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Browsing by Author "Trivedi, Pankaj, committee member"

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    A modeling-experimental (ModEx) approach to advance understanding of global controls and microbial contributions to particulate and mineral-associated organic matter storage
    (Colorado State University. Libraries, 2024) Hansen, Paige M., author; Cotrufo, M. Francesca, advisor; Schipanski, Meagan, committee member; Wallenstein, Matt, committee member; Trivedi, Pankaj, committee member
    As soils are the largest terrestrial pool of carbon (C) and provision many ecosystem services, including nutrient cycling and maintenance of plant productivity, soil C sequestration represents a promising technology to help meet urgent needs to draw down atmospheric carbon dioxide (CO2) and prevent acceleration of climate change, as well as to help feed a rapidly growing global population. Given this, a comprehensive understanding of the mechanisms underpinning observed patterns of soil C storage is necessary to ensure a sustainable future for all. In response to this need, recent breakthroughs in our understanding of soil organic matter (SOM) dynamics have led to the development of multiple frameworks articulating how climate, soil, plant, and microbial properties interact with one another to control the formation of the two SOM constituents, particulate (POM) and mineral-associated organic matter (MAOM). Despite this, environmental controls that act on POM and MAOM storage at the global scale, as well as microbial functionality, is noticeably absent from our empirical understanding of SOM fraction formation and persistence. More advanced knowledge of these controls would enable more robust identification of where SOM is most vulnerable to loss, as well as more informed implementation of 'multi-pool' management practices aimed at enhancing C storage in both POM and MAOM. In this vein, this dissertation explores global controls on and microbial mediation of SOM dynamics at multiple scales through a combination of synthesis, modeling, and experimental (i.e., ModEx) approaches. Specifically, I first synthesized climate, soil property, and fraction C data to understand global controls on C storage in POM and MAOM. I then applied a previously developed individual-based model (Kaiser et al., 2015) to determine how emergent microbial community properties resulting from microbial social dynamics (i.e., interactions among microbes that produce enzymes at different rates) impact POM retention under varying degrees of MAOM saturation. Lastly, I investigated the relevance of hypothesized microbial copiotrophic and oligotrophic life history strategies to changes in POM and MAOM storage. Results from these projects indicate that global POM and MAOM storage is controlled by disparate suites of environmental variables, with POM being primarily controlled by variables that modulate microbial activity, and MAOM being controlled by a combination of C inputs and soil properties related to the potential to stabilize new MAOM. Additionally, flexible enzyme production in response to the availability of easily-assimilable, soluble substrates may contribute to POM retention under varying degrees of MAOM saturation and POM carbon:nitrogen ratio (C:N). However, variation in microbial function does not always result in changes in POM and MAOM storage – differences in growth rate, our proxy for copio- and oligotrophy, was unrelated to changes in POM and MAOM. Despite this, this dissertation indicates that microbial functions and environmental properties controlling microbial activity rates (i.e., controls on C outputs from the soil) mediate POM storage, but that MAOM is more reflective of C inputs to the soil. This indicates that microbial interventions to support soil C storage may want to focus on ecosystem-specific microbial manipulations that support community efficiency and modulate exo-enzyme production. In combination with other management strategies that increase soil C, these types of microbial interventions may help ensure that new soil C is retained in the soil for longer periods of time. Additionally, given that microbial activity is generally expected to increase with climate warming, these results indicate a premium need to preserve existing POM stocks.
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    Abiotic and biotic factors influencing western United States coniferous forests
    (Colorado State University. Libraries, 2019) Lalande, Bradley, author; Stewart, Jane, advisor; Stromberger, Mary, committee member; Tinkham, Wade, committee member; Trivedi, Pankaj, committee member
    In the next decade, climate models suggest that global temperatures will continue to rise. In the western United States, increases in temperatures and changes in precipitation patterns will escalate the risk of drought conditions. These potentially warmer, drier conditions could induce physiological changes within trees, subsequently increasing stress on coniferous forests that are adapted to cool, wet environments. The abiotic stress accompanied by drought conditions can predispose susceptible hosts to biotic stress of insect and disease populations. In particular, high elevation subalpine fir (Abies lasiocarpa) have encountered higher than average mortality rates throughout the western United States in association with abiotic and biotic agents. Chapter 2 of this thesis investigated the potential drivers of subalpine fir mortality and determined how climatic factors and site and stand characteristics influenced the presence of mortality and biotic agents. The objectives were to identify factors driving subalpine fir mortality in Colorado and included 1) determine abiotic and biotic factors that directly and indirectly affect subalpine fir mortality, 2) determine factors associated with the presence of D. confusus or Armillaria spp., and 3) determine if climate variables were correlated to subalpine fir mortality or the presence of D. confusus and Armillaria spp. I hypothesized that sites with a higher density (i.e. basal area, trees per hectare, or canopy closure) would experience greater mortality due to decreased growth rates from competition and that D. confusus or Armillaria spp. prevalence would be a function of tree stress (i.e. increased density), elevation, slope, and departures from normal precipitation (i.e. drought), and minimum and maximum temperatures. Stand health monitoring plots found that the most relevant factors to subalpine fir mortality are the presence of D. confusus (p = 0.003) and the percent subalpine fir on plot (p = <0.0001). I identified that stand density (p = 0.0038), elevation (p = 0.0581), and Armillaria spp. (p = 0.0006) were the greatest influences on the presence of D. confusus, while the largest influences on the presence of Armillaria spp. are warmer maximum summer temperatures (p = 0.0136) and the presence of D. confusus (p = 0.0289). Results indicated that increased subalpine fir mortality was attributed to high stand density as a predisposing factor, warming temperatures as an inciting factor, and bark beetles (Dryocoetes confusus) and root disease (Armillaria spp.) as contributing factors. The combination of predisposing, inciting, and contributing factors suggests that subalpine mortality can be defined as subalpine fir decline. Management strategies used to reduce the impact of subalpine fir decline will need to address ways to improve stand health, while decreasing populations of both, D. confusus and Armillaria spp. In regards to Armillaria, the inability to successfully manage the disease using current techniques highlights the need to find novel management strategies to minimize its impacts. Since this disease is a root pathogen, soil microbes likely influence its growth and survival. Utilizing soil microbial communities as biocontrols may assist in management of Armillaria. Field sampling within the Priest River Experimental Forest in northern Idaho provided the opportunity to observe how soil microbial communities are associated with two species of Armillaria, A. solidipes (primary pathogen) and A. altimontana (weak pathogen). My research objective for Chapter 3 was to identify the soil fungal communities associated with tree health status (healthy, moderate and dead) and each Armillaria species, A. solidipes and A. altimontana, both of which have differing ecological behaviors (virulent pathogen and non-pathogen, respectively) on western white pine. I hypothesized that soil microbial communities associated with virulent A. solidipes and non-pathogenic A. altimontana would differ in fungal richness and diversity with the latter having a greater richness and diversity due to its beneficial qualities to tree health. While richness and diversity is likely to shift among tree health with a greater diversity and richness for soils associated with healthy trees due to root exudate production near the rhizosphere. Soil samples were collected alongside western white pine (Pinus monticola), while Armillaria rhizomorphs were excavated near the roots. The most abundant fungal taxon was Mortierella spp., which functions as saprophyte decomposing dead and down wood. No significant differences in fungal diversity or richness were found in soils associated with Armillaria species, but, although not significant, there where slight differences between soils associated with moderate and dead trees with a greater diversity and richness in soils with dead trees (p = 0.18). Additionally, soil pH was significantly influenced by soil carbon, nitrogen, and organic matter, while moisture significantly influenced soil carbon, nitrogen, and organic matter, acting as indicators to overall health in the stand. Although not significantly different, more Hypocreaceae (Trichoderma), a known biocontrol for root pathogens, were found within soils associated with A. altimontana and healthy trees. More research is needed to solidify differences, yet these factors give insight into potential beneficial aspects of soil fungal communities in association with Armillaria species and tree health. Changing climates regimes outside of 30-year averages cause increased stress to forests. This stress may predispose trees to a greater abundance biotic agents such as bark beetles and secondary pathogens, such as Armillaria root disease specifically in association with subalpine fir in Colorado. Understanding the role that soil fungal communities play in association to Armillaria root disease and tree health may assist in forest management practices to increase the health of high elevation forests.
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    Cover crops for ecological management of U.S. agricultural systems: quantifying ecosystem services across multiple scales
    (Colorado State University. Libraries, 2023) Eash, Lisa, author; Fonte, Steven J., advisor; Schipanski, Meagan E., committee member; Trivedi, Pankaj, committee member; Mooney, Daniel, committee member
    Managing agricultural systems to provide multiple ecosystem services (ES) beyond food provisioning has gained considerable attention in recent years. The integration of cover crops (CC) into U.S. cropping systems presents an opportunity to support multifunctional agricultural systems, which alleviate negative environmental impacts of agriculture, mitigate greenhouse gas (GHG) emissions and support sustained crop production. However, CC impacts on these ES are variable and depend on management and site characteristics, contributing to uncertainty surrounding to what extent CC can improve ES. Reducing this uncertainty is critical to both identify appropriate environmental and management conditions for CC adoption and improve the estimated potential for CC to improve multifunctionality of U.S. cropping systems. This dissertation aims to quantify CC impacts on ES at multiple scales, exploring benefits to the soil microbiome, at the farm level, and nationally. Throughout this assessment I explore how these effects are influenced by climate and soil characteristics and how management can be leveraged to optimize the provision of ES. Chapter two estimates the potential for widespread adoption of CC to increase soil organic carbon (C) stocks and mitigate GHG emissions in the U.S. Analysis using current U.S. crop management data and a biogeochemical model revealed that the mitigation potential over a 20 year period is lower than previous estimates due to regional variability, decreasing rates of C accrual over time, and limited CC integration. Changes in N2O emissions did not offset C sequestration but introduced large uncertainty surrounding total national mitigation potential. Soil C gains due to CC offer important co-benefits to U.S. cropping systems, but the contribution of CC to achieving U.S. emissions targets will likely be lower than previously anticipated. Our spatially-explicit analysis also highlights regions where adoption of CC can have greater relative contributions to GHG mitigation. I then quantify a larger suite of ES in dryland wheat systems of the semi-arid western U.S., a particularly challenging context for CC due to lower potential productivity and associated economic trade-offs. I used two existing field trials to monitor CC impacts on soil health, cash crop productivity, and economics over a period of six years. No-till, CC planting window, and the sale of CC biomass as forage were also explored as strategies to optimize ES provision and economic viability. Chapters three and four demonstrate that the integration of CC amidst water limitations can benefit erosion control and soil structure, but also present significant productivity and economic trade-offs. The integration of fall-planted CC, no-till management, and the use of CC for forage provided the greatest potential for maximizing ES benefits in an economically viable manner. In Chapter five, I conducted a greenhouse study to examine the impact of CC type and functional diversity on microbial community composition and associated ES. Plant functional types (Poaceae, Brassicaceae, and Fabaceae) were associated with distinct increases in ES proxies, which appear to be mediated by shifts in microbial community composition. Specifically, Fabaceae (legume) CC enhanced the presence of copiotrophic microbes, which were associated with improvements in soil structure and high enzyme activity, a proxy for nutrient cycling. Poaceae and Brassicaceae led to improvements in microbial diversity. Ecosystem service benefits and microbial community shifts were conserved in diverse CC mixtures, contributing to increased multifunctionality. Across studies and scales, CC were observed to support a number of ES that address environmental concerns resulting from modern intensive agricultural practices. However, slight benefits and substantial productivity trade-offs in water-limited systems may limit the extent to which CC can mitigate GHG emissions and restore soil C reserves nationally. Management choices, such as CC composition and diversity, no-till management, and the sale of a portion of CC biomass as forage, can be leveraged to optimize the provision of ES in an economically viable manner. Overall, CC effectively contribute to multifunctional agroecosystems whose ES extend beyond food provisioning.
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    Determination of spatial distribution, dissipation, and efficacy of insecticides used for control of citrus greening disease
    (Colorado State University. Libraries, 2022) Rehberg, Rachelle Anne, author; Borch, Thomas, advisor; Henry, Chuck, committee member; Bailey, Travis, committee member; Trivedi, Pankaj, committee member
    Citrus greening disease has devastated citrus production globally. While Florida growers explore management strategies, Asian citrus psyllids (ACP) continue spreading this detrimental disease. Determining the efficacy of insecticides applied in citrus groves is a necessity. In these field studies, the efficacies of foliar insecticide treatments to citrus trees were investigated with liquid chromatography tandem mass spectrometry. Insecticide spatial distribution, dissipation, degradation, and effectiveness at reducing ACP were quantified over time after commercial application at a field site in Florida. Citrus leaves, and sample discs attached to leaves, were collected at specific times and locations within individual citrus trees. ACP were inspected before and after treatments to quantify reductions associated with insecticide concentrations over time. We investigated several insecticides commonly used against ACP including malathion, imidacloprid, dimethoate, and one newer insecticide, afidopyropen. Our findings showed highly variable spatial distribution of insecticides throughout individual trees and rapid dissipation within 24 hours after application. Inadequate distribution to different sides of the leaf and tree canopy areas was observed for all aerial and ground spraying methods tested. Fast degradation rates were observed in sampling discs and citrus leaves with half-lives ranging from 0.6 to 4.0 hours while metabolite concentrations increased. Results showed faster dissipation rates during warmer months (July) and in younger-aged trees ground sprayed with the speed-sprayer. A wide range of insecticide efficacy was observed, with ACP reductions of 63 to 100%. When ACP remained after treatment, effectiveness decreased over time and ACP increased (e.g. from 6 to 172% after afidopyropen treatment). The observed variable spatial distribution, rapid insecticide dissipation, and inadequate efficacy allow remaining ACP or ACP from surrounding groves to continue spreading citrus greening disease, leaving citrus trees unprotected. For contact, or semi-systemic insecticides like afidopyropen, full coverage to both sides of the leaves and tree canopy is crucial to effectively manage ACP populations. ACP regeneration suggests lower metabolite toxicity or pest resistance development and reveals ineffective pest management. This research not only helps inform citrus growers of actual insecticide efficacy in the field, which may influence their pest and disease management strategies, but also provides better understanding of insecticide dissipation from citrus leaves, which assists those advancing predictive models for agricultural applications. Additionally, these results help inform insecticide manufacturers of their products' performance in field conditions which can be compared to laboratory studies. Lastly, this work reveals information on the fate of insecticides in the field which could be used to evaluate its impact on other species and the environment.
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    Developing paper-based devices for mapping agricultural pesticides and environmental contaminants
    (Colorado State University. Libraries, 2021) Menger, Ruth F., author; Henry, Charles S., advisor; Borch, Thomas, advisor; Ravishankara, A. R., committee member; Neilson, James R., committee member; Trivedi, Pankaj, committee member
    The detection of environmental contaminants is important to ensure the health of both humans and the environment. Currently, detection is done by instrumentation like liquid or gas chromatography coupled with mass spectrometry. While sensitive and selective for multiple analytes, these instruments suffer from disadvantages like large size, high sample cost, and the need for a trained analyst to run the samples. As an alternative, microfluidic paper-based analytical devices (µPADs) are becoming more common as inexpensive, fast, easy to use devices to detect and quantify a variety of analytes. My research has been focused on developing µPADs for three different analytes: pesticides, PFAS, and heavy metals. In order to ensure proper crop protection and pest management, it is important to manage and optimize pesticide application. Currently, this is done by water-sensitive papers, which often inaccurately portray the presence of pesticide due to humidity and extraneous water droplets that are not pesticide. In Chapter 2, I have developed a method that uses filter paper to capture a fluorescent tracer dye that has been mixed with the pesticide and then sprayed over the crop. The filter papers are imaged with a lightbox and Raspberry Pi camera system and then analyzed to determine percent coverage. After optimization and validation of the method to WSP, the filter paper method was used to evaluate pesticide distribution in a citrus grove in Florida (Chapter 3). The data from these field studies was used to make recommendations for which application method is best for the different types of pesticides. Paper-based devices are inherently limited by the inability to control fluid properties like mixing. In order to incorporate mixing but also retain a small device that does not require external power to initial flow, a microfluidic device was fabricated out of two glass slides. A staggered herringbone pattern is laser ablated into the slides, and a channel is formed by double-sided adhesive (Chapter 4). Mixing was quantified using blue and yellow dyes. A reaction between horseradish peroxidase and hydrogen peroxide was used as a representative enzymatic reaction and also to determine enzyme kinetics. Since the microfluidic device is made of glass, it is also compatible with non-aqueous solvents. Paper-based devices do not work well with organic solvents because the hydrophobic wax on the paper is dissolved by the solvent. In Chapter 5, the dissertation returns to traditional µPADs for environmental contaminants. Per- and polyfluoroalkyl substances (PFAS) are class of compounds that are highly persistent, toxic, bioaccumulative, and ubiquitous. While multiple instrument-based methods exist for sensitive and selective detection in a variety of matrices, there is a huge need for a fast, inexpensive, and easy-to-use sensor for PFAS detection. This would enable widespread testing of drinking water supplies, ensuring human health. A µPAD was developed for the detection of perfluorooctane sulfonate (PFOS) where the ion-pairing of PFOS and methylene green forms a purple circle. The diameter of the purple circle can be measured by the naked eye with a ruler or with the help of a smartphone to correlate the diameter back to PFOS concentration. At a cost of cents per sample, this µPAD enables fast and inexpensive detection of PFOS to ensure safe drinking water. A common issue with environmental µPADs is the relatively high limits of detection compared to what is needed for regulatory purposes. It can be challenging to lower the limits of detection without incorporating an external pretreatment and/or preconcentration step. As µPADs are small and handle only a small volume of sample (<120 µL), there is the possibility of increasing the sample capacity of the device but without significantly increasing the device size or analysis time. By adding multiple layers of absorbent filter paper underneath radial device for heavy metal detection, the sample volume increased to 1 mL, decreasing the limit of detection for a radial copper detection card from 100 ppb to 5 ppb (Chapter 6). The research presented here achieves the goal of developing µPADs for environmental contaminants. They can be used in different ways to visualize the presence of the contaminant for monitoring and management purposes, ultimately ensuring human and environmental health.
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    Evaluating Bouteloua gracilis cultivars' performance after drought; The role of the soil microbiome
    (Colorado State University. Libraries, 2024) Donne, Carina, author; Smith, Melinda, advisor; Havrilla, Caroline, committee member; Trivedi, Pankaj, committee member; Metcalf, Jessica, committee member
    Drought has affected the Great Plains throughout history, most notably during the Dust Bowl of the 1930's. While most drought events are not as severe as the Dust Bowl, they still cause significant agricultural losses every year. As research has begun to uncover the mechanisms and responses of drought, there are still unanswered questions. For instance, the mechanisms of ecosystem recovery after drought ends remain relatively unexplored. It is possible that intervention methods such as reseeding will need to be done to help restore ecosystem structure and function after drought. After the Dust Bowl, it was a common practice to reseed native grasses, such as Blue Grama (Bouteloua gracilis), in sites severely impacted by the drought. Given forecasts of droughts on par or even more severe than the Dust Bowl, reseeding may need to be employed more frequently in the future to enhance post-drought recovery. However, with reseeding efforts, it is imperative to understand the adaptability of cultivars to the environmental conditions in which they are planted. One aspect of environmental conditions that has rarely been examined the soil microbiome. Here, I used a common garden experiment that included two cultivars of B. gracilis that were planted with soil microbial inocula extracted from either previously droughted or non-droughted soils. These soils were collected from a recently ended four-year drought experiment in the shortgrass steppe of northeastern Colorado, which caused the widespread loss of B. gracilis. The goal of the greenhouse experiment I conducted was to examine whether the post-drought legacy of altered soil microbial communities affected the growth and performance of two common cultivars of B. gracilis. I assessed plant performance by measuring weekly height to estimate relative growth rate and at the end of the experiment, I measured plant above- and belowground biomass. I found no significant differences in relative growth rate or plant biomass, and minimal differences in the bacterial community composition between the two cultivars. These results suggest that the post-drought legacy of altered soil bacterial communities did not differentially affect growth and performance of the two common B. gracilis cultivars evaluated in this study, and that the growth of these cultivars did not differ in their effects on the soil bacterial communities found under ambient vs. previously droughted conditions. Overall, both cultivars may be suitable for reseeding in the shortgrass steppe grassland after extreme drought, yet further studies are needed to examine a broader range of B. gracilis cultivars and whether soil bacterial communities previously exposed to extreme drought would allow for improved growth and performance of different cultivars to future drought conditions.
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    Growing deeper: pathways to enhancing soil organic matter in annual and perennial dryland grain agroecosystems
    (Colorado State University. Libraries, 2022) van der Pol, Laura Kathryn, author; Cotrufo, M. Francesca, advisor; Schipanski, Meagan E., committee member; Trivedi, Pankaj, committee member; Crews, Timothy E., committee member
    The story of agriculture and human civilization is one of loss: loss of soil structure, soil carbon, ecosystem function, and diversity. As we find ourselves at the nexus of intersecting global challenges of radically altered biogeochemical cycles and anthropogenic climate and productivity influence, we urgently need to alter our relationship with the soil and biosphere that sustain our human systems. In this dissertation I evaluate two management strategies for enhancing soil organic matter (SOM) in dryland, grain fields in the U.S.: legume integration and perennial grains. These strategies have been part of traditional farming practices, but they are not commonly utilized by commodity farmers for reasons I explore in Chapter 5. I conclude with policy recommendations for one way that might lead to systemic change that would value soils and their vital role in our human systems more appropriately. Here I provide a brief synopsis of each chapter: In the introduction (Ch. 1) I provide some historical context of human reliance on grain agriculture and the reasons that legumes and perennials might enhance SOM. I also describe the framework of SOM formation used in this research and provide an overview of the components of SOM I measured in this research. The first study (Ch. 3) is an observational study of conventional, dryland wheat farmers in semi-arid Colorado and Nebraska. I examine the 'soil carbon (C) dilemma' (Janzen 2006): How can SOM be increased, while also increasing the release of nutrients that accompanies decomposition? We specifically tested whether incorporating legumes into a continuous rotation influences the form and amount of SOM as well as productivity in farms of the central Great Plains region of the U.S. by contrasting three, no-till rotation systems: 1) conventional wheat-fallow; 2) continuous grain-only rotations, and 3) continuous grain rotations that incorporate a legume crop. We sampled on-farm fields and experimental agricultural research station plots that had received one of these rotations for at least eight years. We found that intensifying the rotation with continuous grains led to 1.5-fold increase in aggregate size but did not change SOC stocks. Incorporating a legume to the continuous grain rotation resulted in 1 Mg C ha-1 more SOC on average in surface soil compared to wheat-fallow rotations. In chapter 3, I use a similar approach to assess whether conversion from annual to perennial grains such as intermediate wheatgrass Kernza® could sequester soil organic carbon (SOC). We sampled three sites with paired fields under annual grains and converted to Kernza 5-17 years ago to 100-cm and compared their SOC stocks as distributed between mineral-associated (MAOM) and particulate organic matter (POM). POM-C was higher under Kernza cultivation but total and MAOM-C were similar. Our findings suggest Kernza increases SOC at depth as POM. Further study is needed to assess whether this will result in long-term SOC sequestration. In order to quantify the effect of legume incorporation and ability of Kernza to form SOC, I performed a mechanistic study to quantify the formation of SOM from Kernza and alfalfa tissues under contrasting N management (Ch. 4) Using continuously labeled 13C/15N plant residues, we tested the effect of litter inputs of contrasting composition (shoot and root material from Kernza® and alfalfa, a perennial legume) under management of Kernza where N was (1) not added, (2) added as urea, or (3) fixed by an alfalfa intercrop. We selected Kernza for its theoretical potential to build SOM due to deep root systems and long growing season. We hypothesized that the higher quality litter from alfalfa shoots would lead to greater MAOM formation due to its higher density of metabolic components promoting enhanced microbial C use efficiency, while root tissues may more likely become stabilized within aggregates as oPOM due to increased contact with soil surfaces. We predicted that the management with N addition may enhance MAOM-formation by alleviating microbial N-limitation and leading to enhanced microbial C use efficiency. We found that overall Kernza promoted greater SOM formation, in both MAOM and oPOM, with 20% of roots stabilized and 12% of shoot stabilized after 27 mo compared to 10% for alfalfa roots and shoots. Finally, in chapter 5, I propose a pilot crop insurance and research program in the U.S. Northern Plains to promote practices that enhance soil health, farm income, resilience, and mitigate climate change. Such a program could inform nationwide adoption of such practices.
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    Ice nucleating particles in the Arctic: measurement and source tracking
    (Colorado State University. Libraries, 2024) Barry, Kevin Robert, author; Kreidenweis, Sonia, advisor; DeMott, Paul, advisor; van den Heever, Susan, committee member; Fischer, Emily, committee member; Trivedi, Pankaj, committee member
    The Arctic landscape is rapidly changing in a warming climate, with sea ice melting and permafrost thawing. Its near-surface air temperature is warming 3.8 times faster than other regions around the world. This rapid warming is known as Arctic amplification. Clouds contribute to this amplification, with their presence and phase is important for determining the surface energy budget. Arctic mixed-phase clouds can last for several days but are not represented well in climate models. Special aerosols, called ice nucleating particles (INPs) trigger ice formation in the atmosphere at temperatures warmer than -38 °C, and thus are important for determining the initiation, lifetime, and radiative properties of these clouds. Observations of INPs, especially over the central Arctic, are limited, and many sources are unknown. This dissertation has the overarching goal of increasing understanding of Arctic INPs. This is achieved through first presenting a full year of INP measurements in the central Arctic, as well as a full year of their composition, using coincident sampling of bacteria and fungi to gain insight into airmass origin. Next, some of the potentially most active Arctic INP sources are explored. Permafrost, which was known previously to contain high levels of INPs, was tested for its activity and persistence in water, and ability to be aerosolized through bubble bursting over several weeks. Then, sources of INPs were surveyed in a region that is controlled by permafrost (a thermokarst landscape). This included field measurements of permafrost, vegetation, sediment, active layer soil, water, and aerosol samples. A high temperature heat test was developed as a diagnostic tool to differentiate sources. Coincidentally, clean working methods to measure INPs were optimized, as efforts to reduce contamination are needed to accurately sample in this region. The main findings from this work suggest a regionally relatively homogenous population of Arctic INPs at most times of year, which is encouraging for efforts to represent them in numerical models across scales and understand their changes in the future. Permafrost-sourced INPs showed high activity and were enhanced near the coast. Unexpectedly, other components of the thermokarst landscape were found to be rich, organic INP reservoirs, emphasizing that the Arctic tundra is a diverse collection of potential contributors to the aerosol.
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    Influence of habitat complexity on diversity and community structure of arboreal spiders in grassland-shrub systems
    (Colorado State University. Libraries, 2023) Knutson, Eric M., author; Charkowski, Amy, advisor; Aldridge, Cameron L., committee member; Trivedi, Pankaj, committee member; Hufbauer, Ruth, committee member
    Revealing the ecological drivers of species distribution is one of the central issues in ecology. The ecological niche concept recognizes that distribution of species is influenced by abiotic (e.g., temperature, landscape characteristics, and nutrients) and biotic (e.g., food availability) factors through both direct and indirect mechanisms. Many of these niche factors can influence the spatial position of plants in a landscape. Plant communities often determine the physical structure of the environment (microclimate, plant architecture) and therefore, have a considerable influence on the distribution of animal species, such as arthropods, and on local community structure. For instance, vegetation structure provides spatial complexity by creating microenvironments that may enable more interactions with other species that live on plants or allow resource partitioning. In grasslands, much of the arboreal habitat is in the form of shrubs, but the role and importance of shrubs in distribution and diversity of arthropods in grasslands is unknown. Spiders are a useful indicator for examining the role of shrubs in arthropod ecology because they are genetically and behaviorally diverse predators and prey that can be captured and counted with a single method. Spiders are a key component of invertebrate communities of grasslands and arboreal spiders of grasslands provide a unique ecological system to study habitat association and community assemblage. However, most spider studies in prairie ecosystems have focused on ground dwelling taxa or those associated with agroecosystems. Only limited data exist for shrub-dwelling species and few studies have compared arboreal spider occupancy across different grassland shrub species. I endeavored to understand this system in more detail by investigating how arboreal spider community structure responds to native shrub species, plant community composition and landscape complexity. Since landscape complexity can be evaluated at multiple scales, landscape characteristics can be significant predictors of presence and abundance for a variety of taxa. I collected and identified 3,053 specimens to family, genus or species level and found that presence of certain shrub species predicted spider species occurrence and suggested diversity community structure patterns. I found that habitat association to combinations on shrub species indicated habitat specific niche partitioning of arboreal spiders in two Colorado grassland systems. Because shrub species occurrence is largely dependent on elevation and moisture gradients, spider occupancy may also be tied to similar gradients correlated with these landscape factors. Changes in the topography of the sampling area affected the local plant communities of shrubs across a recognized elevational gradient, which correlated to habitat zones for arboreal spiders in the local area.
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    Microbial succession in human rib skeletal remains and fly-human microbial transfer during decomposition
    (Colorado State University. Libraries, 2022) Deel, Heather Leigh, author; Metcalf, Jessica L., advisor; Wilusz, Carol, committee member; Trivedi, Pankaj, committee member; Pante, Michael, committee member
    Human decomposition is a dynamic process partially driven by the actions of microbes. It can be defined by the fresh, early decomposition, advanced decomposition, and skeletonization stages. The microbial communities that facilitate decomposition change in a predictable, clock-like manner, which can be used as a forensic tool for estimating postmortem interval. Chapter 1 introduces this concept by describing the stages of decomposition in detail and how high-throughput sequencing methods can be used with microbes to develop models for predicting postmortem interval. Chapter 1 also describes which sample types are most useful for predicting postmortem interval based on the stage of decomposition, the knowledge gaps in the field, and the steps necessary for adoption of this tool into the justice system. During fresh and early decomposition, microbial succession of the skin and soil sample types are most predictive of postmortem interval. However, after approximately the first three weeks of decomposition, the changes in the microbial communities that are used for predictions begin to slow down and the skin and soil sample types become less useful for estimating postmortem interval. Chapter 2 of this dissertation shows that microbial succession of the bone microbial decomposer communities can be used for estimating postmortem interval during the advanced and skeletonization stages of decomposition. First, the bone microbial decomposer community was characterized using 16S ribosomal RNA sequencing from six human donor subjects placed in the spring and summer seasons at the Southeast Texas Applied Forensic Science Facility. A core bone decomposer microbiome dominated by taxa within phylum Proteobacteria was discovered, as well as significant overall differences in the bone microbial community between the spring and summer seasons. These microbial community data were used to develop random forest models that predicted postmortem interval within +/- 34 days over a 1–9-month time frame of decomposition. To gain a better understanding of where the microbes in the decomposed bone were coming from, as healthy, living bone is typically sterile, SourceTracker2 was used with paired skin and soil samples taken from the same decedents. Results showed that the bone microbial decomposer community is likely sourced from the surrounding environment, particularly the skin and soil communities that occur during the advanced stage of decomposition. Chapter 3 of this dissertation focuses on the influence of the blow fly (Calliphoridae) microbiome on human cadaver microbial community assembly. In early decomposition, volatiles attract blow flies to the cadaver, which serves as a source of nutrients and a safe place to lay eggs. It is likely that during this interaction between hosts, there is a mechanical transfer of microbes that subsequently alters each of their microbial communities. While studies have shown that blow flies have their own microbiome, they were not conducted in a decomposition environment. First, Chapter 3 shows the characterization of the blow fly microbiome by organ and season in a terrestrial, human decomposition environment. This was performed by placing ten cadavers across the winter, spring, and summer seasons at the Southeast Texas Applied Forensic Science Facility, collecting the first wave of colonizing flies for each cadaver, and sequencing the 16S ribosomal RNA gene of the labellum (mouth parts), tarsi (leg parts), and oocytes. Results showed that the previously defined universal fly microbiome persists even in a decomposition environment, with notable differences still present between organs and seasons. Additionally, results from using the tool SourceTracker2 showed that the labellum and tarsi act as substantial bacterial sources of the human decomposer bacterial community, and this source contribution varies by season. In summary, this dissertation provides the first quantitative estimate of postmortem interval of terrestrially decomposed human skeletal remains using microbial abundance information. This is a significant contribution to the criminal justice system; anthropologists typically use visual evidence to provide postmortem interval estimates of skeletal remains with errors ranging from months to years, whereas our approach provides estimates with errors of approximately one month. Furthermore, this dissertation shows evidence that there is a mechanical transfer of microbes between blow flies and human cadavers during the early stage of decomposition, which provides ecological insight into human cadaver microbial community assembly.
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    Plant-mediated interactions between herbivory and soil microbial communities in biocontrol programs of Russian knapweed
    (Colorado State University. Libraries, 2024) Matos Franco, Giovana, author; Ode, Paul, advisor; Pearse, Ian, committee member; Smith, Melinda, committee member; Trivedi, Pankaj, committee member
    Russian knapweed (Rhaponticum repens) is an invasive noxious weed present in the United States and two insect biocontrol agents have been released to assist with its management: the gall midge (Jaapiella ivannikovi) and the gall wasp (Aulacidea acroptilonica). Since their establishment, no concrete impacts of biocontrol agents onto Russian knapweed have been measured, neither their impacts on interactions between Russian knapweed and local microbiomes. To address this knowledge gap, observational and manipulative studies were conducted to investigate the effects of biocontrol agents on Russian knapweed fitness as well as its associated microbiomes. We found that Russian knapweed associates with a core microbiome that can assist with invasion in the introduced range as well as, in root samples collected from sites where gall wasp were present, lower microbiome diversity was observed, indicating potential negative effects on overall plant health. In garden conditions, water availability positively correlated with plant growth, negatively correlated with insect establishment, and shaped microbiomes in root associated tissues. Results of this dissertation highlights how introduction of biocontrol agents shifts pre-established relationships between invasive plants and microbiomes as well as how such relationships could be impacting the success of biocontrol programs.
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    Roles of residue management, microbes and aggregation in soil carbon stabilization under semiarid, irrigated corn
    (Colorado State University. Libraries, 2021) Oleszak, Hanna, author; Cotrufo, M. Francesca, advisor; Stewart, Catherine, advisor; Trivedi, Pankaj, committee member
    With atmospheric carbon dioxide levels continuously on the rise, it is critical that we focus our efforts on sequestering carbon (C) to slow global warming. To maximize these efforts, it is furthermore important to understand the pathways by which plant C inputs form soil organic carbon (SOC), as these pathways may inform the efficiency and duration of C stabilization. No-tillage is often recommended as a universal tool to draw C into the soil, yet literature reports mixed effects of tillage practices on C accrual. To maximize our efforts and best recommend agricultural practices for C sequestration, it is important to understand how the incorporation of residue within the mineral soil and disturbance associated with tillage impact plant residue C dynamics, as mediated by changes in microbial community and soil structure. While microbes play the active role in decomposing organic matter, soil structure can act as a gatekeeper to microbial accessibility to organic matter; thus, the effects of disturbance and residue incorporation upon the interplay of these two variables is highly important to consider. We used 13C labeled plant residue to track the movement of residue C in incorporated vs. surface-applied residue treatments in irrigated, semiarid corn for a period of 30 months. Both carbon dioxide (CO2) fluxes and soil cores were tested for total C and 13C enrichment to quantify residue-derived C contribution to CO2 efflux and to C accrual in the mineral soil over time, respectively. Furthermore, aggregate size fractionation and microbial community (via phospholipid fatty acids, PLFAs) were analyzed to assess how residue placement location and disturbance affect the mechanisms behind residue decomposition, and ultimately soil C stabilization. The incorporation of residue in the mineral soil resulted in significantly greater SOC formation efficiencies and greater SOC accrual in the first year, compared to the surface-application of residue. However, differences in SOC accrual subsided after 30 months, even though higher CO2 losses were measured in the surface applied residue treatments after 30 months. Residue-derived microbial biomass was greater in INC than SA or SA-NR at all timepoints, although this was only significant at 6 and 12 months. Residue-derived microbial community composition differed between early and later stages of decomposition, as well as between disturbed and undisturbed treatments. Mean weight diameters of aggregates featured a seasonal trend, with greater mean weight diameters in the fall. Furthermore, INC had significantly higher MWD at 5-10 cm at 6 months compared to surface-applied treatments, while disturbed treatments (INC and SA-NR) had significantly higher MWD's at depth at 12 months than SA. MWD was strongly correlated to residue-derived SOC in incorporated treatments, but not in surface-applied treatments. Finally, SOC formation efficiencies were more strongly correlated to residue-derived F:B in the incorporated treatment, compared to surface-applied treatments. Residue C recovery, SOC formation efficiencies, and residue-derived microbial biomass indicate that the incorporation of residue stimulates SOC formation through the DOC-microbial pathway and the physical transfer path concurrently, while the surface-application of residue follows a shift in SOC formation pathways from DOM-microbial SOC formation to physical transfer of residue. Additionally, correlations between residue-derived SOC, residue-derived F:B, and MWD indicate that the protection of residue C largely relies on aggregation when residue is incorporated.
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    Soil degradation and water scarcity: the importance of soil organic matter and reuse of non-traditional water sources within agricultural systems
    (Colorado State University. Libraries, 2023) Stokes, Sean, author; Borch, Thomas, advisor; Trivedi, Pankaj, committee member; Ippolito, Jim, committee member; Fonte, Steve, committee member
    Our exponentially growing world will demand approximately 70% more agriculture production by 2050, yet according to the Food & Agriculture Organization of the UN, ~33% of land worldwide is experiencing soil degradation and by 2050, over 90% of soils could be degraded. Exacerbating problems with soil degradation are droughts that are becoming more common with a warming climate. According to the National Oceanic and Atmospheric Administration, ~60% of the USA experienced drought in 2022 and over 90% of the Western US is under drought conditions, including one of the largest agricultural regions in the world, California. Therefore, in order to address these urgent issues of soil degradation and water scarcity, agriculture needs to adapt to more sustainable management practices that emphasize the importance of maintaining soil health, specifically, soil organic matter (SOM), and implement treatment processes to utilize non-traditional water sources (i.e., wastewater from various sectors). This dissertation is a combination of two different research projects that focus on these topics. Two chapters are focused on soil degradation in agriculture in collaboration with an industry partner, Cutrale Citrus, and two chapters are focused on the reuse/treatment of non-traditional water sources in collaboration with the Department of Energy's National Alliance for Water Innovation (NAWI).Our scope within the NAWI project was to develop a baseline paper (i.e., a review) for this concept within agriculture, specifically the reuse of agricultural wastewater and the treatment of produced water (PW) for use as irrigation water. Since agricultural water quality has large regional variability, we focused on two agricultural regions, the Midwest and California. The Midwest has runoff primarily contaminated with nutrients that lead to eutrophication in the major water bodies of this region, while California has saline runoff that in some cases is too toxic to be released to the environment. California's agricultural runoff requires advanced treatment techniques while the Midwest could use existing tile drainage systems to capture runoff and re-apply it to cropland since the main contaminants are nutrients. The reuse of PW is more complicated since its often highly saline and contains other toxic organic compounds or metals. Kern County, CA has been reusing PW for over 20 years but only because their PW has low salinity, this allows them to implement low-cost treatments focused on dilution, but this reuse has been controversial. Our analysis showed there are many unknowns related to the toxicity of PW, so we also develop a path forward through the implementation of an "Adverse Outcomes Pathway" approach that could be utilized to minimize any risks associated with the reuse of this water for irrigation. The research focused on soil health utilizes soil from a citrus grove in SW Florida managed by Cutrale Citrus. The first study focused on why tree size varied between areas of the grove with identical management practices and trees of the same age. Based on these observations it was clear that soil health varied between these areas, so we endeavored to understand what components of the soil, including both physiochemical parameters and biological indicators, were showing significant differences between the productivity regions. The results showed that SOM concentrations, enzyme activity, and microbial diversity were the components of the soil that were significantly different between these areas. Additionally, these trees were all infected with Citrus Greening disease, so we developed a hypothesis based on how this phloem-limiting infection could also be impacting soil health or conversely, how soil health could impact the progression of this disease. Based on these results, the second study focused on how we could regenerate the SOM in this soil and improve soil health through the addition of different organic amendments (biochar and compost). A 400-day greenhouse study was conducted to look at changes to the SOM; we combined typical soil science analysis of SOM such as concentration and mineralization rate with molecular level analysis using high-resolution mass spectrometry (FT-ICR MS). Analysis of microbial diversity was also conducted but those results will not be finished in time to be included in the dissertation and will be included only in the published paper. The soils showed clear differences in molecular composition at both the start and finish of the study depending on which amendment was added. Overall, the compost soil showed an initial spike in activity followed by degradation and loss from the system while the biochar showed slower increases in activity and more stability in the soil. The molecular analysis clearly showed the shift of compost towards more oxygenated molecules and a decrease in the number of different chemical formula present, while the biochar soils had transformation occurring without much loss and contained molecules that were more reduced. Overall, this study showed how biochar is an effective amendment when considering the long-term impacts that one application could have compared to compost which has greater stimulation of the soil in the short term but quickly degrades and needs to be reapplied frequently. When considering the issues facing agriculture in the 21st century it is important to take an all-inclusive approach because agriculture is comprised of interconnected systems. For example, if soil health and SOM are not properly considered then that soil might have less ability to store and absorb water so more erosion or nutrient leaching might occur. Or conversely, if water of poor quality is applied to a field, then salts could build up and degrade the soil. However, if we continue to have devastating droughts in the Western US then we might need to consider reusing alternative water sources to irrigate our fields and we should begin to prepare for that possibility as our high-quality freshwater supplies dwindle.
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    Soil microbial communities associated with forest root diseases and Rocky Mountain forests
    (Colorado State University. Libraries, 2022) Lalande, Bradley, author; Stewart, Jane, advisor; Stromberger, Mary, committee member; Tinkham, Wade, committee member; Trivedi, Pankaj, committee member
    To view the abstract, please see the full text of the document.
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    The curious case of chemotaxis in soft rot Pectobacteriaceae
    (Colorado State University. Libraries, 2021) Nasaruddin, Afnan Shazwan, author; Charkowski, Amy O., advisor; Leach, Jan E., committee member; Trivedi, Pankaj, committee member; Heuberger, Adam L., committee member
    Soft rot Pectobacteriaceae, Dickeya and Pectobacterium, are notorious for causing blackleg and soft rot diseases on more than 50% angiosperms such as potato, tomato, carrot, cabbage, and rice. In the United States, soft rot Pectobacteriaceae causes at least $40 million losses of potato each year. Flagellar motility is important for soft rot Pectobacteriaceae virulence. Chemotaxis, which controls flagellar motility towards a conducive environment or away from hostile conditions, is essential for initial stages of infection. Chemotaxis is mediated by chemoreceptors known as methyl-accepting chemotaxis proteins. Genomic analyses of soft rot Pectobacteriaceae and closely related animal pathogens and non-pathogenic bacteria in order Enterobacteriales showed that soft rot Pectobacteriaceae genomes are enriched in methyl-accepting chemotaxis proteins. Furthermore, soft rot Pectobacteriaceae methyl-accepting chemotaxis proteins contain more diverse ligand binding domains compared to other species in Enterobacteriales. This study suggests the importance of chemotaxis for soft rot Pectobacteriaceae pathogenicity and opens up possibilities for future research in targeting chemotaxis for plant disease management. In E. coli, the alternative sigma factor FliA is required for transcription initiation in motility and chemotaxis genes. To determine how chemotaxis is regulated in Dickeya, we conducted an RNA-sequencing experiment using a wild-type strain and a fliA mutant of D. dadantii 3937 grown in minimal media with glycerol or glucose. We found that the FliA sigma factor did not regulate methyl-accepting chemotaxis genes in Dickeya, several virulence genes were upregulated in glucose, and some genes postulated to be regulated by PecS were upregulated in glycerol. It is still a mystery as to which sigma factor regulates the chemotaxis genes in Dickeya, however, my work demonstrates that the regulation of chemotaxis in plant pathogens differs from closely related animal pathogens in the same order.