Theses and Dissertations

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Open Access
Modifications to temperature-based estimates of consumptive water use by mountain meadows
(Colorado State University. Libraries, 2008) Temple, Darcy G., author; Smith, Dan H., advisor
Legal and engineering water communities in Colorado utilize the original Blaney-Criddle method to manage competing demands for water in mountain meadows, yet Blaney-Criddle underestimates in semi-arid, high-elevation environments. Blaney-Criddle consists of a consumptive use (CU) term, f, that is the product of mean monthly temperature, t, and percentage of daylight hours; and a crop coefficient, k, which accounts for crop variation and additional meteorologic effects. Low night temperatures at high elevations incorrectly weight f, and year-to-year variability among k values often results in significant variation between computed consumptive use and lysimeter measurements. Three modifications of the Blaney-Criddle temperature expression were tested against two existing temperature methods (Blaney-Criddle with conventional mean t, and Hargreaves) using lysimeter measurements from nine irrigated grass meadow sites in the upper Gunnison River basin (1999-2003). Use of two modified temperature expressions resulted in improved correlation of estimated Blaney-Criddle f with lysimeter CU. These improvements were similar to those observed when estimating with Hargreaves, which incorporates an additional term, Tdiff, the difference between maximum and minimum daily temperature. Climatological sources of variability in the crop coefficient, k, were also examined. The May-September crop coefficients k were better correlated with Tdiff (r = 0.28 to 0.54) than with mean t (r = 0.01 to 0.43). Specific regression equations based on Tdiff were used to develop crop coefficients from a dataset comprising the current study and three previous calibration studies in Colorado mountain meadows. Based on the standard error of estimate (SEE), estimates using the modeled coefficients more closely predicted CU than did estimates based on averages of locally calibrated k's (SEE difference of up to 5 mm mo-1). Correlations of solar radiation (Rs, the primary energy input to evapotranspiration) with alternative temperature expressions and Tdiff were improved over correlations of Rs with mean t, supporting the improved prediction performance of alternative temperature expressions and of the modeled k based on Tdiff. Those modifications can be applied successfully throughout Colorado mountain basins, and it is hoped that the same technique can be applied to other areas of the western U.S.
Open Access
Ground based active remote sensors for precision nitrogen management in irrigated maize production
(Colorado State University. Libraries, 2009) Shaver, Timothy Michael, author; Westfall, Dwayne G., advisor; Khosla, Rajiv, advisor
Precision agriculture can increase farm input efficiency by accurately quantifying variability within a field. Remotely sensed normalized difference vegetation index (NDVI) has been shown to quantify maize (Zea mays) N variability. Ground-based active remote sensors that can determine NDVI are commercially available and have been shown to accurately distinguish N variability in maize. There are several active sensors available but no studies directly comparing active sensors have been reported. Therefore, a study was conducted to evaluate active sensor performance and develop an in-season maize N recommendation algorithm for use in Colorado using NDVI. Previous studies have demonstrated an association of active sensor NDVI with maize N content and height. However, the NDVI from a GreenSeeker™ green NDVI prototype active sensor had not yet been tested when our study began. Therefore, the green sensor was evaluated to determine if differences in plant growth across MZ could be determined by the active sensor. Results show that the prototype active sensor did not record NDVI values that were associated with MZ. The NDVI from two different sensors (Crop Circle™ amber NDVI and GreenSeeker™ red NDVI) were then examined under greenhouse and field conditions. Results show that NDVI from the amber and red sensors equally distinguished applied N differences in maize. Each active sensor's NDVI values had high R2 values with applied N rate and plant N concentration. Results also show that each sensor's NDVI readings had high R2 values with applied N rate and yield at the V12 and V14 maize growth stages. An N recommendation algorithm was then created for use at the V12 maize growth stage for both the amber and red sensors using NDVI. These algorithms yielded N recommendations that were not significantly different across sensor type suggesting that the amber and red NDVI sensors performed equally. Also, each N recommendation algorithm yielded unbiased N recommendations suggesting that each was a valid estimator of required N at maize growth stage V12. Overall results show that the amber and red sensors equally determine N variability in irrigated maize and could be very important tools for managing in-season application of N fertilizer.
Open Access
A mechanistic approach to modeling saturation and protection mechanisms of soil organic matter
(Colorado State University. Libraries, 2009) Olchin, Gabriel Peter, author; Paustian, Keith, advisor
Simulation models have been used extensively as a research tool in the field of soil organic matter (SOM) dynamics and should embody our best understandings of the processes and mechanisms controlling these dynamics. Our objective was to develop and evaluate a SOM model based upon measureable soil organic carbon (SOC) fractions and optimize it against long-term tillage experiments in North America. This model will include (1) soil aggregate dynamics, with direct influence from tillage events; (2); and the mechanisms of SOM stabilization; and (3) explicitly address the concept of potential SOC saturation. The major proposed mechanisms for SOM stabilization-physical occlusion, organic recalcitrance, and organo-mineral interactions-have limited explicit inclusion in current SOM models.
Open Access
Precision manure management across site-specific management zones
(Colorado State University. Libraries, 2009) Moshia, Matshwene Edwin, author; Khosla, Rajiv, advisor
In the western Great Plains of the USA, animal agriculture is an important contributor to the agricultural economy, and many livestock farms are close to water bodies where manure can potentially contaminate the environment. The objectives of the study were to (i) assess the influence of variable rate applications of animal manure on grain yield in continuous maize production fields across management zones (MZs) in dryland and limited irrigation cropping systems, (ii) to study the effects of variable rate application of animal manure on selected surface soil quality parameters across MZs, (iii) to evaluate the variable rate application of manure using environmental risk assessment tools of N leaching and P runoff indices and to understand its impact on environmental quality, and (iv) to evaluate and compare the nitrogen (N) mineralization of variable rates of dairy cattle manure applied on low, medium and high MZs in a controlled environment. To accomplish objectives (i) through (iii), the study was conducted under a continuous maize cropping system on dryland and limited furrow-irrigated fields in northeastern Colorado, USA. For objective (iv), a 120 day laboratory incubation study was conducted. The results of this project indicated that using animal manure alone for maize grain yield production was economically inefficient using enterprise budget analysis. The study suggests that manure can, therefore, be used in conjunction with synthetic N fertilizer to meet crop N requirements at early growth of maize, while animal manure improve soil quality of low productivity soils over time. This can potentially help to limit the amount of N and P lost into the environment. For N mineralization, the study showed a significant difference (P≤0.05) in mineralized N across zones when dairy animal manure treatments were compared. However, N from animal manure does not mineralize differently between low, medium and high management zones. The key in precision manure management was to find a balance between economically, agronomically and environmentally sound manure management strategies across spatially variable soils.
Open Access
Pedological and ecological controls on biogenic silica cycling in grass dominated ecosystems
(Colorado State University. Libraries, 2009) Melzer-Drinnen, Susan E., author; Kelly, Eugene F., advisor
The biogeochemical behavior of silica is closely linked to the carbon cycle as marine Si-based diatoms are a major control on the distribution of silica in oceans, and play a major role in controlling atmospheric pCO2 via the "biological pump." The importance of biological controls on silica cycling in the terrestrial environment has only recently been known and our studies point to grasslands and grass dominated ecosystems as important repositories. Although the structure and ecological functioning of these ecosystems are strongly influenced by fire and grazing, the role of these key ecological drivers in the production and storage of Si represents a significant knowledge gap. Additionally, the effect of biogenic silica dissolution on the weathering of rock with different mineral assemblages is also insufficiently understood. I evaluated the effects of fire, grazing and parent material on the range and variability of plant derived biogenic silica stored in plant biomass and soils by sampling plants and soils in the mesic grasslands of North America and savannas of South Africa. Using these and other intensive study sites, along with extant productivity and soil texture data I estimated the global Si storage based on two approaches: "measure and multiply" and "paint by numbers".
Open Access
An NLR gene likely underlying RMES1 provides global sorghum resistance bolstered by RMES2
(Colorado State University. Libraries, 2023) VanGessel, Carl, author; Morris, Geoffrey, advisor; Nalam, Vamsi, committee member; Roberts, Robyn, committee member; Mason, Esten, committee member
Breeding for aphid host plant resistance in sorghum has been an area of interest since the emergence of Melanaphis sorghi in North America a decade ago. In order to develop durable sorghum aphid resistance, breeders must be equipped with tools (trait package) and knowledge (molecular mechanisms) of host plant resistance. In this dissertation, I characterize the current state of sorghum aphid breeding and propose a genotype to phenotype map for the major source of global resistance, Resistance to Melanaphis sorghi 1. Relying on near-isogenic lines, I demonstrate that RMES1 is applying selection pressure to sorghum aphid through reduction in fecundity that discriminates among aphid species. In global sorghum lines, RMES1 is rare whereas a second resistance source, RMES2, is common and present in historic breeding germplasm. I mapped RMES2 in Haitian breeding populations where it contributes fitness increases while lacking antagonistic pleiotropy and is selected for alongside RMES1. These results suggest breeding programs may unknowingly be deploying both sources of resistance which in combination are reducing the likelihood of M. sorghi biotype shifts to overcome RMES1. As aphid resistance may rely on phytochemical and/or induction with extended phenotypes regarding aphid populations, I used pan-genomic, transcriptomic, and metabolomic resources to describe the molecular mechanism of RMES1. Structural variation at the Chr06 locus underlies presence/absence variation of several nucleotide-binding leucine-rich repeat receptor (NLR) genes. Two of these candidate genes, SbPI276837.06G016400 and SbPI276837.06G016600, are representatives of two orthologous NLR groups which have genomic and transcriptomic evidence of underlying RMES1 resistance. The PAL branch of the salicylic acid pathway is the primary phytohormone pathway responsible for RMES1-induced resistance. Finally, metabolome reorganization mirroring transcriptome changes suggest RMES1 is inducing multiple downstream mechanisms responsible for reducing aphid fecundity. While the causal gene underlying RMES1 remains to be cloned and the eliciting aphid factor is unknown, this research suggests that gene-for-gene dynamics could lead to resistance-breaking biotype shifts and combining RMES1 with additional resistance genes e.g. RMES2, will help achieve durability.
Open Access
Metagenomic insights into microbial colonization & persistence in subsurface fractured shales
(Colorado State University. Libraries, 2023) Amundson, Kaela K., author; Wilkins, Michael J., advisor; Wrighton, Kelly C., committee member; Borch, Thomas, committee member; Ross, Matthew, committee member
Microorganisms are pervasive yet important components of hydraulically fractured shale systems. Subsurface shales harbor oil & gas and require unconventional techniques, such as hydraulic fracturing, to access these trapped hydrocarbons. Shale microbiomes are of crucial importance as they can directly impact the recovery of oil & gas and associated infrastructure. The overarching theme of this dissertation was to characterize the metabolisms and key traits that underpin the colonization and persistence of fractured shale microbiomes using a multi-omic approach to better understand the microbial impact on this important ecosystem. In Chapter 1, I first discuss the importance of subsurface shales as an important energy reserve, summarize what is known about microorganisms in these ecosystems, and highlight the strength of using a metagenomic approach to studying shale microbiomes. Subsurface shales are heterogeneous – varying in their mineral content, temperature, and other physiochemical conditions. The microbial communities that persist can have substantial impact on the fractured shale ecosystem and contribute to common challenges in hydrocarbon recovery such as corrosion, souring, and bioclogging. The literature review presented here highlights the need to study the functional potential of shale microbiomes as most studies have mostly focused solely on taxonomic composition of persisting microbial communities, and a vast majority of these studies have focused on samples from wells in the Appalachian Basin. However, functional potential of shale microbiomes across a variety of physiochemical conditions must be considered in order to gain an understanding of the role of microorganisms and what possible influences they may have on hydraulically fractured shales systems. Here, I highlight the need (1) to study the whole community at a functional scale and (2) apply a metagenomic approach to a variety of less characterized shale basins to gain a holistic understanding of shale microbiomes and the effects they may have on the broader ecosystem. In Chapter 2, I apply this metagenomic approach to study the persisting shale microbiomes of three fractured shale wells in the Anadarko Basin – a western shale basin characterized by elevated temperature and salinity. No studies using metagenomics had been applied to shale basins in the western United States prior to this research. We sampled five wells in the Anadarko basin over a timeseries >500 days and preformed NMR metabolomics and metagenomic sequencing to uncover the dominant metabolisms, community composition, and other functional traits of the Anadarko shale microbiome. This system was dominated by a fermentative microbial community and a less-abundant sub-community of inferred sulfate reducing microorganisms. Using paired NMR metabolomics and metagenomics, I demonstrated how many fermentative microorganisms have the potential to degrade common complex polymers, such as guar gum, and have potential to produce organic acids that may serve as electron donors for sulfate and thiosulfate reducing microorganisms. Thus, in this study I provided a framework for how carbon may move through the closed fractured shale ecosystem to sustain the microbial community. Finally, I investigated viral presence and diversity across all thirty-six metagenomes and found that inputs were large sources of viral diversity, but that only an extremely small proportion of viruses recovered from produced fluids were genetically similar to viruses previously reported from fractured shales. I observed that a majority of the dominant and persisting genomes encoded a CRISPR-Cas viral defense system, likely in response to the viral community. This highlights viral defense as another key trait for persisting microorganisms, as viruses are the only predators to bacteria and archaea in fractured shale ecosystems. Overall, this study expanded our knowledge of sulfate and thiosulfate reducing microorganisms in fractured shales, demonstrated the potential for common chemical inputs such as guar gum to be utilized by shale microbiomes, and highlighted how other key traits, such as CRISPR-Cas viral defense systems, may be a crucial trait for persisting shale microbiomes. Building on results from viral analyses in Chapter 2, in Chapter 3 I next sought to investigate the temporal dynamics between hosts and viruses to better understand the role of microbial defense against viruses in fractured shale ecosystems. To do this, I sampled six shale wells in the Denver-Julesburg Basin for >800 days, performed metagenomic sequencing, and identified host (bacterial & archaeal) and viral genomes from this data. I observed evidence of ongoing host defense to viral predation at both the community and genome-level through quantifying spacers from CRISPR arrays in metagenomic reads and MAGs. Through these analyses leveraging timeseries sampling and age differences between the shale wells, I provided evidence that suggested migration toward CRISPR arrays that may be more efficient at protecting the microbial host against a wider suite of viruses. Finally, I observed a temporal increase in host-viral co-existence in the closed, fractured shale ecosystem – suggesting the CRISPR defense does not entirely protect against viral predation. Chapter 4 ultimately leverages the approaches, insights, and data gained from Chapters 2 and 3 to study shale microbiomes at a cross-basin, geographic scale. Here, I collected samples from many collaborators who have previously worked in shale systems, performed metagenomic sequencing, and processed all samples in a standardized pipeline to build a comprehensive genomic shale database. In total, this database contains 978 unique MAGs and >7 million unique genes recovered from 209 metagenomic samples obtained from 36 fractured shale wells spanning eleven shale basins from North America, China, and the United Kingdom. In this chapter I analyze the functional potential of shale microbiomes at a genome-resolved level to better understand the geographic distribution of microbial metabolisms and other key traits that likely contribute to colonization and persistence of microorganisms. Here I also leveraged bioinformatic tools to build a custom annotation summary toolkit to process and analyze the large amount of sequencing data for traits of interest. The complete absence of a taxonomic core microbiome across shale basins illustrated in this chapter underscores the necessity of a genome-resolved and functional approach to studying shale microbiomes. Results from analyzing shale microbiomes at this scale could ultimately help to inform microbial management of fractured shale systems. The final chapter of this dissertation (Chapter 5) summarizes the key findings of my research into fractured shale microbiomes, and the mechanisms that may promote microbial colonization, persistence, and survival in these relatively harsh and economically relevant ecosystems. In this chapter I conclude this work by discussing future directions and lingering knowledge gaps for studying fractured shale microbiomes, as well as implications of these findings for other subsurface engineered ecosystems. Ultimately, this body of work contributes a substantial amount of new and informative insights into the functional potentials of persisting shale microbiomes across broad geographic scales.
Open Access
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.
Open Access
The effects of irrigation retirement on soil carbon dynamics of a continuous maize agroecosystem
(Colorado State University. Libraries, 2023) Mendoza-Martinez, Violeta, author; Schipanski, Meagan, advisor; Wrighton, Kelly, committee member; Prenni, Jessica, committee member
Over half of the world's fresh water is used in crop production and, in some key agricultural regions, use far exceeds local water availability and recharge rates. With the increasing strain on freshwater resources caused by climate change and a growing population, agriculture is under pressure to reduce its water consumption and large areas of currently irrigated farmland across the Western U.S. will likely transition into dryland agriculture over the coming decades. The effects this will have on global soil carbon (C) dynamics, however, remain unclear. In 2016, a study was established in Northern Colorado to understand how stopping irrigation affects soil C turnover in a no-till, continuous maize agroecosystem. Earlier results showed limited responses of the soil microbial community to irrigation retirement, but differences in soil heterotrophic respiration (Rh) rates were detected after two years of accumulated differences in plant residue inputs, thus suggesting a possible co-limitation of water and available C to the microbial community. We continued this experiment through 2022 to further explore the relationship between soil moisture and C inputs in shaping the soil microbial community under the new watering regimes and the consequential effects on soil respiration (Rs) as an indicator of soil organic C (SOC) turnover rates. Two seasons of data collection in 2021 and 2022 showed decreases in available soil water, bacteria, fungi, protozoa and actinomycetes fatty acid methyl ester (FAME) biomarkers, activities of four extracellular enzymes and soil autotrophic respiration in response to both reductions in irrigation and plant inputs, with strong interactive effects between the two factors. However, plots under dryland conditions had higher concentrations of dissolved organic carbon (DOC) and muted differences in soil Rh when compared to their irrigated counterparts; differences in Rh between fallow treatments with (YF) and without residue inputs (LTF), on the other hand, were more pronounced. Soil Rs in fallow plots was consistently, positively correlated with field soil temperature, while correlations with moisture were weak or even negative, thus suggesting soil moisture was not a strong direct driver of Rh. We investigated the direct and indirect influences of variables collected monthly across two seasons on soil Rh to test our hypothesized model using structural equation modeling. In contrast to the cumulative treatment level impacts of plant inputs and irrigation, monthly soil moisture measurements had a stronger, direct effect on Rh than substrate availability as estimated by water-extractable DOC. The final model only explained 24% of the variability in soil Rh. Changes in global C dynamics can be expected with transition of land areas from irrigated to dryland agriculture. However, focusing on soil health, resource conservation practices and the resiliency of the soil microbiome can be the key to minimize the potential negative impacts of this transition.
Open Access
Intercropping alfalfa with select grass species for increased yield and quality under deficit irrigation
(Colorado State University. Libraries, 2023) Doyle, Hunter, author; Brummer, Joe, advisor; Cabot, Perry, committee member; Ippolito, Jim, committee member
Drought and water scarcity have plagued the Western US for decades. As these issues become more prevalent, we must explore possibilities to utilize available water more efficiently. The objective of this study was to: Evaluate the ability of mixed and stripped intercropping alfalfa with grasses to increase yield and quality of the forage produced under deficit irrigation. Alfalfa (Medicago sativa) is the most common forage grown in the West and is known for its high-water use. Intercropping alfalfa with perennial grasses can potentially improve water use efficiency. Orchardgrass (Dactylis glomerata), meadow brome (Bromus biebersteinii), and tall fescue (Festuca arundinacea) were mixed on the same bed or strip intercropped on alternating beds with alfalfa under 100% and 60% ET irrigation regimes using subsurface drip irrigation. Three cuts occurred in 2021 and 2022, with deficit irrigation starting after cut one. Yield, crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), neutral detergent fiber digestibility (NDFD), and relative feed value (RFV) were analyzed in this study. During year one, irrigation did not have a significant impact on yield due to high precipitation and the fact that alfalfa performs well under deficit irrigation. Quality was not affected by irrigation treatments throughout both years of this study. Planting treatments significantly impacted yield and all quality parameters throughout this study. In 2021, mixed intercropping treatments averaged 14,210 kg ha-1, stripped treatments averaged 12,285 kg ha-1, and alfalfa averaged 13,406 kg ha-1; significant differences were not present. All mixed treatments, tall fescue stripped, and meadow brome stripped yields were similar to alfalfa in 2021. In 2021, quality was generally only reduced in mixed intercropping treatments compared to alfalfa in the first cutting. The inclusion of grasses with alfalfa reduced crude protein content and increased neutral detergent fiber content during cutting one, overall reducing quality. In cuttings two and three, mixed intercropping did not generally reduce quality. Stripped treatments also reduced quality in cutting one but did not have a large effect on quality in subsequent cuttings. Relative feed value, a common parameter used among producers, was similar among all treatments for all cuttings in 2021. In 2022, deficit irrigation had a significant impact on yield in cuttings two and three. Yields due to deficit irrigation were reduced by 22% and 35% in cuttings two and three, respectively. Total yearly yields were reduced by 12.5% between irrigation treatments. Total yields in mixed intercropping treatments were significantly higher than the alfalfa monoculture, especially the tall fescue and orchardgrass. Meadow brome generally had a higher yield than alfalfa, though not always significant. Mixed treatments averaged 13,308 kg ha-1 and stripped treatments averaged 9,488 kg ha-1 compared to alfalfa at 10,758 kg ha-1. Similar to 2021, quality was only reduced in intercropping treatments during the first cutting. Crude protein and RFV decreased while NDF and ADF increased in intercropping treatments compared to alfalfa alone, resulting in reduced quality. In subsequent cuttings, quality was generally similar among intercropping treatments and alfalfa alone. Mixed intercropping demonstrated to be more productive throughout both years of this study compared to stripped intercropping. Advantages from intercropping were reduced in stripped treatments due to independent cultivation and limited species interactions. Grass species did not have as large of an effect on yield and quality compared to intercropping method. Tall fescue typically performed the best of the grasses, yet all grasses in mixed intercropping performed well compared to alfalfa. Mixed intercropping grass with alfalfa can lead to increased yields with minimal effects on forage quality compared to alfalfa alone. As severe drought continues in areas across the Western US, mixed intercropping could be an option for maintaining or improving yields while producing similar forage quality compared to alfalfa alone under deficit irrigation.
Open Access
The influence of aeolian dust on the biogeochemical and physical characteristics of soils across three bioclimatic domains of the western U.S.
(Colorado State University. Libraries, 2023) Callen, Jessica, author; Kelly, Eugene, advisor; Melzer, Suellen, advisor; Butters, Gregory, committee member; Magloughlin, Jerry, committee member
This study investigates the impacts of dust generation and deposition on the biogeochemistry of soils in the western U.S., where aeolian processes are increasing due to climate change and human activities. Contemporary techniques for collecting and analyzing erosion and deposition were utilized at three locations (Moab, Niwot, CPER) to determine the amount and properties of dust present in three bioclimatic domains (Colorado Plateau, Rocky Mountains, Great Plains). The processes that contribute to the aggradation and degradation of the soil were assessed and used to determine the role of dust in the soil-forming processes at each site. These results indicate that the high amount of soil eroding at Moab (160 times more erosion than deposition) was causing a decrease in the soil volume and creating a loss of clay and plant essential nutrients within the surface horizon. For both Niwot and CPER, the soils were formerly in an aggrading phase but the measurements from soil erosion samplers at these sites indicate the contemporary system are now degrading. The chemical characteristics of deposited dust compared to the soil at Niwot suggest that the Southern Rocky Mountains are receiving dust from non-local sources, specifically Moab within the winter season. The results from CPER suggest deposition is from local dust generation. Based on these findings, it can be inferred that the impact of aeolian processes on the soils varies across bioclimatic domains.
Open Access
Phenotyping tools and genetic knowledge to facilitate breeding of dhurrin content and cyanogenic potential in sorghum
(Colorado State University. Libraries, 2023) Johnson, Kristen, author; Morris, Geoffrey, advisor; Mason, Esten, committee member; Prenni, Jessica, committee member
Cyanogenic glucosides are important secondary compounds found in plants serving roles such as plant defense, pollinator attraction, nitrogen (N) sources, and drought tolerance. Sorghum (S. bicolor [L.] Moench), an important grain crop predominantly grown in drought-prone environments, contains a cyanogenic glucoside known as dhurrin where it functions as a source of hydrogen cyanide (HCN) after the leaf tissue is disrupted. Dhurrin has been hypothesized to serve as an osmoprotectant, N turnover source, and sorghum aphid resistance mechanism. In addition, dhurrin concentrations can vary due to growth stage, environment, and genotype, and this variability can cause limitations for effective dhurrin phenotyping. To facilitate the breeding of dhurrin and HCNp, we developed a semi-quantitative phenotyping method to detect HCNp and investigated the genetics of dhurrin and HCN variation in global sorghum germplasm. In the first study, we developed a simple, semi-quantitative, high-throughput phenotyping method to detect HCNp in sorghum leaf tissue. Biochemical methods have been used to determine dhurrin content quantitatively, however these methods are laborious and costly. As a result, we developed a semi-quantitative phenotypic assay using commercial test strip paper to measure HCNp utilizing a F13 Stg Recombinant Inbred Line (RIL) population with previously reported dhurrin concentrations. We found that later sampling time improved the detection of HCNp variation with broad-sense heritability (H2) values highest at flowering. In addition, we found that other covariates such as leaf number may play a role in effective phenotyping. Altogether this assay can be used to screen a sorghum breeding population in both a greenhouse and field setting for smallholder breeding programs looking to advance their breeding generations more efficiently. In the second study we sought to understand the genetics underlying HCN and dhurrin variability, as well as investigate the relationship between drought and dhurrin using diverse sorghum landraces. We found no direct correlation between dhurrin and drought, but the slight positive correlation could suggest other environmental factors, such as pest pressures, are driving HCN and dhurrin variation. To further understand the biological relationship between dhurrin and HCN, we conducted a genome-wide association study (GWAS) for HCNp and dhurrin. We identified several significant associations between HCNp and known dhurrin biosynthetic and catabolic genetic markers, but major biosynthesis loci were not all significantly associated with HCNp. In addition, we performed a GWAS on dhurrin and found peaks associated with the dhurrin biosynthetic gene cluster, as well as other unknown loci that could contribute to dhurrin variation. This suggests that genetic variation for genes in the dhurrin biosynthesis, catabolism, and recycling pathway contributes to HCNp variability, and they are not direct proxies for each other. As a result, breeders should de-couple phenotyping methods for dhurrin and HCNp depending on the trait of interest.
Open Access
Unlocking sorghum adaptive potential through investigations into pleiotropic control of chilling tolerance by Tannin1
(Colorado State University. Libraries, 2023) Schuh, Anthony, author; Morris, Geoffrey, advisor; Argueso, Cristiana, committee member; Wrighton, Kelly, committee member
Chilling tolerant crops can positively impact agricultural sustainability through lengthened growing seasons and improved water and nitrogen use efficiency. In sorghum (Sorghum bicolor [L.] Moench), the fourth most grown grain, coinheritance of qSbCT04.62, the largest effect chilling tolerance locus, with Tannin1, the major gene underlying undesirable grain proanthocyanidins, has stymied breeding for chilling tolerance. To investigate the genetic basis of qSbCT04.62, including its coinheritance with Tan1, we developed near isogenic lines (NILs) with chilling tolerant haplotypes around qCT04.62. In the first study we genotype the NILs and investigate the introgressions physiological control over the cold stress response. Genome sequencing revealed that the CT04.62+ NILs introgressions on chr04 include Tannin1, a homolog of Arabidopsis cold regulator CBF, peak SNPs for qCT04.62 from multi-family NAM, and 61.2-62 Mb of HKZ ✕ BTx623 NAM family qCT04.62 confidence interval. Grain tannins were correlated with Tan1 genotype, revealing heterogeneity in one NIL at Tannin1. Controlled environment chilling assays found no genotype by environment interaction on growth by chilling per se in parents or NILs. Cold germination was reduced at 15°C and superior at 20 and 25°C in the chilling tolerant parent compared to chilling sensitive, but unchanged between NILs. The introgression also did not regulate a chilling induced increase in non-photochemical quenching. In the second study we investigated Tan1 function with a transcriptome analysis of the NIL's response to chilling stress. Tannin1 was widely expressed in sorghum tissues but did not promote a transcriptional response in chilling tolerance related molecular pathways including lipid remodeling, phytohormone signaling, CBF upregulation, photoprotection, and ROS mitigation. GO analysis also found no significant term enrichments at the p < 0.1 threshold. Only 17 genes had expression patterns regulated by polymorphisms in the introgressions, seven cis, and ten trans, with little evidence of co-regulation. Further, Tannin1 was functionally divergent from its Arabidopsis ortholog TTG1 and other WD40 orthologs in regulating leaf anthocyanin biosynthesis. Overall, these findings suggest that linkage, not pleiotropy, underpins the coinheritance of Tan1 and CT04.62+, unlocking the use of CT04.62+ for sorghum improvement. Further, these results imply a lack of deleterious fitness effects of tan1 alleles in commercial grain sorghum varieties and suggest the possibility of an unknown cold tolerance regulator which, if identified, could have implications for crop improvement of chilling tolerance outside sorghum.
Embargo
Innovative tools for maize water use assessment
(Colorado State University. Libraries, 2023) Capurro, Maria Cristina, author; Andales, Allan A., advisor; Ham, Jay M., advisor; Comas, Louise, committee member; Chávez, José L., committee member
Modern agriculture is facing a scenario of decreased water availability and sustainability concerns. Accurate estimation of crop transpiration is crucial to improve agricultural water management. However, transpiration estimation is challenging due to the difficulty in modeling canopy conductance (gc). There is currently no standardized approach for the calculation of gc. Additionally, direct measurements of gc and transpiration at the field scale are difficult. There are few commercially available sensors that measure transpiration, and those available are expensive. For gc, most of the equipment available use manual or indirect approaches. Meanwhile, during the past years there has been a dramatic development of sensor technology and communications. The expansion of low-cost circuit boards and 3D printing development and the Internet of Things (IoT) has led to a decrease in the cost of sensors and facilitated data acquisition and fabrication of research-grade instruments. The purpose of this study was to develop low-cost tools to measure actual crop transpiration and gc and contribute to the improvement of water use estimation in irrigated fields. We developed two types of IoT plant-based devices using 3D-printing and low-cost electronics and sensors: a sap flow gauge (SFG) and an artificial reference surface (ARS) system. We developed a new theory for a heat pulse method for calculation of transpiration rate that was coupled with a new type of sap flow gauge. The gauge is easy to build and adaptable to a range of stem sizes. We calibrated and validated the sensors in maize (Zea mays L.) plants in the greenhouse and tested them in a well-watered maize field in two locations in northern Colorado, for two years. The sap flow sensors calibration coefficient and standard deviation (SD) was 1.28 g/h ± 0.2, used to convert heat velocity to transpiration flow. A higher calibration coefficient was found in 2019 when a longer heating time was applied, confirming that the coefficient takes into account wounding effects on the plant. The data collected allowed the calculation of the maize transpiration every 15 minutes and showed that they were in good agreement with estimated transpiration from plants on weighing scales from greenhouse studies, from field measurements with commercially available sap flow gauges and with estimations with the Penman-Monteith (PM) approach in field conditions. Daily transpiration from SFGs compared with measured values in the greenhouse had a root mean squared error (RMSE) of 15.4% and a mean absolute error (MAE) of 12.1% of the mean T value in 2020. In 2019 the RMSE was 12.4% and the MAE was 10.2% from the mean T value. In field conditions, when SFGs were compared to daily transpiration estimates using the PM approach, the RMSE and MAE were 0.70 mm and 0.56 mm, a 13.2% and 11% error, respectively. When compared to commercially available SFGs, the RMSE and MAE were 0.66 mm and 0.54 mm (12.4% and 10.2% from the mean T value), respectively. In 2020, daily transpiration estimation in the field with the developed SFGs had a precision of ±1.04 mm SD and when compared to the PM approach had an RMSE and MAE of 0.62 mm and 0.48 mm, respectively (both were within 10% of mean transpiration). Results also showed that error in estimations decrease with additional sensors deployed in the field. More than 4 sensors should be deployed in the field to obtain estimations of corn transpiration with less than 20% error. The required number of gauges varies according to the accuracy desired for transpiration measurements. The ability of the sap flow sensors to measure plant transpiration directly make them powerful tools for multiple applications. They can capture the effects of the environment and characteristics of the plant. Therefore, they are valuable for assessing the partitioning of total crop evapotranspiration (ETc) into plant transpiration and soil evaporation. They can be used for local basal crop coefficient estimations and for fine-tuning local irrigation applications. They can also provide valuable information for ground-truthing complex multi-layer models and simulations that aim to estimate actual transpiration from the field. The use of the sap flow sensors for site-specific basal crop coefficients (Kcb) derivation was tested. Locally derived Kcb values from Trout and DeJonge (2018) for maize was verified using our low-cost sap flow sensors for a period of 22 days in 2020 and for a period of 17 days in 2019. The period was divided into mid-season, beginning of late-season and end late-season. Mean Kcb values from SFGs for mid-season and beginning of late season agreed with those from Trout and DeJonge (2018). Locally derived Kcb was 1.05 and 0.82, while Kcb from SFGs were 1.08 and 1.06 for mid-season during 2019 and 2020 and 0.82 for beginning of late season in 2020. However, end of late-period Kcb from sap flow data in 2020 was higher than the tabulated value (0.62 vs 0.4). This was probably due to the fixed end-of-cycle-date for the maize growing season in contrast to variable growing degree days. This approach is especially useful for low budget and rapid evaluations. We described the advantages of using Kcb curves for estimation of crop water requirements and highlight the benefits of using sap flow gauges for its derivation. The second device was an ARS that consisted of a plastic hemispherical surface that allowed monitoring of dry leaf temperature. This temperature was used to estimate actual maize transpiration, gc and to detect and monitor water stress in field conditions. The hemispherical ARS closely mimicked the temperature of non-transpiring leaves (R2=0.99) in a field study conducted in 2020 at Fort Collins, CO. Actual maize transpiration was adequately estimated for a 14-day period using the thermal approach with the ARS temperature. Comparisons with transpiration calculated from SFGs and the ASCE standardized tall reference ET (ASCE, 2005) with local basal crop coefficient (Kcb) values for maize showed a root mean square error (RMSE) of 0.61 mm and margin of error (ME) of 0.53 mm, representing a 12% and a 10% error of the method in relation to the Penman-Monteith approach and a RMSE and ME of 0.78 mm and 0.73 mm in relation to actual maize transpiration from SFGs. Differences from the total transpiration were within 7.5%. Absolute hourly values of gc were also calculated with this approach during the daytime, showing a pattern and values similar to the conductance derived from the SFGs for a 6-day period. However, underestimations were observed at the beginning and end of the day. When mean mid-day values of gc were compared to sap flow measurements, the MAE and RMSE were 0.51 mm/s. and 0.72 mm/s, representing 8.1% and 11.6% error, respectively. The method was also tested in a deficit-irrigated maize field, showing a reduction in transpiration and in gc due to soil water depletion and demonstrating the sensitivity of the method to detect water stress in the field. However, transpiration values were severely underestimated due to the similarity of the temperatures from the ARS and canopy. Changing the color of the ARS might reduce these errors. Results suggest that a darker color should be used. A simple thermal method for water stress detection was also tested. Its strong correlation with gc (R2=0.7) demonstrated that it could be a method to detect the onset and development of plant water stress in the field. The use of the dry ARS could be a practical approach for maize transpiration, gc and water stress estimation since it requires less weather data. Its simplicity of fabrication, implementation, and low requirements for maintenance during the season are also valuable advantages of the method. We were able to develop versatile low-cost IoT tools for real time monitoring of crop transpiration and gc. These tools can be used for multiple purposes and have the potential to improve our ability to estimate maize crop water requirements.
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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.
Open Access
Parent material-topographic-management controls on organic and inorganic nutrients in semiarid soils
(Colorado State University. Libraries, 1984) Aguilar, Richard, author; Heil, Robert D., advisor; Barbarick, K. A., committee member; Schumm, S. A., committee member; Franklin, W. T., committee member
Paired native grassland and cultivated landscapes were characterized to evaluate parent material and topographic controls on organic matter and phosphorus along catenary sequences in southwestern North Dakota. Site selection was based on parent material (sandstone, siltstone, and shale residuum), similar cropping history (44-yr wheat-fallow rotation), and uniform range management. Parent material-soil process relationships were established by evaluating chemical and physical data for soil profiles at the native-summit landscape segments on the three contrasting parent materials. The effects of topography on the amounts and vertical distribution of organic matter and phosphorus were evaluated by studying soil profiles at various geomorphic landscape components along the catenas. The effects of 44 years of cultivation were evaluated by comparing cultivated and virgin soils at each landscape segment using the soils on native pasture as benchmarks. The finer textured soils weathered in shale were found to have much higher levels of organic C, N and Total P. Soils weathered in sandstone were found to have more uniform decreases in organic matter with profile depth and the highest quantities of organic P. On the native pastures, quantities of organic matter were much higher in the lower landscape segments because of higher moisture contents and/or the deposition of organic matter-enriched soil. Soils at lower landscape segments (lower backslopes, footslopes) have been enriched with Total P at the expense of soils at the upper portions of the catenas. Changes in organic and inorganic soil constituents resulting from cultivation were found to vary as a function of parent material and topography. Mineralization losses of organic constituents appear to have been higher in the sandstone soils. The fine-textured shale soils, which appear to have a large proportion of highly humified, clay associated organic matter, lost the lowest quantities of organic constituents relative to total soil loss. Losses of organic matter were generally lower at the lower landscape segments in all three sites, reflecting soil deposition. Redistribution of soil material by both mechanical (tillage practices) and natural processes (wind and water erosion) must be considered when evaluating cultivation-induced changes in soil properties along catenary sequences.
Open Access
Utilizing plant genetic resources for pre-breeding of water-efficient sorghum: genetics of the limited transpiration trait
(Colorado State University. Libraries, 2022) Cerimele, Gina, author; Morris, Geoffrey, advisor; Cotrufo, Francesca, committee member; McKay, John, committee member
Shifting precipitation patterns driven by the changing climate threaten productivity of dryland agricultural systems. Increasing the efficiency of water use by crops grown in dryland regions, such as sorghum (Sorghum bicolor), is a target for plant breeding to address this issue. c variants conferring efficient water use in sorghum may be found within collections of plant genetic resources (PGR). However, tropical sorghum PGR require adaptation to the target temperate environment to begin the pre-breeding trait discovery process. The landmark Sorghum Conversion Program unlocked diverse sorghum genetics for temperate breeding by adapting tropical African lines to temperate height and maturity standards. In the U.S. Sorghum Belt, spanning South Dakota to central Texas, the limited transpiration (LT) trait could provide growers a 5% yield increase in water-limited conditions with high vapor pressure deficit (VPD) according to crop modeling. To transfer the LT trait into commercial breeding programs, an elite donor line must be developed. Characterizing the genetic architecture of LT informs markers and breeding strategy for development of an elite donor. To characterize the genetic architecture of LT, two biparental recombinant inbred line (RIL) mapping families were developed from crossing putative LT parents SC979 and BTx2752 by putative non-LT parent RTx430. For this study, the families were grown together as a mapping population in three locations (continental-humid eastern Kansas, semi-arid western Kansas, and semi-arid Colorado) in one year. The families were phenotyped for the LT trait using UAS- collected thermal imaging and canopy temperature as a proxy. The families were initially designed with the goal of controlling phenotypic covariates of canopy temperature associated with height and flowering time, like neighbor-shading and artifactual temperature inflation related to panicle imaging. To test whether the family design controlled for height and flowering time covariates, the populations were phenotyped for both traits. High broad-sense heritability (H2) > 0.86 for all traits and families across locations indicates that the traits are not fixed. However, phenotypic distributions reveal that most lines are within an agronomically-relevant range that limits confounding covariates. Using DArTseq-LD genotyping data, GWAS analyses of height and flowering time reveal putatively significant marker-trait associations (MTA) with known loci underlying height and maturity in sorghum. These results collectively indicate that, while genetic variation for height and flowering exist in the LT mapping families, the resulting phenotypes are homogeneous enough to be suitable for LT genetic mapping. To test hypotheses on the monogenic, oligogenic, or polygenic architecture of the LT trait, canopy temperature data collected by the UAS-thermal imaging missions was used. Non-zero H2 of canopy temperature in most location-timepoints indicates genetic variation is present for LT in the population. Continuous phenotypic distributions imply a quantitative architecture. GWAS analyses revealed moderate marker-trait association peaks visible within timepoints and across locations, indicating oligogenic architecture of LT. Some of those peaks also colocalize with sorghum homologs of aquaporin genes in Arabidopsis thaliana, suggesting that aquaporin variation could be a molecular basis underlying the trait. These results provide a basis for marker-assisted selection in developing an LT donor line.
Open Access
Alfalfa water use under deficit irrigation for farm savings
(Colorado State University. Libraries, 2022) Sitterson, Jan, author; Andales, Allan A., advisor; Mooney, Daniel F., committee member; Brummer, Joe E., committee member
Colorado water law allows for water rights to be leased between agriculture and municipality users. Decreasing the consumptive use (CU) of agricultural land while maintaining profits and yields will allow farmers to lease their water rights for revenue. Deficit irrigation is a water-saving approach to avoid the complete dry up of irrigated farmland while providing profitable yields and monetary gains from water transfers. To maximize water savings, efficient irrigation systems such as subsurface drip irrigation (SDI) are used to prevent water losses from soil evaporation. This study evaluated the feasibility of using SDI with deficit irrigation practices to grow alfalfa (Medicago Sativa L.) at production scale in northeast Colorado (2018 – 2022). Alfalfa was found to have good potential for decreasing CU due to its drought tolerance, multiple harvests per season, and improved quality of hay with less irrigation water. The Water Irrigation Scheduler for Efficient Application (WISE) model was also found to be a useful tool for estimating CU of deficit irrigated alfalfa and the regrowth phases after multiple harvests in a growing season. Mid-season corrections of the soil water deficit in WISE improved the accuracy of modeled CU. Overall the water savings from deficit irrigation at low, medium, and high irrigation levels with an SDI system can be profitable when prices for leasing water exceed hay prices per unit area of production.
Open Access
The effects of soil structure on soil organic matter: a mechanistic approach
(Colorado State University. Libraries, 2022) Even, Rebecca, author; Cotrufo, M. Francesca, advisor; Conant, Richard, committee member; Paustian, Keith, committee member
Two key factors theorized to affect soil organic carbon (SOC) dynamics are type of plant carbon (C) inputs and soil structure (i.e., soil aggregation), both are influenced by management practices and are considerably intertwined. Research surrounding these factors has increased in the last several decades as the threat of climate change has forced policy makers to find natural based solutions to rising CO2 levels in Earth's atmosphere. Given that soil acts as the largest terrestrial C pool but has lost substantial amounts of C due to land use change and unsustainable agriculture, focus has shifted towards identifying better ways to manage arable lands that improve SOC storage. Among the conventional management practices tillage is likely the most studied, because of its damage to soil structure, leading to soil C losses. However, while research centered on tillage effects on soil aggregation and SOC cycling is vast, few studies explore how plant C input type (i.e., soluble versus structural) and disturbance (i.e., tilling) together affects SOC in soils with different degrees of aggregation. We examined the effects of soil texture, disturbance, and plant input type on soil aggregation, C mineralization, and formation and persistence of plant input-derived SOC to better understand the mechanisms by which soil aggregates help form and protect SOC, specifically as particulate and mineral associated organic carbon (POC and MAOC). POC and MAOC are expected to be formed by distinct pathways, respectively from structural and soluble inputs. Because of their different mechanisms of protection, POC and MAOC are also expected to respond differently to plant inputs and management practices, like tilling, that disturb soil aggregates. We aimed to parse the formation and persistence of POC and MAOC by adding 13C labeled plant residue separated into soluble and structural plant constituents to determine how these physically distinct plant compounds contribute to either pool when soil is intact or disturbed. In an in-lab incubation using 13C enrichment, we traced SOC over the course of one year in a factorial design with four factors: soil type*disturbance*plant input*harvest. Our results showed, as expected, that hot-water extractable (HWE) plant inputs contributed substantially to MAOC while structural plant components (SPC) inputs preferentially formed POC. Interestingly, we found that disturbance resulted in less HWE mineralized to CO2 and more MAOC formation in the highly aggregated (HA) soil suggesting that increased mineral surface area caused more efficient dissolved OM sorption. Moreover, HWE-derived MAOC persisted in both the undisturbed (U) and disturbed (D) HA soils but not in low aggregation (LA) soils, indicating that persistence of MAOC is dependent on soil type and aggregation (i.e., soil physical structure). Although we did not observe significant differences in aggregate-occluded POC (oPOC) formation between HAD and LAD soils, we did see higher oPOC persistence in HAD soil compared to LAD soil. Greater accumulation oPOC in HAD from day 22 to the end of the incubation suggests, again, that soil type influences the persistence of POC through occlusion in aggregates. To corroborate this, we also found that LAD soil had the highest CO2 mineralization of SPC plant inputs as SPC was left more unprotected in the soil with a low capacity to aggregate. Disturbance did not affect microbial biomass in either HA or LA soils. We saw more plant-derived microbial biomass C from HWE inputs compared to SPC inputs in the bulk soil, indicating that HWE inputs are assimilated into microbial biomass, thus incorporated into SOC with higher efficiency. Lastly, there was a significant drop in % plant-derived microbial biomass C in the bulk soil overtime, as expected. However, because the % HWE-derived MAOC persisted in HA soils regardless of disturbance, we illustrated the importance of microbial necromass in addition to direct DOC sorption for SOC stabilization as MAOC. Overall, my study provides mechanistic understanding for the role of soil structure and aggregation on POC and MAOC formation and persistence which can help improve the representation of these processes in models, to provide better predictions of SOC changes with changes in management practices affecting disturbance.
Open Access
Putting microbial polyphenol metabolism on the map: using microbiome science to revise soil chemical paradigms
(Colorado State University. Libraries, 2022) McGivern, Bridget B., author; Wrighton, Kelly C., advisor; Hagerman, Ann, committee member; Borch, Thomas, committee member; Prenni, Jessica, committee member; Wilkins, Michael J., committee member
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