 2 represents the distal expression of the base of a highstand systems tract. In contrast to Interval 1, the Interval 2 mudstones are generally characterized by high clay content, low radiolaria productivity, and intermittent colonization of the sea floor by bivalves and millimeter to centimeter-scale burrowing organisms during higher order sea level lowstands. Core descriptions, radiolaria distribution patterns, x-ray diffraction data and comparisons to other shale plays in the United States of America suggest that mature mudstones in the Interval 1 part of the succession outside of the depocenter, and in isolated silt-rich sub-basins, might be sufficiently brittle and permeable to exploit for hydrocarbons utilizing horizontal drilling and hydraulic fracturing technologies.Item Open Access Soil nitrogen cycling in agroecosystems as modified by biochar amendment and plant processes(Colorado State University. Libraries, 2019) Rocci, Katherine, author; Cotrufo, M. Francesca, advisor; Fonte, Steven, advisor; von Fischer, Joseph, committee memberEcosystem productivity is dependent upon cycling of nutrients, such as nitrogen (N). In agricultural systems, humans have greatly altered N cycling through the application of synthetic fertilizers such that soil N in agroecosystems is lost at higher rates than N in unmanaged systems. A variety of strategies have been assessed to reduce losses of soil N through nitrous oxide (N2O) emissions and leaching, which can negatively impact climate and water quality, respectively. The application of biochar, a carbon-rich soil amendment, has shown promise for increasing N retention in agricultural systems, but field and greenhouse studies often present less dramatic and often conflicting effects, suggesting the need for greater study in these environments. Further, the effects of biochar do not occur in isolation, but rather depend on plant processes that may affect soil N dynamics. This thesis explores these ideas through: (1) a greenhouse study considering the effects of different biochar types on N cycling with and without plants and (2) a field study looking at seasonal patterns of N cycling and fixation in alfalfa as altered by strategically-placed, low rates of biochar application. Study 1 sought to determine differential effects of biochar and plants, and raw and engineered biochar, on both fertilizer and innate soil N cycling using isotopically labelled fertilizer. While biochar effects on soil-derived N were minimal, we found that engineered biochar led to significantly higher leaching losses of fertilizer N. Plants, in contrast, were found to reduce N loss and increase overall recovery of fertilizer N. Study 2 focused on the effects of low and economically feasible application rates of two different biochars on N fixation, N loss, and mineral N availability over a growing season. We found no biochar effects on any N cycling parameter and, rather, found significant temporal effects in all N pools. Seasonal dynamics suggest connections between SIN availability and N fixation and loss. Indications of increased N loss with engineered biochar in Study 1 urge the need for greater study of biochars in combination with a variety of fertilizer types in order to provide the best recommendations to farmers. Lack of effects with biochar in Study 2 indicate that low application rates of biochar may not be useful for increasing N retention, suggesting the need to find a balance between economic and effective biochar application rates. Since both studies suggest that plant processes have more substantial impacts on N cycling than biochar amendment, via reduced N loss (Study 1) or increased symbiotic N input (Study 2), it is important that plants are included in more biochar studies such that the strength of biochar effects can be more realistically evaluated.Item Open Access The effects of temperature and moisture on alpine microbial processes across a gradient of soil development(Colorado State University. Libraries, 2012) Osborne, Brooke Bossert, author; Baron, Jill, advisor; Cotrufo, Francesca, committee member; von Fischer, Joseph, committee member; Wallenstein, Matthew, committee memberAlpine ecosystems are being transformed by global change. Climate change and atmospheric nitrogen deposition are exposing soils to novel temperature regimes, melting alpine glaciers, altering precipitation patterns, and directly introducing bioavailable nutrients. Because microbial communities are important drivers of nutrient cycling and ecosystem function in the alpine, and because temperature, moisture and nutrient availability are primary controls of microbial abundance and activity, it is likely that microbial linkages exist between global change and ecosystem-level consequences of global change in alpine regions. Deglaciation in high-elevation regions incrementally exposes soils to primary succession, which creates a wide range of soil environments. Yet, little is understood about these unusual environments' respective microbial communities or how they respond to the influence of global change. This research studied the effects of changing temperature and moisture controls on microbial carbon and nitrate (NO3-) processing in a range of alpine soils. The soils were collected from a watershed that exhibits characteristics of nitrogen saturation as a result of atmospheric nitrogen deposition. Glacial outwash, talus, and meadow soils were characterized by physical, chemical and biological properties. Soil temperature regimes were highly variable in the field, with some soils experiencing great diurnal fluctuations, while others remained consistently cold. The response of microbial community size, structure, activity and behavior to warming and changing soil moisture was addressed with laboratory incubations. Microbial community size and nutrient availability increased with increasing soil organic carbon. Microbial activity in all soils increased with temperature and moisture, as evidenced by total and microbial biomass-specific rates of respiration. However changes in microbial biomass carbon and parameters of community structure and behavior differed among the soils. This indicated that the soils responded using individual mechanisms to changing microclimate conditions during the incubations. The net production of NO3- occurred in all soils under all experimental conditions, however the rate at which NO3- was produced responded differently to temperature and moisture treatments. This suggests that global change may affect biological controls of NO3- availability in the alpine.Item Open Access The impacts of deficit irrigation on crop production and sustainable soil management(Colorado State University. Libraries, 2022) Flynn, Nora E., author; Fonte, Steven, advisor; Comas, Louise, committee member; Stewart, Catherine, committee member; von Fischer, Joseph, committee memberGrowing issues of water scarcity around the planet highlight a need for more efficient use of agricultural water. Deficit irrigation (DI) offers a promising option to reduce water use with relatively small impacts on crop yield, when properly managed. However, the impacts of DI management on above and belowground crop growth and the interactions between plants and soil are complex and need further study. There are concerns that DI, because it often reduces crop biomass, could reduce soil carbon (C) stocks, and negatively impact soil processes related to soil health. Additionally, DI alters soil moisture conditions with significant implications for soil C turnover and for the movement, transformation, and fate of soil nitrogen (N). At the same time soil N could buffer crops from water stress. Therefore, the goal of this research was to examine the potential impacts of DI on crop production and water stress and implications for soil C and N dynamics. Chapter 2 explores the effect of DI on maize above and belowground growth, soil microbial community composition, soil aggregation as well as soil C concentrations in surface soils (0-20 cm) and at depth (40-60 cm). Deficit irrigation increased root length density in deep soils (40-60 cm), with a trend towards higher soil C in treatments with the most root growth. Deficit irrigation also reduced total microbial biomass in the surface layer and led to shifts in microbial community composition. While aggregation and soil C were not strongly impacted by DI here, increased root growth under DI could eventually increase soil C and benefit a range of soil health related parameters, which are advantageous for crop production in water-limited systems. Chapter 3 quantifies greenhouse gas emissions from DI compared to full irrigation and suggests that DI can reduce both N2O and CO2. While this is a promising result, we also found that yields were reduced under DI, such that yield-scaled emissions were higher under DI compared to FI. The tradeoff between reducing emissions at the cost of reducing yield is important to recognize in the development of more sustainable agricultural practices. An additional important observation in this study was that emissions from this drip-irrigated maize system appeared to be much lower than from sprinkler or furrow irrigated maize systems reported elsewhere in the Great Plains. Chapter 4 sought to elucidate the impact of DI on the fate of N and the interactions between water and N in a drip-irrigated maize system. Yield and the amount of N at the end of the growing season in the harvested material vs. N lost via N2O emissions or remaining in the soil. Deficit irrigation reduced grain yield compared to full irrigation was quantified. Less N was taken up by maize under DI, leaving more residual nitrate in the soil at the end of the growing season, which is vulnerable to subsequent loss via leaching or emissions. While DI reduced consumptive water use in this experiment, yields were also reduced, thereby reducing water use efficiency. Overall, the findings of this study suggest that farmers should apply less fertilizer when utilizing DI. Chapter 5 examines the impact of DI and N level on above and belowground growth of five different sorghum genotypes in a greenhouse experiment. We found that DI led to an increase in root biomass allocation for all the sorghum genotypes, and that a low N treatment further increased root biomass allocation and specific root length (SRL) compared to a high N treatment under DI. Importantly, increasing root biomass allocation did not decrease aboveground biomass which is a common tradeoff in drought-stressed agriculture. In summary, this research indicates that DI alters crop growth in important ways beyond just grain yield. Deficit irrigation can increase maize and sorghum root growth, which has important implications for water and nutrient acquisition and for building soil C. This finding is especially significant in semi-arid systems, where maintaining and building soil C presents a significant challenge for long term soil health. We also showed that DI can be used to reduce greenhouse gas emissions, but it is important to note that such management can also reduce yield. Overall, this research will help inform farmers and policymakers in making decisions around the adoption of DI practices. Most importantly, this work suggests that proper implementation of DI offers promise to maintain crop growth with less water and that doing so could maintain or increase soil C stocks and would require less N fertilizer application compared to full irrigation.