- ItemOpen AccessSoil 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 memberOur 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.
- ItemOpen AccessThe 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 memberOver 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.
- ItemOpen AccessIntercropping 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 memberDrought 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.
- ItemOpen AccessThe 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 memberThis 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.
- ItemOpen AccessPhenotyping 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 memberCyanogenic 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.