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

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Open Access
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
Crop domestication impacts on rhizosphere interactions and nitrogen acquisition
(Colorado State University. Libraries, 2024) Hwang, Siwook, author; Fonte, Steven J., advisor; Machmuller, Megan B., committee member; Crews, Timothy E., committee member; Wrighton, Kelly C., committee member; Boot, Claudia M., committee member
Synthetic nitrogen (N) fertilizer is an essential pillar of modern industrial agriculture. Production and application of synthetic N fertilizer, however, are two of the most expensive, energy intensive, and environmentally deleterious processes in agriculture. Therefore, alternative means of providing N in an agroecosystem are of great interest in sustainable agriculture. While many solutions – from cover cropping to intercropping – have been suggested over time it remains unclear if the modern high-yielding crops can thrive in these alternative N conditions. Decades of breeding under high synthetic N input as well as the inherently annual nature of these modern cereal crops may prevent them from fully taking advantage of these alternative N sources. In this dissertation, I explored the impact of domestication on crop rhizosphere interactions and N acquisition, in both retrospective and prospective terms. First, I investigated how modern maize (Zea mays subsp. mays), and its wild relative Teosinte (Zea mays subsp. parviglumis) differed in their ability to adapt to, and take up, cover crop residue N and synthetic N inputs. We designed a 13C (carbon)/15N dual isotope labeling experiment in which we compared the C allocation patterns of modern maize and teosinte in response to synthetic (urea) and organic (cover crop residue) forms of N. Teosinte responded to organic N by increasing its biomass root-to-shoot (R:S) ratio by 50% compared to synthetic N, while modern maize maintained the same biomass R:S ratios in both N treatments. Recent photosynthate R:S ratio (measured using 13C-CO2, 7 weeks after establishment) was greater in organic N than in synthetic N treatments for both modern maize and teosinte (91% and 37%; respectively). Label-derived dissolved organic C (DOC), representing recent rhizodeposits, was 2.5 times greater in the organic N treatments for both genotypes. Modern maize took up a similar amount of organic N as teosinte using different C allocation strategies. Our findings suggest that intensive breeding under high N input conditions has not affected this modern maize hybrid's access to organic N sources while improving its ability to take up synthetic N. Next, I shifted my focus to the novel perennial grains Kernza and perennial wheat. Kernza® is a domesticated intermediate wheatgrass (IWG, Thinopyrum intermedium). Perennial wheat is a hybrid between Kernza/IWG and modern annual durum wheat (Triticum turgidum subsp. durum). Kernza, in addition to being a perennial, may still possess beneficial belowground traits that may have been lost in modern cereals through millennia of aboveground-focused plant breeding. If so, such traits may be passed down to perennial wheat. To characterize root architecture, exudate profiles, and microbial communities of Kernza and perennial wheat in relation to annual wheat, I conducted a greenhouse experiment. We grew three genotypes/species (Kernza, perennial wheat, annual wheat) and collected their root exudates after 8 weeks of growth. The exudates were analyzed via LC-MS/MS for their chemical composition. We extracted DNA from rhizosphere soils and sequenced them for 16S and ITS profiles. Lastly, we scanned the roots to analyze root distribution across different diameter classes. We found that perennial wheat invested more heavily into very fine (< 250 µm) roots compared to annual wheat and Kernza. Perennial wheat also exuded at a greater rate of exudates per amount of root biomass. We suspect that the greater proportion of very fine roots in perennial wheat led to greater surface area and greater specific exudation rate, and that this may be related to hybrid vigor. We did not find evidence of a genotype effect on root exudate or microbial community composition. However, root exudates (overall metabolite profiles) significantly correlated with root architecture (distribution of root volume over different diameter classes) and the microbial community composition. These interactions represent a potential pathway through which plants can exert influence over the rhizosphere microbial community. Overall, these results emphasize the importance of root architecture in mediating belowground interactions. Understanding rhizosphere dynamics and the response to domestication and hybridization can guide further development of robust perennial cereal crops. In a third experiment, I studied how Kernza, perennial wheat, and annual responded to cereal-legume intercropping (biculture) in the field. To do so, we planted each of the three genotypes in monoculture or in biculture with alfalfa (Medicago sativa). We sampled their rhizosphere over two growing seasons and extracted soil DNA to construct rhizosphere 16S and ITS profiles. We hypothesized that 1) rhizosphere microbial community composition of annual wheat and Kernza will be most dissimilar from each other with perennial wheat intermediate, and 2) microbial community composition will shift in biculture, with the greatest change in Kernza and the smallest in annual wheat. We found that the rhizosphere 16S profiles differed significantly from the other two genotypes but the 16S profile of perennial wheat did not differ from that of annual wheat. Perennial wheat seemingly inherited microbial recruitment traits of its annual parent more so than its perennial parent's. Interestingly, inclusion of legumes led to the convergence, rather than divergence, of 16S profiles among genotypes. We postulate that the competitive pressure of alfalfa may have led to this convergence of 16S profiles across genotypes. The fungal community did not show evidence of genotype effect. However, the fungal community composition changed over two years in monoculture but not in biculture. This result implies that fungal community may become distinct over time if it is influenced by only one genotype (i.e., monoculture) rather than two (i.e., biculture). In conclusion, we found evidence of genotype-driven microbial community assembly that changed with legume's competitive pressure. The inheritability of microbial assembly was present but skewed towards the annual parent. Our study demonstrates the importance of including rhizosphere interactions in our evaluation of novel cereal crops in and out of cereal-legume biculture. In a final study, I investigated how rhizosphere microbial ecology of these three genotypes (Kernza, annual wheat, and perennial wheat) could be linked to their ability to acquire N from neighboring alfalfa plants. We designed a greenhouse study in which we planted all three cereals in monoculture or in biculture with alfalfa and used 15N leaf feeding technique to track the movement of N from alfalfa to cereals. In addition, we also extracted DNA from the soil and sequenced it for 16S rRNA profiles. Arbuscular mycorrhizal fungi (AMF) infection rate was also measured on all cereals and legumes. We hypothesized that: 1) annual wheat would produce the greatest biomass but Kernza would have highest proportion of legume derived N in its biomass, 2) all microbial communities will shift in biculture, with the greatest change in Kernza and the smallest in annual wheat, and 3) Kernza would have the highest rate of infection from AMF, especially in biculture. Surprisingly, we found no evidence of genotype or cropping system (monoculture or biculture) effect on either proportion or absolute amount of N derived from legume. We did find, however, that DOC concentration was higher in cereal rhizosphere grown in biculture than in monoculture, suggesting greater belowground investment in exudates when the grasses are grown with a legume. Despite this trend, annual wheat had much lower microbial biomass carbon (MBC) level in its rhizosphere compared to the perennials, in biculture. We contended that this may be due to substrate suitability of annual wheat's rhizodeposit. We also found that AMF infection rate was in fact the lowest in Kernza. Lastly, we found that 16S profiles of all three cereals shifted towards that of alfalfa in biculture. This trend might suggest microbial spillover, wherein rhizosphere microbial community of one genotype colonizes that of a neighboring plant, from alfalfa rhizosphere. Overall, we demonstrated that quantifying the N transfer in the rhizosphere can provide important insight into how these genotypes may be inducing changes in soil biogeochemistry in response to neighboring legumes. In summation, this dissertation provides links between crop genotype, root exudate chemistry and rate, microbial community assembly, and their biogeochemical consequences, in alternative N environments. Deepened understanding of how complex rhizosphere interactions may affect internal N cycling could be leveraged to further optimize these unique systems such as perennial cereal-legume biculture. In doing so, we will be one step closer to a more sustainable future, that is less reliant on synthetic N fertilizers.
Open Access
Cropping system, site and topographic impacts on deep soil carbon dynamics in no-till dryland agroecosystems
(Colorado State University. Libraries, 2024) Landers, Carolita E., author; Fonte, Steven J., advisor; Schipanski, Meagan, advisor; von Fischer, Joe, committee member
Long-term research of no-till management in the US Great Plains has shown that increasing cropping intensity can potentially increase soil organic carbon (SOC) and crop yields compared to traditional winter wheat (Triticum aestivum L.)- fallow management systems. However, due to varying climate and topographical factors, SOC accrual rates may change with time and soil depth. We sampled SOC in a long-term experiment 36 years after its establishment. The study is located across three sites in eastern Colorado, and it characterizes a gradient of potential evapotranspiration (PET) with multiple slope positions at each site. Thus, the objectives of this study are to understand 1) the effects of different crop rotations and cropping system intensification on SOC after 36 years in the surface soil in a no-till, dryland system., and 2) how climate and topography influence SOC and SIC dynamics in deeper layers (> 20 cm) and potentially interact with management. The cropping rotations examined were wheat-fallow, wheat-corn (Zea mays L.)-fallow, continuous summer cropping and a grass strip to represent the Conservation Reserve Program, all planted across three sites with similar annual precipitation but increasing PET and a slight slope gradient. We found cropping intensity, slope position, soil depth, and site (PET) all independently impacted SOC and SIC concentration (g kg-1) and stocks (Mg ha-1). Aside from the perennial GRASS treatment that consistently had higher SOC to depth, the management effect was seen most pronounced in the surface layers of the soil, but beyond 20 cm, SOC and SIC were influenced more by site and slope. As previously seen, the toe slope accumulated the most SOC in the surface layers; however, it did not persist in the deeper layers where the summit and side slope positions accumulated more. The findings of this research contribute to addressing the information gap surrounding deep SOC and SIC dynamics and their interactions with climate and management of no-till in dryland agroecosystems. We revealed that while the surface soil SOC responds to intensification, deeper SOC and SIC layers show a more complex interplay between climatic and topographic factors. These insights are crucial for developing sustainable agricultural practices and enhancing carbon sequestration to inform climate change mitigation strategies in the Great Plains.
Open Access
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.
Open Access
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.
Open Access
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.
Open Access
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.
Open Access
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.