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Browsing by Author "Fonte, Steven J., advisor"

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    Cover crops for ecological management of U.S. agricultural systems: quantifying ecosystem services across multiple scales
    (Colorado State University. Libraries, 2023) Eash, Lisa, author; Fonte, Steven J., advisor; Schipanski, Meagan E., committee member; Trivedi, Pankaj, committee member; Mooney, Daniel, committee member
    Managing agricultural systems to provide multiple ecosystem services (ES) beyond food provisioning has gained considerable attention in recent years. The integration of cover crops (CC) into U.S. cropping systems presents an opportunity to support multifunctional agricultural systems, which alleviate negative environmental impacts of agriculture, mitigate greenhouse gas (GHG) emissions and support sustained crop production. However, CC impacts on these ES are variable and depend on management and site characteristics, contributing to uncertainty surrounding to what extent CC can improve ES. Reducing this uncertainty is critical to both identify appropriate environmental and management conditions for CC adoption and improve the estimated potential for CC to improve multifunctionality of U.S. cropping systems. This dissertation aims to quantify CC impacts on ES at multiple scales, exploring benefits to the soil microbiome, at the farm level, and nationally. Throughout this assessment I explore how these effects are influenced by climate and soil characteristics and how management can be leveraged to optimize the provision of ES. Chapter two estimates the potential for widespread adoption of CC to increase soil organic carbon (C) stocks and mitigate GHG emissions in the U.S. Analysis using current U.S. crop management data and a biogeochemical model revealed that the mitigation potential over a 20 year period is lower than previous estimates due to regional variability, decreasing rates of C accrual over time, and limited CC integration. Changes in N2O emissions did not offset C sequestration but introduced large uncertainty surrounding total national mitigation potential. Soil C gains due to CC offer important co-benefits to U.S. cropping systems, but the contribution of CC to achieving U.S. emissions targets will likely be lower than previously anticipated. Our spatially-explicit analysis also highlights regions where adoption of CC can have greater relative contributions to GHG mitigation. I then quantify a larger suite of ES in dryland wheat systems of the semi-arid western U.S., a particularly challenging context for CC due to lower potential productivity and associated economic trade-offs. I used two existing field trials to monitor CC impacts on soil health, cash crop productivity, and economics over a period of six years. No-till, CC planting window, and the sale of CC biomass as forage were also explored as strategies to optimize ES provision and economic viability. Chapters three and four demonstrate that the integration of CC amidst water limitations can benefit erosion control and soil structure, but also present significant productivity and economic trade-offs. The integration of fall-planted CC, no-till management, and the use of CC for forage provided the greatest potential for maximizing ES benefits in an economically viable manner. In Chapter five, I conducted a greenhouse study to examine the impact of CC type and functional diversity on microbial community composition and associated ES. Plant functional types (Poaceae, Brassicaceae, and Fabaceae) were associated with distinct increases in ES proxies, which appear to be mediated by shifts in microbial community composition. Specifically, Fabaceae (legume) CC enhanced the presence of copiotrophic microbes, which were associated with improvements in soil structure and high enzyme activity, a proxy for nutrient cycling. Poaceae and Brassicaceae led to improvements in microbial diversity. Ecosystem service benefits and microbial community shifts were conserved in diverse CC mixtures, contributing to increased multifunctionality. Across studies and scales, CC were observed to support a number of ES that address environmental concerns resulting from modern intensive agricultural practices. However, slight benefits and substantial productivity trade-offs in water-limited systems may limit the extent to which CC can mitigate GHG emissions and restore soil C reserves nationally. Management choices, such as CC composition and diversity, no-till management, and the sale of a portion of CC biomass as forage, can be leveraged to optimize the provision of ES in an economically viable manner. Overall, CC effectively contribute to multifunctional agroecosystems whose ES extend beyond food provisioning.
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    Evaluation of spring wheat genotypic response to soil health promoting management practices
    (Colorado State University. Libraries, 2017) Junaidi, Fnu, author; Fonte, Steven J., advisor; Byrne, Patrick F., committee member; Paschke, Mark W., committee member
    Growing efforts to restore soil organic matter and overall soil health are likely to enhance soil biological communities and promote positive interactions between plants and soil communities. However, modern genotypes bred under intensive management practices may not be able to benefit fully from soil health promoting practices if they have lost their ability to effectively interact with key soil organisms. The purpose of this study was to explore this idea by studying how spring wheat genotypes with different breeding contexts and histories respond to improved soil health achieved via additions of organic matter and soil fauna. A greenhouse experiment with a full factorial complete randomized design was carried out at Colorado State University, Fort Collins, between June and November, 2016. The treatment factors included spring wheat genotype, as well as compost and earthworm additions. The genotypes included a wild ancestor of wheat, Aegilops tauschii, two older genotypes of spring wheat, Gypsum and Red Fife, and two near-isogenic modern genotypes, Scholar Rht2M and Scholar Rht2W, that differ only by the presence of the semi-dwarf allele Rht-D1b in ScholarRht2M. Each wheat genotype was grown in rootboxes (24.5 x 3.5 x 38.0 cm) that received either soils amended with composted manure or not, and with or without the addition of earthworms (two Aporrectodea caliginosa per box). Measurements included plant growth (heading date, number of tillers), biomass (aboveground and root biomass, root:shoot ratio), root morphology (root length and diameter), yield-related traits (number of seeds, seeds weight, average weight per seed, harvest index), nitrogen content (vegetative aboveground and grains), and nitrogen uptake. Findings indicate that interactions between genotypes and soil treatments were inconsistent, and the original hypothesis, that older wheat genotypes would show a greater response to improved soil biological conditions relative to newer genotypes, was not well supported. Overall, the aboveground and yield responses to compost were small compared to the root responses. Composted manure additions, increased root length, biomass, and diameter only in the wild accession (Ae. tauschii) and older Gypsum wheat variety. Modern genotypes, on the other hand, exhibited little root trait plasticity except in root diameter, which decreased with compost additions. Except for a decrease observed in Red Fife, compost effects on aboveground biomass were not significant for most genotypes. Genotype x earthworm interactions were only observed in the vegetative biomass N uptake, and earthworm effects in general were low due to low survival of the earthworms. Ae. tauschii and Gypsum had a more positive response to compost addition for both aboveground and root biomass, indicating that these genotypes may better take advantage of soil health promoting practices. While Gypsum had a similar response to the wild accession when compost was added, Red Fife tended to respond more like the modern genotypes. Overall, my findings suggest that different wheat genotypes can respond distinctly to changes in soil management and biological activity. Only a few genotypes were tested, but a number of clear genotype x soil biology interactions highlights the importance of considering soil management practices, environmental context, and breeding history for different wheat lines, so that we can better manage plant x soil interactions.
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    Exploring the role of planned and unplanned biodiversity in the soil health of agroecosystems
    (Colorado State University. Libraries, 2021) Kelly, Courtland, author; Fonte, Steven J., advisor; Schipanski, Meagan E., committee member; Wallenstein, Matthew, committee member; Hall, Ed, committee member
    To view the abstract, please see the full text of the document.
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    Factors contributing to maize and bean yield gaps in Central America vary with site and agroecological context
    (Colorado State University. Libraries, 2018) Eash, Lisa, author; Fonte, Steven J., advisor; Khosla, Raj, committee member; Davis, Jessica G., committee member
    In Central America, the population and associated food demands are rising rapidly, while yields of their staple crops, maize and beans, remain low in a global context. To identify the main limiting factors to crop production in the region, field trials were established in six priority maize- and bean-producing regions in Guatemala, Honduras and El Salvador. Potential yield-limiting factors were evaluated in the 2017 growing season and included: nutrient management, irrigation, planting arrangement, and/or pest and disease control. When considering all sites, improved fertilization and pest and disease control significantly improved yields in maize by 11% and 16% respectively, but did not have a significant overall effect in beans. Irrigation had no effect in the year studied, due to sufficient and evenly distributed rainfall over the growing season. Optimized planting arrangement resulted in an average 18% increase in maize yield overall, making it the most promising factor evaluated in this study. However, the effectiveness of each factor varied across sites and no factor was effective at increasing yield consistently across all sites. Increased production was not always associated with net economic gains due to the relatively high costs of inputs and technology in the region. The study demonstrated that production constraints are highly dependent on local management practices and agroecological context. Therefore, public and private development efforts that seek to increase production should seek to identify site-specific limitations pertinent to each area in question.
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    Feeding the soil to feed the planet: soil health outcomes from novel amendments to residue management
    (Colorado State University. Libraries, 2021) Olayemi, Oladapo Peter, author; Wallenstein, Matthew D., advisor; Fonte, Steven J., advisor; Schipanski, Meagan M., committee member; Trivedi, Pankaj T., committee member; Conant, Richard T., committee member
    Healthy soils are the foundation for the continued capacity of agricultural lands to supply essential ecosystem services while also meeting demands for food, fuel and fiber. From academia to policymakers and other key stakeholders, attention towards soil health continues to rise due to global environmental challenges such as climate change and food security that can be potentially mitigated through the sustainable and innovative management of soils. Specifically, the application of organic inputs including composts and animal manures can help enhance water holding capacity, organic matter accumulation and crop production. However, the heterogeneous nature of soils and diversity of production systems precludes a single ‘silver bullet' solution to optimize soil health. In addition, outstanding questions persist on the differences in spatiotemporal effects of different organic inputs and their application frequency as well as the linkages between different soil health properties. This dissertation examines soil health under two different organic input management regimes including a novel soil amendment derived from cheese manufacturing as well as corn residue management in semi-arid agroecosystems. Both the novel soil amendment and corn residue management approaches were established with the goal of conserving soil water in these water limited systems. The novel soil amendment approach involved the one-time, direct application of a byproduct from cheese production known as lactobionate (LB) to soils through an agronomic trial irrigated with wheat and corn. I found that LB applied to soils increased the water retention capacity as well as the microbial biomass content of soils in the 5-15 cm soil zone under the wheat trial. I also found a non-statistically significant 14% increase in corn yield for LB-amended plots. However, I did not observe any difference in wheat yield and some soil properties (soil pH, soil carbon (C), soil nitrogen (N), and soil ammonium concentration for both trials) with lactobionate addition. My observations suggest the potential for lactobionate to modify soil water content, microbial biomass, nitrate, and yield but outcomes varied by crop trial and amendment rates. This implies that while recycling industrial food processing waste for use as a soil amendment may have benefits for key soil properties, the timing, mode and application rate need to be optimized for maximal effects on soil properties. Due to the effect of LB on soil health observed in the field trials, I conducted an 84-day laboratory incubation experiment to understand specific mechanisms of how LB influences soil organic matter (SOM) decomposition and accumulation via different SOM fractions. I collected soils from the field and split them to add 13C lactobionate to some soils and water only to other soils. I found that about 53% of added lactobionate was respired over 84 days, and observed a positive priming effect after 14 days. In response to LB addition, the total C content of the water extractable organic matter (WEOM) fraction increased by 100% at the initial stage of the incubation but declined exponentially and quicker than other SOM fractions. In addition, the total C content of the light-fraction particulate organic matter (LF-POM) fraction also declined, while both the sand-sized POM and mineral-associated organic (MAOM) C fractions strongly increased relative to unamended control. My results suggest that while lactobionate can help improve soil water retention, it also presents an avenue to building more persistent C through its impacts on the internal cycling of SOM fractions and more importantly on the mineral-associated organic matter fraction considered more relevant to SOC long-term persistence and relative resilience to disturbance. The corn residue management study included a four-treatment combination of residue management (residue retained versus residue harvested) and tillage (no-tillage versus conventional tillage) implemented in the field consistently for 6 years, in contrast to the one-time application of lactobionate. My results showed that the most significant differences across soil properties measured were more apparent at the 0-10 cm zone and were mainly driven by residue retention with minor tillage effects. Regardless of tillage mode employed, retaining residues in the 0-10 cm soil layer led to higher soil water content, soil C, aggregate stability, available phosphate, soil macrofauna and fungal abundance and diversity. Furthermore, residue retention was the main driver of macrofauna and microbial community composition; however, an interaction between tillage and residue management suggested that the effect of tillage on microbial communities was most pronounced when residues were retained. I also found significant covariation between soil physicochemical, macrofauna and microbial datasets, indicating a strong association between different soil properties and cascading effects of management on multiple soil properties. Overall, my findings suggest the impact of both novel amendment and corn residue inputs on soil health varied with application strategy, as the corn residues applied consistently for 6 years had a stronger effect on soil health in the top layer of soils (0 – 15 cm) as compared to lactobionate which was applied one-time. Certain soil properties also responded more quickly to management as compared to others. In addition, while organic inputs are usually applied to target a specific soil health property, other soil health elements can also be affected in a similar magnitude and direction due to latent linkages between different soil properties.
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    Impacts of cropping system and nutrient management on soil health and soil-borne pathogens in smallholder systems of western Kenya
    (Colorado State University. Libraries, 2024) Mutai, Joyce Chelangat, author; Fonte, Steven J., advisor; Vanek, Steven, advisor; Stewart, Jane E., committee member; Schipanski, Meagan E., committee member
    Crop production in smallholder farms is often limited by low soil fertility and the presence of soil-borne pathogens. Both challenges are associated with limited nutrient inputs, low rotational diversity, as well as small land holdings and the associated need for continuous cultivation in many smallholder systems. This dissertation explores the varied ways in which cropping systems and nutrient management strategies influence key soil health parameters and relationships with key soil-borne pathogens. Additionally, this research tests a suite of soil health bioassays to facilitate farmers' understanding of soil-borne pathogen status on their farms. I utilized a mix of observational research, short-term on-farm experiments, and long-term cropping system trials to understand: 1) the potential of simplified soil pathogen tests (for Fusarium, Pythium, and plant parasitic nematodes (PPN)) to provide insight on soil pathogen pressure, 2) the impact of dis- tinct nutrient management strategies (organic vs. synthetic inputs) on key soil health parameters and associated soil-borne pathogens, and 3) effects of cropping system (mono-cropping vs. more complex systems) on key soil health parameters and soilborne pathogens. To address these objectives, I first validated a suite of simplified soil bioassays to screen for PPN (e.g., Meloidogyne, Pratylenchus) and other key soilborne pathogens (Pythium and Fusarium) against formal laboratory methods. I collected soils across eleven on-farm trials in western Kenya (66 plots total), examining the impact organic vs. synthetic nutrient inputs on bean production. The soil nematode bioassays involved counting lesions on soybean roots and galls on lettuce roots and were strongly correlated with the abundance of gall forming, root-knot nematodes (Meloidogyne) and root lesion nematodes (Pratylenchus) recovered in laboratory-based extractions. Effectiveness of a Fusarium bioassay, involving the counting of lesions on buried soybean stem, was validated via DNA sequencing to identify Fusarium taxa and a pathogenicity test of cultured Fusarium strains. Finally, a Pythium soil bioassay using selective media clearly showed presence of the pathogen, with seed rotting and colonies observed. When examining nutrient management impacts on nematode communities, soils amended with manure had fewer PPN and considerably more bacterivores and fungivores compared to soils amended with synthetic N and P. Similarly, Pythium presence was lower in soils amended with manure, and higher levels of Fusarium in the same plots, likely due to the ability of various Fusarium taxa to exist as a saprophyte. Our findings suggested that relatively simple bioassays can be used to help farmers assess soilborne pathogens with minimal costs, thus enabling them to make informed decisions on soil health and pathogen management. In a second study, I used an exploratory approach to examine common cropping systems in western Kenya smallholders including: maize monocultures, maize-legume intercrops, maize in rotation with legumes and vegetables, and horticultural systems based on perennial crops and vegetable production. I sampled 35 farms to understand the impact of cropping system diversity and associated nutrient management on the abundance of Fusarium pathogens and LN. I found that organic inputs led to fewer lesion-causing nematodes compared to the inorganic inputs system, but an inverse relationship with Fusarium pressure was observed. Permanganate oxidizable C (POXC), particular organic matter (POM), total C, and soil pH were highly correlated with each other and negatively associated with LN pressure, while POM was positively correlated with Fusarium pressure. In a third study, I leveraged a long-term (18-year) field trial in western Kenya, testing cropping systems representative of smallholder farms. The long-term trial evaluates three cropping systems: 1) continuous maize monocrop, 2) maize in rotation with the woody legume, Tephrosia (T. candida), and 3) maize intercropping with soybean, and two nutrient management strategies: 1) application of farmyard manure (vs. not), and retention or removal plant residue, with all plots receiving regular fertilizer inputs. I sampled soil from 40 plots and measured soil physical (texture, POM), aggregate stability, bulk density), chemical (pH, total C, available P, POXC), and biological (Fusarium, Pythium, RKN, LN) properties. Results indicated that long-term manure significantly improved soil properties including pH, POXC, POM, total C, and soil aggregation. Moreover, manure significantly reduced Pythium and RKN pressure. Soil pH and POXC were associated with Pythium and RKN, such that plots with low pH and POXC levels had high abundance of these soilborne pathogens. Fusarium abundance on the other hand, was higher with manure and associated variables (aggregation, POXC, total C). In a fourth study, I utilized a long-term trial (45 years) in Kabete, central Kenya focused on integrated soil fertility management in continuous maize-bean rotation and the resulting impacts on soil characteristics was well-suited to this goal. I examined the effects of dry manure application, maize stover management (incorporated vs. removed), and synthetic fertilizers (N and P applied vs. no application) in a full-factorial experiment on a range of soil physical, chemical, and biological properties. Results indicated that application of organic inputs, especially manure, greatly improved soil organic matter (SOM) pools, soil pH, aggregate stability, and decreased bulk density, compared to synthetic fertilizers. At the same time, manure significantly reduced Pythium and LN pressure, while plant residues reduced RKN and Pythium considerably. In summary, the simplified soil pathogen bioassays and soil health analyses considered in this dissertation offer a powerful set of tools to help smallholder farmers and the local research or extension organizations that they work with to monitor and anticipate soil related challenges in their fields, thus supporting agricultural livelihoods and resilience. Additionally, these findings suggest that continuous mining of nutrients and minimal returns of organic matter (i.e. removal of crop residues and no manure application) appears to drive the decline of important soil health properties (pH, POXC, POM, aggregation, and total C), with important implications for soil-borne pathogens.