Browsing by Author "Schipanski, Meagan, committee member"
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Item Open Access 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 memberAs 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.Item Open Access Control of Meloidogyne chitwoodi (Columbia root-knot nematode) by microbial soil inoculants in potatoes (Solanum tuberosum)(Colorado State University. Libraries, 2022) Gross, Gary Edward, author; Wallner, Stephen, advisor; Vivanco, Jorge, advisor; Schipanski, Meagan, committee memberColumbia root-knot nematode (Meloidogyne chitwoodi Golden et al) is a major pest in commercial potato production in the northwestern, United States of America. M. chitwoodi infestation is widespread throughout the potato (Solanum tuberosum) growing regions of the U.S and other areas of the world. Meloidogyne spp. causes severe crop damage and economic losses in a broad range of economically important crops. Traditionally, M. chitwoodi has been controlled by the applications of chemical-based soil fumigants and nematicides. Chemical based controls have shown good effect at controlling M. chitwoodi, but due to their human toxicity, possible damage to the environment, development of nematode resistance to chemical nematicides, decreased availability of labeled chemical nematicides and the high cost of chemical nematicides there is a need for alternative methods to control M. chitwoodi. Specific soil microorganisms have been found to be antagonistic and parasitic to M. chitwoodi and other Meloidogyne spp. in potatoes and several other crops. It has also been proposed that the use of soil microorganisms that are antagonistic and parasitic to plant parasitic nematodes are an essential component to long term sustainable Integrated Nematode Management (INM). Due to the agricultural need for the development of alternative control methods of Meloidogyne spp. in crop production worldwide two commercially available microbial soil inoculant products were tested under greenhouse and open-field conditions. The two commercially available microbial soil inoculant products that were tested are NemaRoot, which contains Purpureocillium lilacinus (formally known as Paecilomyces lilacinus) and BioFit N, which contains Azotobacter chroccum, Bacillus subtilis, Bacillus megaterium, Bacillus mycoides, and Trichoderma harzianum. Previous findings have shown that Bacillus subtilis, Bacillus megaterium, Trichoderma harzianum and Purpureocillium lilacinus all have the ability to control Meloidogyne spp. to varying degrees in a number of diverse crops. The greenhouse experiments that were conducted for this research showed that NemaRoot was able to reduce M. chitwoodi root galling by 64% (P < 0.001), eggs by 74% (P < 0.001) to 91% (P < 0.001), second-stage juveniles in the substrate by 80% (P < 0.001), the reproductive factor by 67% (P < 0.001) to 80% (P < 0.001) and potato tuber damage by 77% (P < 0.001) to 82% (P < 0.001) in potatoes. The greenhouse experiments also showed that BioFit N was able to reduce M. chitwoodi root galling by 73% (P < 0.001, eggs by 81% (P < 0.001) to 97% (P < 0.001), second-stage juveniles in the substrate by 81% (P < 0.001), the reproductive factor by 82% (P < 0.001) to 87% (P < 0.001) and potato tuber damage by 78% (P < 0.001) to 78% (P < 0.001) in potatoes. The commercial open-field potato experiment showed that 2, 3 and 4 applications of BioFit N at a rate of 1.12 kg/ha per application were able to control M. chitwoodi tuber damage as well as 2 applications of Vydate (Oxamyl) at a rate of 2.2 L/ha per application. These results show that biocontrol of M. chitwoodi with microbial soil inoculants are an effective control method; especially, when used as a part of an Integrated Nematode Management (INM) strategy.Item Open Access Ecovoltaics and grassland responses to solar energy co-location(Colorado State University. Libraries, 2024) Sturchio, Matthew Anders, author; Knapp, Alan K., advisor; Ocheltree, Troy, committee member; Schipanski, Meagan, committee member; Mueller, Nathan, committee memberThe mitigation of climate change requires a transition to renewable sources of energy, and of all available options solar photovoltaic (PV) energy generation has the greatest potential to reduce CO2 emissions by the year 2030. Even so, ground mounted PV is land use intensive, and ideal locations for solar development often overlap with sensitive natural ecosystems and highly productive agricultural land. A scalable approach with potential to alleviate the land use tension created by solar development is the co-location of PV arrays and grassland ecosystems. While this approach has many positive implications for land sparing, the ecological consequences of PV presence above grassland ecosystems are not well understood. In this dissertation I discuss how the unique microenvironments created by PV arrays alter patterns of productivity, physiological response, and forage quality in a semi-arid grassland in Colorado, USA. I also outline a new approach to PV development, Ecovoltaics, that is informed by several fundamental ecological concepts. An Ecovoltaic approach to solar development co-prioritizes energy generation and ecosystem services by intentional design and management through all aspects of array development. With this work, I hope to inform a more sustainable future for solar energy.Item Open Access Effects of cyanobacterial fertilizer, commonly-used organic fertilizers, and plant growth regulators on yield and growth characteristics of carrots (Daucus carota var. sativus), cucumbers (Cucumis sativus), and bell peppers (Capsicum annuum)(Colorado State University. Libraries, 2016) Wickham, Allison, author; Davis, Jessica G., advisor; Schipanski, Meagan, committee member; Bartolo, Michael, committee memberNitrogen (N) is arguably the most important agricultural nutrient. More money and resources are spent on N management in agricultural systems than any other nutrient. Producing N fertilizer for agricultural use accounts for more than half of the carbon footprint of crop production. Nitrogen plays a crucial role in plant growth, and adding N fertilizers to agricultural systems can lead to noticeable increases in productivity. Nitrogen fertilizers commonly used in organic production are often energy intensive to produce and expensive to transport. Cyanobacteria fertilizer (cyano-fertilizer) produced on-farm could decrease fertilizer impacts on the environment as well as reduce production costs for organic farmers. In addition, cyanofertilizer may perform similarly to products marketed to increase production via plant growth hormones such as seaweed extract, which is shipped all over the world from coastal regions. The effects of common organic fertilizers as well as organic liquid cyano-fertilizer on carrot (Daucus carota var. sativus) and cucumber (Cucumis sativus) growth and yield characteristics were tested during field experiments at the Horticulture Field Research Center in Fort Collins, CO in 2014 and 2015. Bell peppers (Capsicum annuum) were grown in a greenhouse experiment in 2015 at the Colorado State University Plant Growth Facility. Cyano-fertilizer was produced and evaluated in this study to compare effects of farm-grown cyano-fertilizer and commonly-used organic fertilizers. The purpose of this study was to identify fertilizer and foliar seaweed application effects on yield, stress, and growth characteristics of all three plant species. In all experiments, hydrolyzed and non-hydrolyzed fish fertilizers, and cyano-fertilizer treatments were applied at prescribed N rates throughout the growth period approximately every 10 days. Control treatments received no supplemental N. Each treatment, including the control, was repeated with the addition of two forms of concentrated organic seaweed extract applied foliarly. Neptune’s Harvest and Seacom PGR brand seaweeds were used for their lack of N content. Seaweeds were applied at the manufacturers’ recommended rates. Phytohormones were detected in all N fertilizers and in the PGR seaweed. No phytohormones were detected in the Neptune’s Harvest seaweed. In 2014, carrot length and yield were increased by the addition of cyano-fertilizer compared to the unfertilized control. All fertilizers increased post-season soil N compared to the control. Nitrogen fertilizers increased carrot leaf tissue Mg concentrations compared to the control. Nitrogen fertilizers and foliar seaweed influenced the number of carrots with deformities, and a significant interaction between N fertilizers and seaweed with regard to stress indicated a stress response to the addition of both fish fertilizer and a foliar seaweed application. In 2015, cyano-fertilizer produced a higher carrot yield than hydrolyzed fish fertilizer. Nitrogen fertilizers impacted the total number of cucumbers harvested as well as total cucumber yield, but the results were not consistent across years. The majority of significant differences occurred in the pepper study. Nitrogen fertilizer had an effect on leaf tissue nutrient concentrations as well as phytohormone content. Nitrogen fertilizer also impacted flower death and leaf abscission as well as plant stress. Foliarly applied seaweed treatments had very little significant influence in the carrot or cucumber field studies, but did have an effect on pepper shape and color (crop quality). Pepper yield was impacted by the addition of N fertilizers. Foliar seaweed impacted pepper branching behavior as well as fruit color and shape. Based on these experiments, it can be concluded that cyano-fertilizer can be used as a N source in place of commonly-used organic fertilizers. With regards to plant growth characteristics, it is unclear that any of the products applied consistently impacted plant growth characteristics in a way that improved yield or quality.Item Open Access Evaluation of stress coefficient methods to estimate crop evapotranspiration(Colorado State University. Libraries, 2015) Kullberg, Emily G., author; Chávez, José L., advisor; DeJonge, Kendall, committee member; Niemann, Jeffrey, committee member; Schipanski, Meagan, committee memberIncreased competition for water resources is placing pressure on the agricultural sector to remain profitable while reducing water use. Remote sensing techniques have been developed to monitor crop water stress and produce information for evapotranspiration (ET) based irrigation scheduling decisions. Use of stress detection methods allows producers to avoid exceeding set crop water stress levels and keep operations sustainable under limited irrigation despite some yield reduction. Remote sensing data such as spectral reflectance and infrared canopy temperature can be used to quantify crop water stress, often through the use of vegetation indices calculated from the near-infrared and red bands and temperature indices calculated from the thermal wavelength, respectively. Reference ET methods estimate water use based on crop characteristics and climactic parameters assuming optimum soil water conditions. In order to adjust crop ET for water limited conditions such as drought or water allocation restrictions, ET scaling techniques that are sensitive to crop development and stress are necessary. The performance of five remote sensing techniques to estimate corn ET under drought conditions in Northern Colorado were evaluated: one method based on air temperature, canopy temperature and relative humidity (Crop Water Stress Index (CWSI)), three methods based strictly on canopy temperature including Degrees Above Non-Stress (DANS), Degrees above Canopy Threshold (DACT), and Temperature Ratio, and one method based on multispectral vegetation indices (NDVI Ratio). Data were collected during 2010 through 2013 growing seasons at the USDA-ARS Limited Irrigation Research Farm near Greeley, CO. Varying water deficit levels were imposed on corn (Zea mays L.) under pressurized drip irrigation. ET estimates from the five remote sensing techniques were compared to soil water balance (via neutron probe) and ET calculations. Results showed that stress coefficient methods with less data requirements such as DANS and DACT are responsive to crop water stress as demonstrated by low RMSE of ET calculations comparable to more data intensive methods such as CWSI (CWSI = 0.77 mm/day, DANS = 0.80 mm/day, DACT = 0.80 mm/day, Tc Ratio = 0.83 mm/day, NDVI Ratio = 0.85 mm/day). Detailed tables indicate which remote sensing methods are appropriate to use given certain data availability and irrigation level, in addition to providing an estimation of the associated error in ET. Using the most appropriate stress coefficient method has the potential to improve irrigation scheduling and therefore allow crops to reach the maximum possible yield given the level of deficit irrigation. Methods with fewer data requirements, such as DACT with only a single canopy temperature measurement requirement, may be more appropriate to improve on-farm water management in certain situations. Results justify use of simplified measures of stress to improve deficit irrigation water management with limited data.Item Open Access Factors contributing to herbicide response in CoAXium wheat(Colorado State University. Libraries, 2024) Pelon, Amber L., author; Dayan, Franck, advisor; Gaines, Todd, committee member; Schipanski, Meagan, committee memberCompared to other pests, weed competition has the most significant negative impact on wheat grain yield. Understanding the contribution of metabolism in overall tolerance to herbicides can lead to new methods for controlling weeds in wheat. Glutathione S-transferase's (GSTs) role in the detoxification of herbicides has been studied since 1970. Previous literature reported increased resistance to herbicides with higher GST activity in black grass (Alopecurus myosuroides) and Asia minor bluegrass (Polypogon fugax). Resistance could be reversed by inhibiting GST activity. This research assesses the role of Phase 2 plant cell metabolism by testing (GST) inhibition to see if it influences the metabolism of quizalofop P-ethyl (QPE) in winter wheat (Triticum aestivum). We hypothesized that the addition of a safener would make the wheat more tolerant to the herbicide while the addition of a GST inhibitor would make the wheat more sensitive to QPE. Experiments were conducted analyzing the QPE effect on whole-plant biomass and an LC-MS/MS analysis of the amount of quizalofop acid (QZA) found in plant extracts. Safeners enhanced herbicide metabolism which increased CoAXium wheat tolerance to QPE. GST inhibitors, conversely, decreased herbicide metabolism causing CoAXium wheat to be more sensitive to QPE. Understanding the contribution of metabolism in overall resistance to herbicides can lead to breeding improvements for more herbicide-tolerant wheat varieties and new methods for controlling weeds in wheat.Item Open Access Identifying grass-legume bicultures to increase above and belowground biomass production and improve traditional fallows in crop rotations of the Andean Highlands(Colorado State University. Libraries, 2021) Meza Retamozo, Katherin Paola, author; Fonte, Steven, advisor; Schipanski, Meagan, committee member; Davis, Jessica, committee memberIn the high Andes of Peru, intensification of crop rotation and agricultural land-use is reducing the practice and duration of traditional fallow (based on natural establishment of native vegetation). These fallows represent one of the main traditional soil management practices to sustain long-term productivity, while also providing key forage resources in these mixed crop-livestock systems. Improved forage-based fallows, with the intentional seeding of more productive annual and perennial forages, offer great potential for producing forage and contributing to soil restoration under intensified contexts; however, there remains a gap in knowledge about which plant species can best optimize tradeoffs between forage production and belowground inputs to support long-term soil fertility and contribute to the multifunctionality of Andean agroecosystems. To address this issue, a pot study was conducted with two contrasting soils to evaluate the above and belowground productivity of all possible grass-legume pairs involving five grasses (oat (Avena sativa), ryegrass (Lolium multiflorum), festulolium (Lolium x Festuca genera), brome grass (Bromus catharticus), and orchardgrass (Dactylis glomerata), and four legumes (vetch (Vicia dasycarpa ), red clover (Trifolium pratense), black medic (Medicago lupulina), and alfalfa (Medicago sativa)) in comparison to the performance of each species in monoculture. Grass-legume bicultures resulted in significant overyielding, producing 65% and 28% more total dry biomass and total N uptake on average than species in monoculture, respectively. Grass-legume shoot biomass production yielded 67% more compared to monocultures, while root biomass was on average 58% higher in bicultures than in monocultures. For aboveground biomass, production differences between grass-legume bicultures were significantly influenced by the species of legume present, while belowground biomass was more affected by the grass species present in the bicultures. Roughly 80% of the mixtures achieved a mean land equivalent ratio (LER) > 1.0. When examining total biomass production, the most successful bicultures were oat-vetch (LER=1.87), vetch-festulolium (LER=2.31), vetch-orchardgrass (LER=1.87), oat-red clover (LER=1.62), and red clover-ryegrass (LER=1.46). When examining partial LERs (the component of the LER attributed to each species), we found that overyielding in bicultures was mainly driven by increases in the biomass of the component grass species. Our findings suggest that mixtures of key functional species (e.g. grass and legume, annual and perennial species) offer greater promise in improved fallows compared to monocultures of the respective species. Additionally, I suggest that strategically designed improved fallow mixtures, with emphasis on perennial species that support long-term root inputs, can best support soil health and the multifunctionality of Andean agroecosystems.Item Open Access Investigating the relationship between cover crop species diversity, composition and function of the soil microbiome(Colorado State University. Libraries, 2023) Seitz, Valerie, author; Prenni, Jessica, advisor; Wrighton, Kelly, committee member; Schipanski, Meagan, committee member; Nishimura, Marc, committee memberCropping diversification, such as cover cropping, can contribute to sustainable agriculture by enhancing soil health and promoting ecosystem services through interactions with the soil microbial community. One important mechanism through which cover crops impact soil health is via root exudation, the release of organic compounds from plant roots into the soil region surrounding the roots, the rhizosphere. Root exudation varies among cover crop species, growth stages, and edaphic and environmental conditions resulting in a myriad of effects on the rhizosphere. Plant-derived inputs, like root exudates, modulate the soil microbial community, influencing microbial biomass, community structure, and catalyzing biogeochemistry. As a result, cover crops are linked to microbial changes that impact soil nutrient cycling and organic matter decomposition leading to a legacy impact on primary crop yield and health. Understanding the intricate relationship between cover crop root exudation composition and the soil microbiome is crucial for optimizing cover crop selection, management practices, and harnessing cover crops for precision microbiome management in agroecosystems. My dissertation demonstrates that cover crop root exudation differs considerably across cover crop species, and cultivars within species, and reveals cover crop metabolic impacts on soil microbial composition and function, which play a large role in the generation and maintenance of healthy soils to support our agricultural needs.Item Embargo Isolation, interpretation, and implications of physical soil organic matter fractions in soil systems(Colorado State University. Libraries, 2024) Leuthold, Samuel J., author; Cotrufo, M. Francesca, advisor; Lavallee, Jocelyn M., advisor; Mueller, Nathan, committee member; Schipanski, Meagan, committee memberSoil organic matter (SOM) is crucial to sustained ecosystem function, due to its role in regulating nutrient cycling, carbon (C) storage, and soil structure relevant to both food production and climate regulation. Since the early 1990s, physical fractionation methods have been used to separate bulk SOM into discrete components. The central aim of these methodologies is to simplify the complex heterogeneity of the bulk SOM pool by isolating fractions with more homogenous chemistries, formation pathways, and mechanisms of persistence. By understanding the relative distribution of C and nitrogen (N) among these various fractions, we gain appreciable insight into the mechanisms underlying fundamental soil biogeochemical processes. Despite their historic use, however, significant questions remain regarding the means of proper isolation and interpretation. This dissertation looks to these questions directly, reviewing and then interrogating the methods by which fractions separated before applying those fractionation schemes to answer key questions relating SOM to ecosystem function. The first section reviews the history and current state of physical fractionation methodologies, before using a triangulation of experimental evidence, including chemical, isotopic, and spectral indicators, to identify the best practices for laboratory use. These chapters advance our current understanding of SOM biogeochemistry by drawing an explicit link between the conceptual definitions of SOM fractions and the various procedural definitions that have been used historically. Across a range of soils representative of agricultural land in the United States, we show that fractionation methods that separate particulate organic matter (POM) fraction by density isolate fractions more in line with the conceptual definition of POM than the more frequently used size separation. This work aims to unify understanding across the field of soil biogeochemistry and allows for more robust analyses and modeling efforts. The subsequent chapters use this approach to investigate fundamental questions around SOM stability and persistence. The mineral associated organic matter (MAOM) fraction has long been understood to be relatively stable, with slower turnover times and a more homogenous composition as compared to POM. Its accumulation has thus been discussed as a target for climate change mitigation. We leveraged a unique long-term experimental site with archived samples stretching back over 60 years to test this assumption, aiming to identify a dynamic fraction of MAOM by comparing the SOM composition of plots that had not received organic inputs over the course of the experiment against plots that had received regular inputs for six decades. Our spectral and isotopic analyses showed that a dynamic fraction of the MAOM existed and was primarily composed of plant derived compounds. As the exchangeable MAOM pool was exhausted due to a lack of fresh C inputs, we found that the composition of the MAOM pool became more strongly dominated by microbial byproducts. This work represents useful evidence towards a holistic understanding of the dynamic nature of SOM, and forces reimagining of long-held paradigmatic views. One challenge in the current SOM biogeochemistry landscape is that often questions exist downstream of methodologies, such that the fractions that can be isolated drive the research that is conducted. By first identifying robust methodologies, in the second half of this dissertation we were able to ask specific questions about the link between SOM dynamics and ecosystem function. To this end, we pursued three different lines of inquiry: a field study in which the objective was to link the fractional distribution of C and N to yield stability in agricultural systems, a field study that seeks to understand the persistence dynamics of SOM over a decadal scale in grassland systems, and a laboratory incubation that aims to discern the relative contributions of POM and MAOM in regard to plant available N. The first field study used samples from 9 working farms across the Central United States to better understand how SOM might moderate the spatiotemporal stability of crop yields at the field scale. Yield instability is a major cause of economic and environmental distress in row crop systems, and regional studies have suggested that increasing SOM may be able to mitigate variation in yield across time and space. The chapter presented here is the first study that attempts to identify a mechanistic link between SOM fractions and yield stability. In disagreement with regional and county scale studies, we found that SOM abundance was not linked to increased yield stability in cropping systems. Rather, unstable yield zones had significantly higher SOM content than stable zones, particularly in regard to the POM fraction. This work indicates that at the subfield scale, interactions between climate, topography, and management may be driving spatial patterns of both yield stability and SOM accumulation. This is a key insight, implying that some of the relationships between SOM and agronomic outcomes are scale dependent, and highlighting the need for field scale work to maintain relevance to growers. The second field study produced novel insights, tracing isotopically enriched litter and pyrogenic organic matter (PyOM) through various SOM fractions over the course of a decade, one of the longest tracer experiments that has occurred in grassland ecosystems. We found that after 10 years, the majority of the remaining litter derived C and N inputs were stored in the MAOM fraction, a result well aligned with our hypotheses. Interestingly though, the litter derived MAOM fraction formed rapidly (~ 1 year) and persisted at a relatively similar concentration for the duration of the study. This suggests the potential for divergent persistence mechanisms of POM and MAOM, implying less inter-fraction transfer than previous frameworks have proposed and prompting re-evaluation of the mechanisms of MAOM formation and persistence. In contrast, the applied PyOM remained almost completely in the POM fraction over the 10-year period, reinforcing both the heterogeneity of the bulk SOM pool, and the myriad of persistence mechanisms that stabilize various SOM fractions. Given that PyOM is ubiquitous in soil regardless of burn history and can persist for hundreds of years, this result has critical importance for our understanding of turnover time of the POM fraction, and suggests that we may be underestimating the dynamic nature of POM when PyOM is not accounted for. Finally, in a lab incubation experiment, we took advantage of recent advances in isotopic measurement to prove recent theories around MAOM N accessibility. Whereas POM is often thought of as the fraction that provides nutrients in the short term, our two-week incubation showed that under certain conditions, the majority of plant available N may be derived from the MAOM fraction. This work validates proposed frameworks and is an important step towards understanding coupled C and N management in agroecosystems that could improve N use efficiency and increase producer sustainability. Overall, the work in this dissertation aims to provide a comprehensive overview of how fractions can and should be isolated, and the information gained via this fractionation. By clarifying and advancing methodology to quantify SOM components and the understanding of their contribution to critical soil functions for the sustainability of food production and the mitigation of climate change this dissertation represents a major step forward for the study, modeling and managing of SOM in agricultural systems.Item Open Access Mapping evapotranspiration at a high resolution using the surface aerodynamic temperature model and airborne multispectral remote sensing data(Colorado State University. Libraries, 2016) Barlak, Melahat Semin, author; Chávez, José L., advisor; Andales, Allan, committee member; Schipanski, Meagan, committee memberIrrigation is the largest single consumer of water in the world, and with the increasing population, limitation of natural resources, climate change, and global warming, the pressure on water resources has become more significant and attention to agriculture is increasing daily. The limitation of agricultural areas requires efficient use of these areas to obtain a maximum yield. Evapotranspiration (ET) is a major component of the water budget and energy balance. Therefore, exact measurement of plant water use (and thus ET) is vital for efficient use of water resources, planning, and management purposes, especially for arid and semiarid regions. Many methods have been developed for estimating crop ET on a small field scale, such as the Bowen Ratio (BR), the Eddy Covariance (EC), and Lysimeter systems; however, remote sensing-based ET methods have been developed for estimating crop water needs on a regional scale. The energy balance (EB)-based ET algorithms require the computation of net radiation (Rn), soil heat flux (G), and sensible heat flux (H) to solve for latent heat flux or ET as a residual. Values of Rn and G can be estimated with an acceptable accuracy. However, estimation of H is not straightforward. This is because surface aerodynamic temperature (To) is difficult to measure or estimate. Instead, radiometric surface temperature (Ts) is generally used in the estimation of H. However, using Ts may cause overestimation of H, and thus underestimation of ET. To account for those differences between To and Ts, several remote sensing-based algorithms have been developed for mapping ET. The Surface Aerodynamic Temperature (SAT) model is one of them, and was used in this study to estimate sensible heat flux (H) for cotton fields and calculate ET as a residual of the EB for research fields located at the USDA-ARS Conservation and Production Research Laboratory (CPRL) near Bushland, Texas in 2008. By using the SAT model, ET results obtained from the multispectral airborne remote sensing data were compared with ET calculated with model input data collected at the large weighing lysimeters site . Resulting SAT ET values were obtained with a Mean Biased error (MBE) and a Root Mean Squared error (RMSE) of 2.67% and 8.61%, respectively. Then, actual crop ET from the SAT model were compared to measured values from the large lysimeter mass balance. This evaluation resulted in 25.9% MBE and a 44.07% RMSE for the east irrigated fields while for the west dryland fields the error obtained was 42.13% MBE and 42.91% RMSE. In addition, the crop water stress index (CWSI) was used to calculate actual ET using remote sensing inputs and results were also compared to lysimeter measured ET values. Results indicated that the errors were MBE value of 3.77% and an RMSE value of 10.76% for the east fields and 0.89% MBE and 6.0% RMSE for the west fields of the research area, respectively. The results show that the SAT model that was used in this study may not be appropriate for sparse vegetation and heterogeneous surface conditions and that further improvement of the model is required with the application of remote sensing data. On the other hand, the CWSI method performed better than the SAT model for estimating ET and crop water stress levels.Item Open Access Simulating canopy dynamics, productivity and water balance of annual crops from field to regional scales(Colorado State University. Libraries, 2016) Zhang, Yao, author; Paustian, Keith, advisor; Arabi, Mazdak, committee member; Parton, William, committee member; Schipanski, Meagan, committee memberTo provide better understanding of natural processes and predictions for decision support, dynamic models have been used to assess impact of climate, soils and management on crop production, water use, and other responses from field to regional scales. It is important to continue to improve the prediction accuracy and increase the reliability. In this work, we first improved the DayCent ecosystem model by developing a new empirical method for simulating green leaf area index (GLAI) of annual crops. Its performance has been validated using experimental observations from different experimental field locations as well as more aggregate NASS yield data spanning the country. Additionally, sensitivity and uncertainty of important parts of the crop growth model have been quantified. Our results showed the new model provided reliable predictions on crop GLAI, biomass, grain yield, evapotranspiration (ET), and soil water content (SWC) at field scale at various locations. At national scale, the predictions of grain yields were generally accurate with the model capable of representing the geographically-distributed differences in crop yields due to climate, soil, and management. The results indicated that the model is capable of providing insightful predictions for use in management and policy decision making. Although there are challenges to be addressed, our results indicate that the DayCent model can be a valuable tool to assess crop yield changes and other agroecosystem processes under scenarios of climate change in the future.Item Open Access Soil microbial community dynamics associated with agricultural crops(Colorado State University. Libraries, 2018) Lichtner, Franz Johann, author; Broders, Kirk Dale, advisor; Schipanski, Meagan, committee member; Smith, Richard G., committee member; Wallenstein, Matthew D., committee memberIt could be argued that the sustainability of agriculture hinges on our ability to understand and manage the interactions that occur between agricultural crops and microbial communities that reside in the soil. Soil microbes regulate the decomposition of organic matter, the cycling of nutrients to crops and can induce systemic resistance. They also drive global biogeochemical cycles that influence the climate, which in turn determine the growing environment for crops. Soil microbes also interact with crop plants directly via neutral, pathogenic, or beneficial symbioses that can influence plant health as well as resistance and resilience to pests and abiotic stress. Conversely, crop plants, via their growth, root exudation and litter production, are critical to the maintenance and growth of soil microbe populations. Despite their close association and importance to global agriculture, our understanding of the interactions between crop plants and their associated soil microbial communities remains poorly understood. In this dissertation I conducted experiments in two agro-ecoregions (the US Northeast and the Southern mountains of Colorado) to better understand how crop plant composition and management influence soil microbial communities and populations of pathogenic microbes. Data from the first experiment are reported in Chapters 1 and 2. In this experiment I sampled soil microbial communities in a field experiment that was replicated across four locations in the Northeast US. The experimental treatments were plots of perennial ryegrass varying in perennial ryegrass genotypic composition and diversity. My objective was to determine whether the genotypic composition and diversity of the perennial ryegrass stand influenced the structure (Chapter 1) and composition (Chapter 2) of the soil microbial community over the years of the experiment. I found that soil microbial community structure (measured as abundance of bacteria and fungi) and composition was not influenced by the cultivar mixtures, but rather by the year, location, and plant biomass. In chapter 3 I present data from a survey of Helminthosporium solani and Colletotrichum coccodes and a controlled experiment on their effects on potato cultivars in post-harvest storage. The objective of these studies was to understand how specific fungal-fungal and fungal-plant interactions are important in a potato production system where the functional aspects of a specific microbial community is not well understood. Here we see an annual change in soil pathogen presence depending on crop plant in the field. My results show that microbial interactions are polymodal and dependent on host genotype, soil chemical and physical properties and management practices. My final objective in this dissertation was to formally describe a fungal species, Penicillium acequia sp. nov. This fungal species was prevalent in agricultural soils and morphologically and genetically different from its closest relative. This new species has potential to be cultured and utilized as a biocontrol or for production of valuable secondary metabolites. Fungal antagonism as an option for crop plant disease control could reduce overall fungicide use. Inoculation of perennial cropping systems with beneficial microbes at planting over multiple years could harbor a soil microbiome that requires fewer inputs with reduced disease. We have a long way to go in describing the diversity of life in the soil that is critical to our food production system, and must characterize the presence and function of microbes within agricultural systems. Collectively, the data from this dissertation suggests that there are important yet opaque outcomes of microbial interactions influenced by time and location among other variables. Host genetics, including resistance genes, allow for unique microbial interactions and nutrient exchange which may matter more than traditional phenotypic plant traits, though this requires more research. Microbial interactions continue to evolve, the importance of genetic quantity is not to be discounted, rather determining the biologic pathways mediating interactions will provide greater insight into the sustainability of agricultural ecosystems.Item Open Access The cost of consumption: an analysis of the heterogeneous impacts of groundwater availability in the High Plains aquifer(Colorado State University. Libraries, 2019) Moore, Lacey, author; Suter, Jordan, advisor; Goemans, Chris, committee member; Schipanski, Meagan, committee memberNearly 20-percent of the wheat, corn, cotton and cattle produced in the United States are made possible by the hydrologic resources of the High Plains Aquifer (HPA) (NRCS, 2017). Despite being a source of agricultural prosperity, this aquifer has long been subject to overdraft including reductions in saturated thickness exceeding 50m in the southern extents (Haacker et al., 2016). We follow Hornbeck et al. (2014, 2015) in comparing economic outcomes among counties inside the HPA to similar counties within 100km from the aquifer boundary, building on this research by also evaluating the impact of initial groundwater endowments as an exogenous measure of irrigation access. Utilizing a hedonic pricing model based on Ricardian theory of land valuation, we choose to examine irrigation intensity, land values, and population density using census data at the county scale to measure the marginal benefit of groundwater. These economic outcomes are examined across ranked groupings of initial saturated thickness for three distinct time periods: approximate pre-development of the aquifer (1925-1945), during the height of irrigation expansion (1950-1992), and during contemporary time periods of irrigation water shortages (1997-2012). Results indicate that previous studies which have regarded the HPA as a homogeneous unit overlook the true marginal contributions of groundwater. We find that the counties with the largest initial endowments of groundwater in the HPA have increased land values by as much as 42-percent during the height of irrigation expansion, and more importantly have maintained the longest lasting economic benefits compared to counties with lower initial saturated thickness and those outside the aquifer. Our results differ from previous studies (i.e., Feng et al., 2012) as we find no statistical relationship between access to groundwater (or aquifer depletion) and population density.Item Open Access Understanding the disease ecology of the corn bacterial leaf streak pathogen Xanthomonas vasicola pv. vasculorum(Colorado State University. Libraries, 2019) Ortiz Castro, Mary Carmen, author; Leach, Jan, advisor; Broders, Kirk, advisor; Charkowski, Amy, committee member; Schipanski, Meagan, committee memberBacterial leaf streak, caused by Xanthomonas vasicola pv. vasculorum (Xvv), is an emerging disease of corn in North and South America. Based on the combined $52.4 billion value of the corn industry, early reports of Xvv disease severity, and lack of management methods, this emerging pathogen represents an economic threat to corn production in the United States. The primary goal of this research is to provide a basic understanding of the infection ecology and survival of the corn bacterial leaf streak pathogen. Through genetic transformations of the bacteria with fluorescent proteins and confocal microscopy, we were able to show the localization of the bacteria within plant leaves. In addition, we found that there is a significant interaction between Xvv isolates and two corn varieties. By evaluating the bacterial fitness across representative isolates of Xvv, we showed that 22°C is the optimal temperature for bacterial growth in culture. We also evaluated the interaction of Xvv with the endophyte Pantoea ananatis and found that the presence of the endophyte significantly decreases Xvv's disease response. Finally, through litter studies at multiple locations, we demonstrated that infected residue left on the surface of the soil harbored significantly greater quantities of Xvv than infected residue buried 10 cm below the surface. These findings will be useful to understand the bacterial leaf streak disease cycle and aid in the development of management strategies that may limit the distribution of Xvv within corn fields and prevent its spread to other corn producing regions.Item Open Access Using indaziflam for integrated weed management in managed and natural ecosystems(Colorado State University. Libraries, 2020) Seedorf, Rachel H., author; Nissen, Scott, advisor; Tekiela, Daniel, committee member; Schipanski, Meagan, committee memberIndaziflam is a relatively new herbicide for natural area weed management. It is unique because it inhibits cellulose biosynthesis and it controls annual weeds as the seeds germinate. This soil active herbicide provides the opportunity to control winter annual grasses and annual broadleaf weeds without impacting established perennial grasses and forbs. These characteristics are key to managing weeds, while promoting the growth of native vegetation. Indaziflam was a key component in the development of an integrated weed management plan for Denver International Airport (DEN). DEN supports a diverse set of landscapes, from the Pena Boulevard Transport Corridor to shortgrass prairie, natural areas, and riparian corridors. DEN is faced with several challenges when managing vegetation, with weed invasion being one of the most important. Kochia (Bassia scoparia) and downy brome (Bromus tectorum L.) pose the greatest threats to desirable vegetation and healthy, sustainable ecosystems. Kochia is an invasive broadleaf that is a prolific seed producer and can spread quickly. Downy brome is also a highly invasive winter annual grass that can fill open niches in native plant communities. Current vegetation management at DEN does not adequately control weeds and does not promote the growth of desirable vegetation. Therefore, site-specific research assessing passive and active restoration practices was conducted to develop a landscape management plan to help improve and promote native vegetation. Two research studies were established at DEN, both with remnant native grasses that were also invaded by downy brome and kochia. The objective was to demonstrate passive restoration. We hypothesized that weed control using indaziflam and other post-emergent herbicides would provide 2+ years of control. Downy brome, kochia, and perennial grass cover and biomass were collected in 2019 and 2020 to measure herbicide impacts and plant community responses. Averaged across both sites, downy brome cover, 2 years after treatment (YAT), was reduced to < 2% in all indaziflam plots compared to the control (~75% cover). At both sites, perennial grass biomass increased 5- to 10 – fold once downy brome competition was removed. These invaded sites with remnant grass populations responded positively with timely weed management. Active restoration was employed at two sites that were void of desirable grass species. Perennial grasses were drill seeded and protected from weed competition with adaptive weed management, primarily with selective herbicides. With adequate weed control and supplemental irrigation, crested wheatgrass was the only grass that successfully established (83% stand frequency). This study illustrates the challenges associated with revegetating degraded sites and the necessity of providing adaptive weed management. Furthermore, the information derived from these studies was used to develop management prioritization categories to assist DEN in making strategic decisions for managing weeds and restoring sites across the airport property. The final management plan represents the culmination of the site-specific, research-based recommendations made and will be utilized by DEN land management to improve current practices. This project also demonstrated the utility of using indaziflam in a managed ecosystem. In natural ecosystems invaded by downy brome, indaziflam provides similar opportunities for passive restoration. Downy brome produces large amounts of litter in these ecosystems that act as continuous fine fuel. Prescribed burning is often used as a tool to remove plant litter and provide downy brome control and can be followed by herbicide treatments to extend control; however, combining prescribed burning with indaziflam has not been evaluated. We hypothesized that removing the litter layer using prescribed fire before applying indaziflam alone or combined with post-emergent herbicides would increase herbicide efficacy and extend downy brome control. In September 2017, two downy-brome infested sites were burned. In March 2018, indaziflam was applied alone or in combination with post-emergent herbicides to the burned area as well as non-burned plots. Downy brome cover and the desirable plant community responses were evaluated to determine burning and treatment effects. Downy brome cover was reduced in all herbicide treatments in the burned plots compared to the non-burned plots at both sites 2 years after treatment (YAT) (Site 1 - 6.5% ± 1.2 SE vs. 19.8% ± 2.6; Site 2 - 7% ± 1.5 vs. 15.5% ± 1.7). Desirable plant species cover, richness, and diversity were not negatively impacted by burning or herbicide treatments. Perennial cool-season grass cover responded positively to burning at site 1, while the perennial forb community responded positively to burning at site 2. Plant diversity and species richness also increased at site 2 in the burned plots which was due to the increase in the number of native forb species. This study demonstrates that burning extended downy brome control even at lower indaziflam use rates, without reducing the diversity of the desirable plant community. This research also demonstrates the utility of using indaziflam in natural ecosystems.