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Browsing by Author "Cotrufo, M. Francesca, advisor"

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    A modeling-experimental (ModEx) approach to advance understanding of global controls and microbial contributions to particulate and mineral-associated organic matter storage
    (Colorado State University. Libraries, 2024) Hansen, Paige M., author; Cotrufo, M. Francesca, advisor; Schipanski, Meagan, committee member; Wallenstein, Matt, committee member; Trivedi, Pankaj, committee member
    As soils are the largest terrestrial pool of carbon (C) and provision many ecosystem services, including nutrient cycling and maintenance of plant productivity, soil C sequestration represents a promising technology to help meet urgent needs to draw down atmospheric carbon dioxide (CO2) and prevent acceleration of climate change, as well as to help feed a rapidly growing global population. Given this, a comprehensive understanding of the mechanisms underpinning observed patterns of soil C storage is necessary to ensure a sustainable future for all. In response to this need, recent breakthroughs in our understanding of soil organic matter (SOM) dynamics have led to the development of multiple frameworks articulating how climate, soil, plant, and microbial properties interact with one another to control the formation of the two SOM constituents, particulate (POM) and mineral-associated organic matter (MAOM). Despite this, environmental controls that act on POM and MAOM storage at the global scale, as well as microbial functionality, is noticeably absent from our empirical understanding of SOM fraction formation and persistence. More advanced knowledge of these controls would enable more robust identification of where SOM is most vulnerable to loss, as well as more informed implementation of 'multi-pool' management practices aimed at enhancing C storage in both POM and MAOM. In this vein, this dissertation explores global controls on and microbial mediation of SOM dynamics at multiple scales through a combination of synthesis, modeling, and experimental (i.e., ModEx) approaches. Specifically, I first synthesized climate, soil property, and fraction C data to understand global controls on C storage in POM and MAOM. I then applied a previously developed individual-based model (Kaiser et al., 2015) to determine how emergent microbial community properties resulting from microbial social dynamics (i.e., interactions among microbes that produce enzymes at different rates) impact POM retention under varying degrees of MAOM saturation. Lastly, I investigated the relevance of hypothesized microbial copiotrophic and oligotrophic life history strategies to changes in POM and MAOM storage. Results from these projects indicate that global POM and MAOM storage is controlled by disparate suites of environmental variables, with POM being primarily controlled by variables that modulate microbial activity, and MAOM being controlled by a combination of C inputs and soil properties related to the potential to stabilize new MAOM. Additionally, flexible enzyme production in response to the availability of easily-assimilable, soluble substrates may contribute to POM retention under varying degrees of MAOM saturation and POM carbon:nitrogen ratio (C:N). However, variation in microbial function does not always result in changes in POM and MAOM storage – differences in growth rate, our proxy for copio- and oligotrophy, was unrelated to changes in POM and MAOM. Despite this, this dissertation indicates that microbial functions and environmental properties controlling microbial activity rates (i.e., controls on C outputs from the soil) mediate POM storage, but that MAOM is more reflective of C inputs to the soil. This indicates that microbial interventions to support soil C storage may want to focus on ecosystem-specific microbial manipulations that support community efficiency and modulate exo-enzyme production. In combination with other management strategies that increase soil C, these types of microbial interventions may help ensure that new soil C is retained in the soil for longer periods of time. Additionally, given that microbial activity is generally expected to increase with climate warming, these results indicate a premium need to preserve existing POM stocks.
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    Bridging the gap between regenerative agriculture and the biological mechanisms controlling soil organic matter dynamics
    (Colorado State University. Libraries, 2024) Prairie, Aaron, author; Cotrufo, M. Francesca, advisor; Fonte, Steven, committee member; Rosenzweig, Steven, committee member; Hall, Edward, committee member
    This dissertation investigates the complex impacts of regenerative agriculture on soil organic matter (SOM) dynamics and soil fauna biodiversity, addressing a broad range of objectives from uncovering global patterns and policy needs to mechanistic understanding. Through global meta-analyses, policy evaluations, field studies, and mechanistic experiments, this research provides a comprehensive understanding of how regenerative practices influence soil health, carbon sequestration, and biodiversity. Chapter 2 aimed to understand global patterns through a meta-analysis quantifying the effects no-till (NT) and cropping system intensification significantly increase SOM, via impacts on both particulate organic matter (POM) and mineral-associated organic matter (MAOM). The analysis reveals that NT and cropping intensification synergize with integrated crop-livestock (ICL) systems to greatly enhance soil organic carbon (SOC) stocks, highlighting the potential of regenerative practices to mitigate climate change and promote soil health. Chapter 3 sought to evaluate the impacts of diversified agricultural systems on SOC, soil health, and yield across the United States. The findings indicate that diversified systems consistently show higher levels of SOC, improved soil health, and improved agronomic outcomes. The policy recommendations include increasing funding for soil health practices, supporting longer participation of producers in conservation programs, and tailoring these programs regionally to maximize their effectiveness. Chapter 4 focused on field-level impacts by examining the effects of varying degrees of regenerative practice adoption on SOM dynamics and soil fauna biodiversity in 22 farms within the Cheney Watershed, of central Kansas. By developing a Regenerative Farming Index (RFI), the study clearly links regenerative practices to increased carbon and nitrogen stocks in both POM and MAOM, and indicates a positive correlation between regenerative practices and soil biodiversity. Path analysis suggests that soil fauna indirectly influence SOM through their role in enhancing regenerative practices. Chapter 5 aimed to provide a mechanistic understanding of SOM dynamics by exploring the interactions between predatory mites and bacterivorous nematodes. The study highlights how these interactions shape microbial necromass accrual and MAOM formation. The findings underscore the importance of considering the entire soil food web in ecological studies to fully understand SOM formation and stabilization mechanisms. Overall, this dissertation advances the understanding of SOC dynamics under regenerative agriculture, providing valuable insights for sustainable soil management and climate change mitigation. By integrating global and local scales, it offers a holistic view of how regenerative practices can restore soil health and contribute to more resilient and productive agricultural systems.
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    Environmental change impacts on carbon and nitrogen dynamics in soils and vegetation: from global synthesis to local case studies
    (Colorado State University. Libraries, 2022) Rocci, Katherine, author; Cotrufo, M. Francesca, advisor; Baron, Jill S., committee member; Knapp, Alan K., committee member; Lavallee, Jocelyn M., committee member
    Human-induced changes in the Earth system, known collectively as global environmental changes, are modifying terrestrial ecosystems. Feedbacks between land biogeochemistry (e.g., the cycling of elements) and global change are one of the key uncertainties in global climate models, and thus understanding land (e.g., soils and plants) responses to global change will help us predict future climate. In order to advance understating of how soils and plants respond to global changes, we need to work across scales by synthesizing global findings, using experimental networks, and studying context dependent responses at individual sites. Specifically, this dissertation uses this framework to investigate: (1) the responses of carbon (C) in total soil organic matter (SOM) and its fractions to warming, elevated atmospheric carbon dioxide (CO2), altered precipitation regimes, and nitrogen (N) fertilization globally using meta-analysis; (2) SOM C and N stoichiometry and distribution in response to nutrient fertilization in globally-distributed grasslands; (3) plant and soil biogeochemical responses to increased precipitation at a mesic grassland; (4) bulk (wet and dry) N deposition in response to proximity to the road in a topographically complex, subalpine forest. Soil organic matter stores carbon (C) and N and thus helps to control climate and provide energy and nutrients for ecosystem function. Thus, understanding SOM responses to global change will help determine future climate and ecosystem processes. However, SOM is made up of a diverse pool of molecules, and separating SOM into more homogenous functional pools (e.g., particulate and mineral-associated organic matter [POM and MAOM]) can provide clearer understanding of SOM responses to perturbations. By synthesizing global-scale understanding, Chapter 2 showed that POM and MAOM C responded differently to global changes and these responses depended on experiment length, soil depth, and experiment methodology. By investigating how SOM responses to global change varied across a global distribution of grasslands, Chapter 3 found that addition of macro- and micronutrients modified POM and MAOM C:N, depending on ambient environmental conditions, and consistently reduced SOM C stability. By investigating C and N cycling under altered precipitation at a local scale, Chapter 4 showed that studying SOM fractions provided clearer understanding of the mechanisms underlying grassland biogeochemical responses to increased precipitation. Chapters 2-4 all show the value of investigating soil fractions rather than solely the total SOM pool, as studying these fractions provided unique information and greater functional understanding. Global changes are not felt equally by all ecosystems. Ecosystems near sources of N deposition may be especially vulnerable to this global change. The fifth chapter of this dissertation, like the fourth chapter, focused on understanding local responses to global change. The vast majority of roadside N deposition studies find increased N deposition adjacent to roadways, but we did not find this, potentially due to the complex topography at our site or insufficient vehicle emissions. This suggests higher roadside N deposition cannot be assumed for all ecosystems. Altogether this dissertation synthesized and advanced our understanding of global change effects on plant and soil C and N pools and cycling.
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    Evaluating soil productivity and climate change benefits of woody biochar soil amendments for the US Interior West
    (Colorado State University. Libraries, 2018) Ramlow, Matthew Alan, author; Cotrufo, M. Francesca, advisor; Ogle, Stephen, committee member; Rhoades, Charles C., committee member; von Fischer, Joseph, committee member
    Managing our lands to provide for today and the future requires sustainable land management practices that enhance productivity while reducing climate impacts. Proponents claim biochar soil amendments offer a comprehensive solution to enhance soil capacity to deliver water and nutrients to plants while decreasing climate impacts through reduced nitrous oxide (N2O) emissions from fertilizer use and carbon (C) sequestration. This dissertation evaluates such claims for woody biochar applications within the US Interior West; to enhance crop production and reduce N2O emissions in deficit irrigation agricultural systems, and to support forest road restoration efforts. It also employs laboratory incubations and soil biogeochemical modeling to predict and to better understand the controls on biochar's greenhouse gas mitigation potential. The field studies demonstrate that this woody biochar improved soil moisture content but its enhanced capacity to retain water did not alleviate plant water stress when water inputs were low. Similarly, in forest soils, this woody biochar amendment improved plant available N but at levels that did not impact productivity. In lab incubations this woody biochar reduced N2O emissions. While this reduction could not be explained by bulk soil mineral N transformations, the soil moisture regime did affect biochar's ability to reduce N2O emissions. Despite the observed biochar N2O emission reductions in incubated soils, under field conditions biochar effects on N2O emissions were inconclusive. When evaluating biochar's C sequestration potential, soil biogeochemical modeling revealed that 59 percent of the biochar C applied will be sequestered in soils after 100 years. Losses from biochar fragmentation and leaching may constitute a considerable proportion of the C losses. Of the applications considered, C sequestration remains the most promising use for biochar soil amendments within the US Interior West.
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    Fire disturbance belowground: untangling consequences for soil food webs and organic matter
    (Colorado State University. Libraries, 2019) Pressler, Yamina, author; Moore, John C., advisor; Cotrufo, M. Francesca, advisor; Knapp, Alan K., committee member; Balgopal, Meena M., committee member
    Soils and the ecological communities they house provide a diverse array of ecosystem services including the provisioning of food and fiber, decomposition and nutrient cycling, water filtration, and the maintenance of terrestrial biodiversity. These complex belowground communities, and therefore the ecosystem processes they regulate, are increasingly threatened by fire due to climate, land use, and management changes. Fires can have profound effects on the physical and chemical soil environment, with consequences for soil biological communities. Fires cause mortality of soil organisms during the disturbance event, change the soil pH, and alter the quantity and quality of soil organic matter (SOM). In particular, fires transform organic matter into pyrogenic carbon (PyC), a recalcitrant material with a dense aromatic structure and long residence times in soils. In natural ecosystems, soil food webs interact with PyC produced after a fire. In agroecosystems, PyC, in the form of biochar, is also used as a tool to manage soil carbon and fertility. Given the widespread effects of fire on biological, chemical, and physical components of the soil, and the importance of soil communities for the provisioning of ecosystem services, understanding the consequences of fire disturbance for soil food webs and organic matter is an important research objective. My dissertation leverages several different scientific inquiry approaches to understand the consequences of disturbance and management for the ecology of soils. I take a multifaceted approach by considering soil organisms, food webs, and organic matter in the context of fire disturbance and agricultural management. I begin by presenting results from a meta-analysis investigating the effect of fire on soil biota biomass, abundance, richness, evenness, and diversity. Overall, I found a pervasive negative effect of fire on soil microorganisms and conclude that soil fauna are more resistant to fire than soil microorganisms. Then, I present results from a field study investigating the effect of fire frequency on soil food web structure, function, stability, and resilience in an oak-pine savanna. Here, I found that while soil biota biomass and food web function did not differ with fire frequency, food web structure, stability, and resilience did. In particular, soil food webs at intermediate fire frequencies (4-year fire return interval) were the least stable and least resilient to fire. Thereafter, I consider the consequences of fire for SOM composition through the lens of PyC. I seek to understand where and why PyC persists in soils at a continental scale by using multiple analytical techniques to quantify PyC across Europe. I found that PyC may contribute a smaller component of soil organic carbon than previously thought and that organic carbon is the best predictor of PyC at a continental scale. I then consider how agricultural management and PyC in the form of biochar, impacts soil food webs in a semi-arid corn agroecosystem. I did not find any measurable effects of biochar on soil food web structure or function. I conclude that the long-term impact of historical land management on soil food webs far outweighs any impact of short-term management practices involving biochar. I then use this field study as an opportunity to integrate scientific inquiry in middle school classrooms. I present a collection of classroom activities co-developed with secondary educators that lead students to investigate the effect of biochar on soils and plants. I conclude by discussing the themes, patterns, and ideas that emerge from the preceding chapters. I found that the responses of soil ecological communities to disturbance are highly context dependent. This context dependency leads to hidden, unexpected, and even contradictory patterns. I end by reflecting on how completing this work has informed my non-linear approach to science.
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    Forest soil C and N responses to salvage logging and belowground C inputs in bark beetle infested stands
    (Colorado State University. Libraries, 2020) Avera, Bethany N., author; Cotrufo, M. Francesca, advisor; Rhoades, Charles, committee member; Rocca, Monique, committee member; van Diepen, Linda, committee member
    Managing forest ecosystems in this era of global change requires a fundamental understanding of forest soil properties and processes. Forest disturbance events are projected to increase in severity and frequency, requiring a better understanding of how post-disturbance management will impact ecological processes such as soil nutrient dynamics and stocks of soil carbon (C). The research in this dissertation focused on areas of widespread mortality in lodgepole pine (Pinus contorta var. latifolia) in northern Colorado due to the most recent outbreak of the endemic mountain pine beetle (MPB; Dendroctonus ponderosae Hopkins). The goal of this research was to examine soil nitrogen (N) stocks, plant N uptake, and changes in forest soil C stocks in soil organic matter (SOM) due to tree mortality and subsequent salvage logging and from different belowground C inputs. To achieve this aim, I compared the three most prevalent management options: 1) uncut beetle-infested lodgepole pine stands and clear-cut salvage logged areas with either 2) post-harvest residue retention or 3) post-harvest residue removal. To determine the impacts of MPB-infestation and salvage logging on ecosystem N stocks and plant N uptake, I implemented an experimental field study by adding 15N-labeled ammonium sulfate to research plots centered over lodgepole pine seedlings. Measuring N stocks and 15N recovery in soil and vegetation pools over two growing seasons highlighted the coupled nature of forest C and N cycling between plant and soil forest ecosystem compartments. The majority of the 15N label was recovered in the soil and was not impacted by the management treatments. In contrast, the N uptake by lodgepole pine seedlings was driven primarily by the amount of C fixation and the patterns of C fixation, in turn, related to other environmental factors modulated by the management treatment, such as available light. An observational field study sought to quantify changes in forest soil C stocks in the bulk soil and SOM fractions and detect any changes in C chemistry as a result of management that may impact C persistence. In the dry, high elevation forests studied, soil C increased with salvage logging likely due to mixing of surface residues and O horizon C into the mineral soil during logging. The distribution of C stocks among the mineral soil fractions and the chemistry of those fractions indicated that root C accumulation in the particulate organic matter (POM, >53 μm) is an important mechanism of soil C accumulation in these forest soils. A mechanistic laboratory incubation evaluated the efficiency of mineral-associated organic matter (MAOM, <53 μm) formation from root and hyphal necromass inputs with different C chemistries. This study showed that rye root necromass with more labile and less structural C than pine roots, was processed most in the 38-day incubation and contributed much more efficiently to the formation of MAOM than did the pine roots. Despite less processing, the arbuscular and ectomycorrhizal fungal necromass both contributed as efficiently as rye roots to MAOM formation. These results indicate that both C chemistry and C/N ratio exert controls on residue processing and MAOM formation. Together, this dissertation work showed that salvage logging stimulated the growth of lodgepole pine seedlings, resulting in increased storage of both C and N in the plant biomass above- and belowground. As this pine root biomass turns over, the root necromass will contribute C to the POM fraction, the largest pool of soil C in this system. The net increase of forest soil C with salvage logging found in this study is notable as it suggests that the MPB-infested lodgepole pine forests of Colorado can be salvage logged with a low risk of significant soil C loss. Additionally, the highest recovery of the N label was in the soil, thus the high soil N recovery with higher soil C supports SOM is a sink of N reducing N losses. Finally, pine seedling colonization by ectomycorrhizal fungi may further aid with nutrient retention and the efficient formation of MAOM during regeneration.
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    From litter decomposition to soil organic matter formation: using stable isotopes to determine the fate of carbon and nitrogen
    (Colorado State University. Libraries, 2014) Horton, Andrew James, author; Cotrufo, M. Francesca, advisor; von Fischer, Joseph, committee member; Paschke, Mark, committee member
    Litter decomposition releases the energy and nutrients fixed during photosynthesis into the atmosphere and soil. In the soil, carbon and nitrogen from the litter can be stabilized in soil organic matter pools, which globally represent large pools of both carbon (C) and nitrogen (N). Soil organic matter pools are heterogeneous, the product of different stabilization processes and will stabilize C and N for periods of time ranging from years to millennia. A thorough mechanistic understanding of the fate of above-ground litter C and N is essential to understand how climate change could affect both carbon sequestration and soil health. This research studied the fate of litter derived organic matter. Isotopically labeled litter was used in a field incubation to trace litter derived C and N into different SOM pools and soil depths over the course of 3 years. Additionally, naphthalene was used to suppress microarthropods to determine the impact of mesofauna on the fate of litter derived N. In the laboratory, soil from the field experiment was incubated for 150 to determine how different SOM pools contributed to respiration and leaching. Microarthropods do not increase overall N mineralization rates, but do influence the fate of litter derived N. When present, microarthropods increased the amount of litter derived N in the light fractions, suggesting that microarthropods increase litter fragmentation. Surprisingly, litter derived organic matter does not contribute to respiration and leaching equally, suggesting that leaching and respiration are not directly related. Litter derived OM behaves differently than older OM present in the soil, with the newer litter derived C and N being more readily lost from SOM pools. This result supports the onion layering model suggested by Sollins (Sollins et al. 2006). In order to create more accurate models, microarthropods and the onion layering model should be included in future C and N dynamic studies.
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    Growing deeper: pathways to enhancing soil organic matter in annual and perennial dryland grain agroecosystems
    (Colorado State University. Libraries, 2022) van der Pol, Laura Kathryn, author; Cotrufo, M. Francesca, advisor; Schipanski, Meagan E., committee member; Trivedi, Pankaj, committee member; Crews, Timothy E., committee member
    The story of agriculture and human civilization is one of loss: loss of soil structure, soil carbon, ecosystem function, and diversity. As we find ourselves at the nexus of intersecting global challenges of radically altered biogeochemical cycles and anthropogenic climate and productivity influence, we urgently need to alter our relationship with the soil and biosphere that sustain our human systems. In this dissertation I evaluate two management strategies for enhancing soil organic matter (SOM) in dryland, grain fields in the U.S.: legume integration and perennial grains. These strategies have been part of traditional farming practices, but they are not commonly utilized by commodity farmers for reasons I explore in Chapter 5. I conclude with policy recommendations for one way that might lead to systemic change that would value soils and their vital role in our human systems more appropriately. Here I provide a brief synopsis of each chapter: In the introduction (Ch. 1) I provide some historical context of human reliance on grain agriculture and the reasons that legumes and perennials might enhance SOM. I also describe the framework of SOM formation used in this research and provide an overview of the components of SOM I measured in this research. The first study (Ch. 3) is an observational study of conventional, dryland wheat farmers in semi-arid Colorado and Nebraska. I examine the 'soil carbon (C) dilemma' (Janzen 2006): How can SOM be increased, while also increasing the release of nutrients that accompanies decomposition? We specifically tested whether incorporating legumes into a continuous rotation influences the form and amount of SOM as well as productivity in farms of the central Great Plains region of the U.S. by contrasting three, no-till rotation systems: 1) conventional wheat-fallow; 2) continuous grain-only rotations, and 3) continuous grain rotations that incorporate a legume crop. We sampled on-farm fields and experimental agricultural research station plots that had received one of these rotations for at least eight years. We found that intensifying the rotation with continuous grains led to 1.5-fold increase in aggregate size but did not change SOC stocks. Incorporating a legume to the continuous grain rotation resulted in 1 Mg C ha-1 more SOC on average in surface soil compared to wheat-fallow rotations. In chapter 3, I use a similar approach to assess whether conversion from annual to perennial grains such as intermediate wheatgrass Kernza® could sequester soil organic carbon (SOC). We sampled three sites with paired fields under annual grains and converted to Kernza 5-17 years ago to 100-cm and compared their SOC stocks as distributed between mineral-associated (MAOM) and particulate organic matter (POM). POM-C was higher under Kernza cultivation but total and MAOM-C were similar. Our findings suggest Kernza increases SOC at depth as POM. Further study is needed to assess whether this will result in long-term SOC sequestration. In order to quantify the effect of legume incorporation and ability of Kernza to form SOC, I performed a mechanistic study to quantify the formation of SOM from Kernza and alfalfa tissues under contrasting N management (Ch. 4) Using continuously labeled 13C/15N plant residues, we tested the effect of litter inputs of contrasting composition (shoot and root material from Kernza® and alfalfa, a perennial legume) under management of Kernza where N was (1) not added, (2) added as urea, or (3) fixed by an alfalfa intercrop. We selected Kernza for its theoretical potential to build SOM due to deep root systems and long growing season. We hypothesized that the higher quality litter from alfalfa shoots would lead to greater MAOM formation due to its higher density of metabolic components promoting enhanced microbial C use efficiency, while root tissues may more likely become stabilized within aggregates as oPOM due to increased contact with soil surfaces. We predicted that the management with N addition may enhance MAOM-formation by alleviating microbial N-limitation and leading to enhanced microbial C use efficiency. We found that overall Kernza promoted greater SOM formation, in both MAOM and oPOM, with 20% of roots stabilized and 12% of shoot stabilized after 27 mo compared to 10% for alfalfa roots and shoots. Finally, in chapter 5, I propose a pilot crop insurance and research program in the U.S. Northern Plains to promote practices that enhance soil health, farm income, resilience, and mitigate climate change. Such a program could inform nationwide adoption of such practices.
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    Implementing organic amendments to enhance maize yield, soil moisture, and microbial nutrient cycling in temperate agriculture
    (Colorado State University. Libraries, 2018) Foster, Erika J., author; Cotrufo, M. Francesca, advisor; Comas, Louise, committee member; Rhoades, Charles, committee member; Wallenstein, Matthew D., committee member
    To sustain agricultural production into the future, management should enhance natural biogeochemical cycling within the soil. Strategies to increase yield while reducing chemical fertilizer inputs and irrigation require robust research and development before widespread implementation. Current innovations in crop production use amendments such as manure and biochar charcoal to increase soil organic matter and improve soil structure, water, and nutrient content. Organic amendments also provide substrate and habitat for soil microorganisms that can play a key role cycling nutrients, improving nutrient availability for crops. Additional plant growth promoting bacteria can be incorporated into the soil as inocula to enhance soil nutrient cycling through mechanisms like phosphorus solubilization. Since microbial inoculation is highly effective under drought conditions, this technique pairs well in agricultural systems using limited irrigation to save water, particularly in semi-arid regions where climate change and population growth exacerbate water scarcity. The research in this dissertation examines synergistic techniques to reduce irrigation inputs, while building soil organic matter, and promoting natural microbial function to increase crop available nutrients. The research was conducted on conventional irrigated maize systems at the Agricultural Research Development and Education Center north of Fort Collins, CO. The first field experiment tested a temporally limited irrigation strategy with high application rates of organic amendments (30 Mg ha-1) to increase soil moisture, N and P retention, and enhance soil microbial activity. The experiment used biochar created from bio-energy production. The control plots contained 1.49% total soil carbon, and biochar addition increased total carbon to 2.67%. The biochar also had variable impacts on microbial extracellular enzyme activities, causing a 40% reduction in β-1,4-glucosidase and phosphatase activities, with repercussions for hydrolysis of soil P and cellulose. However, the biochar amendment did not enhance yield. This field experiment also found that the limited irrigation technique reduced water inputs by 30% while maintaining yield. The second experiment of the dissertation determined the mechanism behind the decrease in extracellular enzymatic activities after biochar addition. Through a combination of a Bradford protein assay and a fluorometric assay of potential enzymatic activities, the pine wood biochar adsorbed and reduced both β-glucosidase and acid phosphatase activities by 75-100% relative to a control soil. Though highly variable, depending upon pH, the main factor influencing activity levels was the solid phase. The high temperature biochar had a large surface area within micropores. The substrate can diffuse into the micropores, where it is inaccessible to large enzymes; there is lower catalysis of those substrates, which indicates potentially lower nutrient release in the soil. Finally, to examine the agronomic efficacy of biochar, a second maize field trial was developed also implementing full and limited irrigation. This experiment incorporated an engineered coconut hull biochar, characterized by a neutralized pH, removed toxins from the surface, and homogenized pores. The biochar was banded directly onto the seed row at a low application rate (0.8 Mg ha-1). Additionally, a surface applied plant growth promoting P solubilizing bacterial inoculum was tested alone, and in combination with biochar. To determine the efficacy of these amendments to improve soil nutrient availability and maize yields, the soil nutrient supply, crop nutrient concentration and accumulation, and soil bacterial community composition were measured. The bacterial community data was analyzed using a cutting-edge technique based on Exact Sequence Variants to analyze single nucleotide differences, enhancing comparability with future studies. In this experiment the biochar increased soil available K and S which correlated to crop uptake, shifted the early season microbial community, and increased by 20% over the control (+1.95 Mg ha-1). The inoculum and combination treatments did not impact yield, but in these plots we observed the presence of bacterial families that were added in the original inoculum. Overall this work emphasized the efficacy of precision management strategies with biochar application to enhance yield. This dissertation work underlines the importance of contentiously selecting specific amendment type, application rate and method to achieve either agronomic or environmental benefits. Continued research with synergistic approaches will help to develop best practices within the region to manage agroecosystems for improved resilience.
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    Isolation, interpretation, and implications of physical soil organic matter fractions in soil systems
    (Colorado State University. Libraries, 2024) Leuthold, Samuel J., author; Cotrufo, M. Francesca, advisor; Lavallee, Jocelyn M., advisor; Mueller, Nathan, committee member; Schipanski, Meagan, committee member
    Soil organic matter (SOM) is crucial to sustained ecosystem function, due to its role in regulating nutrient cycling, carbon (C) storage, and soil structure relevant to both food production and climate regulation. Since the early 1990s, physical fractionation methods have been used to separate bulk SOM into discrete components. The central aim of these methodologies is to simplify the complex heterogeneity of the bulk SOM pool by isolating fractions with more homogenous chemistries, formation pathways, and mechanisms of persistence. By understanding the relative distribution of C and nitrogen (N) among these various fractions, we gain appreciable insight into the mechanisms underlying fundamental soil biogeochemical processes. Despite their historic use, however, significant questions remain regarding the means of proper isolation and interpretation. This dissertation looks to these questions directly, reviewing and then interrogating the methods by which fractions separated before applying those fractionation schemes to answer key questions relating SOM to ecosystem function. The first section reviews the history and current state of physical fractionation methodologies, before using a triangulation of experimental evidence, including chemical, isotopic, and spectral indicators, to identify the best practices for laboratory use. These chapters advance our current understanding of SOM biogeochemistry by drawing an explicit link between the conceptual definitions of SOM fractions and the various procedural definitions that have been used historically. Across a range of soils representative of agricultural land in the United States, we show that fractionation methods that separate particulate organic matter (POM) fraction by density isolate fractions more in line with the conceptual definition of POM than the more frequently used size separation. This work aims to unify understanding across the field of soil biogeochemistry and allows for more robust analyses and modeling efforts. The subsequent chapters use this approach to investigate fundamental questions around SOM stability and persistence. The mineral associated organic matter (MAOM) fraction has long been understood to be relatively stable, with slower turnover times and a more homogenous composition as compared to POM. Its accumulation has thus been discussed as a target for climate change mitigation. We leveraged a unique long-term experimental site with archived samples stretching back over 60 years to test this assumption, aiming to identify a dynamic fraction of MAOM by comparing the SOM composition of plots that had not received organic inputs over the course of the experiment against plots that had received regular inputs for six decades. Our spectral and isotopic analyses showed that a dynamic fraction of the MAOM existed and was primarily composed of plant derived compounds. As the exchangeable MAOM pool was exhausted due to a lack of fresh C inputs, we found that the composition of the MAOM pool became more strongly dominated by microbial byproducts. This work represents useful evidence towards a holistic understanding of the dynamic nature of SOM, and forces reimagining of long-held paradigmatic views. One challenge in the current SOM biogeochemistry landscape is that often questions exist downstream of methodologies, such that the fractions that can be isolated drive the research that is conducted. By first identifying robust methodologies, in the second half of this dissertation we were able to ask specific questions about the link between SOM dynamics and ecosystem function. To this end, we pursued three different lines of inquiry: a field study in which the objective was to link the fractional distribution of C and N to yield stability in agricultural systems, a field study that seeks to understand the persistence dynamics of SOM over a decadal scale in grassland systems, and a laboratory incubation that aims to discern the relative contributions of POM and MAOM in regard to plant available N. The first field study used samples from 9 working farms across the Central United States to better understand how SOM might moderate the spatiotemporal stability of crop yields at the field scale. Yield instability is a major cause of economic and environmental distress in row crop systems, and regional studies have suggested that increasing SOM may be able to mitigate variation in yield across time and space. The chapter presented here is the first study that attempts to identify a mechanistic link between SOM fractions and yield stability. In disagreement with regional and county scale studies, we found that SOM abundance was not linked to increased yield stability in cropping systems. Rather, unstable yield zones had significantly higher SOM content than stable zones, particularly in regard to the POM fraction. This work indicates that at the subfield scale, interactions between climate, topography, and management may be driving spatial patterns of both yield stability and SOM accumulation. This is a key insight, implying that some of the relationships between SOM and agronomic outcomes are scale dependent, and highlighting the need for field scale work to maintain relevance to growers. The second field study produced novel insights, tracing isotopically enriched litter and pyrogenic organic matter (PyOM) through various SOM fractions over the course of a decade, one of the longest tracer experiments that has occurred in grassland ecosystems. We found that after 10 years, the majority of the remaining litter derived C and N inputs were stored in the MAOM fraction, a result well aligned with our hypotheses. Interestingly though, the litter derived MAOM fraction formed rapidly (~ 1 year) and persisted at a relatively similar concentration for the duration of the study. This suggests the potential for divergent persistence mechanisms of POM and MAOM, implying less inter-fraction transfer than previous frameworks have proposed and prompting re-evaluation of the mechanisms of MAOM formation and persistence. In contrast, the applied PyOM remained almost completely in the POM fraction over the 10-year period, reinforcing both the heterogeneity of the bulk SOM pool, and the myriad of persistence mechanisms that stabilize various SOM fractions. Given that PyOM is ubiquitous in soil regardless of burn history and can persist for hundreds of years, this result has critical importance for our understanding of turnover time of the POM fraction, and suggests that we may be underestimating the dynamic nature of POM when PyOM is not accounted for. Finally, in a lab incubation experiment, we took advantage of recent advances in isotopic measurement to prove recent theories around MAOM N accessibility. Whereas POM is often thought of as the fraction that provides nutrients in the short term, our two-week incubation showed that under certain conditions, the majority of plant available N may be derived from the MAOM fraction. This work validates proposed frameworks and is an important step towards understanding coupled C and N management in agroecosystems that could improve N use efficiency and increase producer sustainability. Overall, the work in this dissertation aims to provide a comprehensive overview of how fractions can and should be isolated, and the information gained via this fractionation. By clarifying and advancing methodology to quantify SOM components and the understanding of their contribution to critical soil functions for the sustainability of food production and the mitigation of climate change this dissertation represents a major step forward for the study, modeling and managing of SOM in agricultural systems.
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    Mechanisms and management for soil carbon sequestration
    (Colorado State University. Libraries, 2020) Mosier, Samantha, author; Cotrufo, M. Francesca, advisor; Paustian, Keith, advisor; Davies, Christian, committee member; Denef, Karolien, committee member
    Soil organic matter (SOM) holds more carbon (C) than the atmosphere and terrestrial aboveground biomass combined. SOM also provides many other co-benefits in the form of ecosystem services. The rate at which we lose or sequester more C in soils is of great importance for mitigating the rising atmospheric greenhouse gas concentrations as well as for maintaining the fundamental services that soils provide to humanity. Many of the mechanisms involved in accruing and storing soil C are not entirely clear, and factors like litter chemistry and minerology can all come into play when determining the sequestration potential of a specific ecosystem. Additionally, not all soil C is equal in its turnover time or in its ability to resist disturbance. Therefore it is crucial that we better understand how functionally different soil C pools form and persist in the soil environment. Several "climate smart" soil management practices have been analyzed for their potential to sequester more C. However there are still gaps in our knowledge regarding soil C sequestration and how it can be impacted by land use management. The southeast US is a region with particularly severe soil degradation from poor agricultural management, but also has a high potential for increased soil C sequestration and overall soil health. This dissertation looks at some potential mechanisms and management practices involved with storing more stable soil C in the southeastern US. Mechanisms include how litter chemistry and soil C saturation can enhance or inhibit soil C sequestration. Then, we evaluated management practices from pine plantations and grassland grazing in the southeastern US to evaluate if improved management could increase soil C stocks, their distribution, and overall soil health.
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    Moving beyond mass loss: advancing understanding about the fate of decomposing leaf litter and pyrogenic organic matter in the mineral soil
    (Colorado State University. Libraries, 2014) Soong, Jennifer L., author; Cotrufo, M. Francesca, advisor; Wallenstein, Matthew, committee member; Knapp, Alan, committee member; Parton, William, committee member
    Leaf litter decomposition recycles the energy and nutrients fixed by plants during net primary productivity back to the soil and atmosphere from where they came. Traditionally, leaf litter decomposition studies have focused on litter mass loss rates, without consideration for where that mass ends up in the ecosystem. However, during litter decomposition by soil microbes a fraction of the litter mass lost is truly lost to the ecosystem as respired CO2, while another fraction remains in the ecosystem stored in the soil as soil organic matter (SOM). SOM is heterogeneous in composition, with various SOM pools remaining stored in the soil for time spans ranging from days to millennia depending on their biochemical and physical properties. Pyrogenic organic matter (py-OM) is the partially combusted plant residue left behind by fires, and has been found to contribute to long term SOM pools. SOM accounts for the largest terrestrial pool of carbon (C) in the global C cycle and stores nitrogen (N) and other nutrients for plant productivity. Therefore the formation of SOM during litter decomposition is critical to terrestrial C and N cycling and its feedback to global biogeochemical cycles. The focus of my dissertation is the study of leaf litter and py-OM decomposition, and quantitatively tracing how much decomposing litter and py-OM is used by soil microbes, how much is lost as CO2, and how much remains in the soil and contributes to SOM formation under different conditions. In order to best address my research questions, I first studied the methods of leaching of dissolved organic carbon (DOC) and 13C and 15N isotope labeling of plant material in the laboratory. Then, I conducted a laboratory incubation where I found that the amount of hot water extractable C and the lignocellulose index (Lignin/(lignin+cellulose)) can be used to predict DOM leaching, and the partitioning of C loss between DOC and CO2 from leaves and py-OM during decomposition. I also conducted two field studies using 13C and 15N labeled Andropogon gerardii leaf litter and py-OM to trace the fate of C and N losses during their decomposition in a fire affected tallgrass prairie, and understand the role of soil microarthropods in this process. I found that soil microarthropods increase the amount of leaf litter C that contributes to stabilized SOM formation during litter decomposition, by increasing litter inputs to the soil where they can be utilized by soil microbes. Finally, I found that frequent inputs of py-OM, rather than litter, due to annual burning of the tallgrass prairie alters the SOM formation process by removing relatively labile litter inputs to the soil and replacing it with py-OM that is unusable by soil microbes. Overall, my dissertation has focused on taking a mechanistic approach to understanding the process of litter and py-OM decomposition, and how their decomposition contributes to SOM formation and ecosystem CO2 fluxes. My results have helped to improve our understanding of terrestrial biogeochemistry, and the processes that control SOM formation during litter decomposition.
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    Pathways of soil organic matter formation in agroecosystems as influenced by litter chemistry, root depth and aggregation
    (Colorado State University. Libraries, 2024) Fulton-Smith, Sarah E., author; Cotrufo, M. Francesca, advisor; Paustian, Keith, committee member; Ojima, Dennis, committee member; Fonte, Steven, committee member
    Soils contain more carbon (C) than any other terrestrial reservoir, and the increase of these C stocks has been targeted as a potential climate solution globally. Agroecosystems play a critical role in our ability to provide these climate solutions through increasing soil organic matter (SOM). There is significant potential for SOM accrual in agroecosystems due to the degradation of SOM typically observed in these systems. One promising approach to increasing soil C sequestration is through the selection of deep-rooted crops, such as Sorghum bicolor. However, significant questions remain about root inputs' ability to contribute to SOM in order to balance the greenhouse gas (GHG) lifecycle of a bioenergy feedstock. My dissertation aims to answer some of these questions as well as to propose a framework to integrate the study of SOM formation from crop inputs with soil aggregate structure. Bioenergy has the potential to emit fewer GHGs than other fuel sources, such as fossil fuels, yet there are some emissions during the transportation production of bioenergy feedstocks and fuels that could be offset by soil C sequestration. However, in annual bioenergy systems, aboveground biomass is typically removed from the system, meaning roots are the primary source of OM available to return to the soil. However, roots and shoots may differ significantly in their ability to contribute to SOM due to differences in litter chemistry. In Chapter 2, I conducted a field incubation to understand how sorghum root versus leaf litter, as influenced by their contrasting chemistry, affect the formation and stabilization of SOM. Using unique soil-biomass microcosms to incubate root or leaf litter in topsoil (0-30 cm) for 19 months in the field, I traced the fate of litter decomposition products by combining stable 13C and 15N isotope labeling with extensive separation of physical soil fractions, free or within different aggregate structures. I found that roots, which were lower quality than leaves, decomposed more slowly but contributed more efficiently to total SOM formation than leaves. However, leaves contributed more to the stable SOM pool (i.e. associated to minerals) while roots contributed more to less stable fractions (i.e. light particulate organic matter). Additionally, sorghum is known to produce roots to a depth of 2 meters. There is limited understanding of how roots deeper in the soil (e.g., below 30 cm) lead to SOM formation and stabilization. In Chapter 3, I used the same microcosm approach as in Chapter 2, with roots that were incubated up to a 90 cm depth to better understand how depth influences the ability of roots to contribute to the formation of SOM and what role aggregates play in this process. Results of this study showed that differences in root decomposition dynamics with depth resulted in greater accrual of root litter C in more stable mineral associated SOM pools in the surface depth while there was slower decomposition and greater accrual in the less stable particulate organic matter fractions in the deep soil. Interestingly, most of the stable fraction was recovered within soil aggregates, particularly microaggregates. The results of these experiments emphasized the important role of microaggregates in modulating SOM dynamics. In Chapter 4, I used the information gleaned from Chapters 2 and 3 as well as advances in the SOM research community to speculate on the role of aggregation, specifically microaggregates, in moderating SOM formation by presenting a conceptual framework that integrates aggregates within our current understanding of particulate and mineral associate SOM dynamics. Overall, my dissertation addresses fundamental questions about our ability to increase SOM levels and resulting soil C accrual through the production of a deep-rooted crop through a field incubation. At the same time, I have connected these relevant results to the broader SOM research community by presenting a novel conceptual model that advances our current SOM framework. My hope is that this will be a valuable contribution to the field and spark discussion and future research.
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    Residue-derived carbon transformations with altered residue management in an irrigated corn system in Colorado
    (Colorado State University. Libraries, 2019) Leichty, Sarah I., author; Cotrufo, M. Francesca, advisor; Stewart, Catherine, advisor; Conant, Richard, committee member
    Soil plays an essential role in storing carbon (C) and nutrients regulating climate and sustaining food production. As such, it is important to understand how human activities affect C cycling in soil. Agricultural lands, particularly croplands, comprise some of the most managed areas of the world. We have the potential to positively impact C sequestration in croplands by understanding how residue management affects the C mineralization as well as the formation and stabilization of soil organic C (SOC). No-till (NT), which leaves residue on the surface, has been proposed as the superior residue management for building SOC due to a decreased rate of residue and existing SOC decomposition. Conventional tillage (CT), which breaks aggregates while incorporating residue into the soil, is thought to result in less SOC storage through increased residue and SOC decomposition, and soil erosion. However, NT does not always result in higher SOC storage than CT when measuring total profile stocks and the gains might not be stable in a changing climate. I studied a semi-arid, irrigated, corn system where gains in surface SOC but losses at depth had been observed because of conversion to NT. I studied the effect of altered residue management by mimicking NT and CT residue placement and soil disturbance and followed the residue-derived C into soil respiration (CO2) and physically defined SOC pools. I applied isotopically labeled (13C) residue either on the soil surface (NT) or incorporated into the soil (CT), which allowed me to track losses and transformations of residue C under different residue placement. A third treatment with surface-applied residue following soil disturbance tested the effect of disturbing aggregates during tillage. I collected soil respiration measurements and determined its isotopic composition for twelve months following residue addition to understand how residue location and soil disturbance affected the rate of total CO2 efflux, and of their component fractions (i.e., derived from residue vs. derived from soil). As reported in Chapter 2, I found that incorporated residue had higher residue-derived respiration in the first six months ("off season"), but surface-applied residue had higher residue-derived respiration during the later six months ("growing season"). Growing season respiration rates were higher and driven largely by warmer temperature and more available water (i.e. irrigation events) than in the off season. Thus, the growing season trend dictated the full year trend with surface residue more vulnerable to loss as CO2 efflux compared to incorporated residue that was likely protected from decomposition by the soil matrix presumably from either aggregation or mineral associations. Following, I tracked the fate of the remaining residue C by measuring SOC pools with varying levels of stability and report these results in Chapter 3. I harvested incorporated and surface-applied residue treatments six months after residue addition. I found that incorporated residue had more residue-derived C in bulk soil compared to surface-applied residue treatments. The larger pool of residue SOC within the incorporated residue treatment was due to increased residue decomposition compared to slower surface residue decomposition. Based on the two pathways of SOC formation proposed in Cotrufo et al., (2015a), residue C was tracked into both minerally-associated and particulate organic matter (MAOM and POM respectively). We hypothesized more MAOM formation due to the importance of the DOC-microbial pathway at the initial stages of decomposition with a smaller pool of POM due to the physical transfer path becoming important later in decomposition. After six months of residue decomposition, residue C was greater in POM than MAOM fractions for all treatments (either marginally or significantly), indicating the importance of POM formation pathways in both surface-applied and incorporated residue treatments. After accounting for differences in decomposition, I found that incorporated and surface-applied SOC formation efficiencies of residue decomposition (i.e., the fraction of residue C decomposed that resulted in SOC versus being lost through mineralization) were similar when SOC pools were summed. However, the SOC formation efficiency of surface-applied residue with soil disturbance was 40% lower than either surface-applied or incorporated residue, indicating that soil disturbance inhibited SOC formation when residue was surface applied. It is surprising that surface-applied residue POM formation was high in the short term because surface residue had to enter the soil matrix over time unlike incorporated residue. The high amount of POM likely formed through biotic transformation by soil fauna in contrast to POM protection likely through aggregation in the incorporated residue treatment. Thus, it appears that POM formation was more important than MAOM formation for both surface-applied and incorporated residue management. My results show that intact NT systems, particularly with earthworms and fungal networks may efficiently transfer POM C belowground during the initial six months of decomposition. At 12 months, I predict that protection of incorporated residue will be more pronounced compared to surface residue, since surface residue appears to be vulnerable to decomposition after irrigation events. Longer-term results (~3 years) will elucidate whether CT residue management continues to store more residue SOC than NT, potentially explaining why irrigated, NT systems might not consistently store more SOC. Climate change will likely increase the use of irrigation to meet crop water needs, thus we need to continue exploring the complexities of SOC formation and stabilization within irrigated NT and CT in order to sequester C for the health of our soil and planet.
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    Roles of residue management, microbes and aggregation in soil carbon stabilization under semiarid, irrigated corn
    (Colorado State University. Libraries, 2021) Oleszak, Hanna, author; Cotrufo, M. Francesca, advisor; Stewart, Catherine, advisor; Trivedi, Pankaj, committee member
    With atmospheric carbon dioxide levels continuously on the rise, it is critical that we focus our efforts on sequestering carbon (C) to slow global warming. To maximize these efforts, it is furthermore important to understand the pathways by which plant C inputs form soil organic carbon (SOC), as these pathways may inform the efficiency and duration of C stabilization. No-tillage is often recommended as a universal tool to draw C into the soil, yet literature reports mixed effects of tillage practices on C accrual. To maximize our efforts and best recommend agricultural practices for C sequestration, it is important to understand how the incorporation of residue within the mineral soil and disturbance associated with tillage impact plant residue C dynamics, as mediated by changes in microbial community and soil structure. While microbes play the active role in decomposing organic matter, soil structure can act as a gatekeeper to microbial accessibility to organic matter; thus, the effects of disturbance and residue incorporation upon the interplay of these two variables is highly important to consider. We used 13C labeled plant residue to track the movement of residue C in incorporated vs. surface-applied residue treatments in irrigated, semiarid corn for a period of 30 months. Both carbon dioxide (CO2) fluxes and soil cores were tested for total C and 13C enrichment to quantify residue-derived C contribution to CO2 efflux and to C accrual in the mineral soil over time, respectively. Furthermore, aggregate size fractionation and microbial community (via phospholipid fatty acids, PLFAs) were analyzed to assess how residue placement location and disturbance affect the mechanisms behind residue decomposition, and ultimately soil C stabilization. The incorporation of residue in the mineral soil resulted in significantly greater SOC formation efficiencies and greater SOC accrual in the first year, compared to the surface-application of residue. However, differences in SOC accrual subsided after 30 months, even though higher CO2 losses were measured in the surface applied residue treatments after 30 months. Residue-derived microbial biomass was greater in INC than SA or SA-NR at all timepoints, although this was only significant at 6 and 12 months. Residue-derived microbial community composition differed between early and later stages of decomposition, as well as between disturbed and undisturbed treatments. Mean weight diameters of aggregates featured a seasonal trend, with greater mean weight diameters in the fall. Furthermore, INC had significantly higher MWD at 5-10 cm at 6 months compared to surface-applied treatments, while disturbed treatments (INC and SA-NR) had significantly higher MWD's at depth at 12 months than SA. MWD was strongly correlated to residue-derived SOC in incorporated treatments, but not in surface-applied treatments. Finally, SOC formation efficiencies were more strongly correlated to residue-derived F:B in the incorporated treatment, compared to surface-applied treatments. Residue C recovery, SOC formation efficiencies, and residue-derived microbial biomass indicate that the incorporation of residue stimulates SOC formation through the DOC-microbial pathway and the physical transfer path concurrently, while the surface-application of residue follows a shift in SOC formation pathways from DOM-microbial SOC formation to physical transfer of residue. Additionally, correlations between residue-derived SOC, residue-derived F:B, and MWD indicate that the protection of residue C largely relies on aggregation when residue is incorporated.
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    Soil nitrogen cycling in agroecosystems as modified by biochar amendment and plant processes
    (Colorado State University. Libraries, 2019) Rocci, Katherine, author; Cotrufo, M. Francesca, advisor; Fonte, Steven, advisor; von Fischer, Joseph, committee member
    Ecosystem productivity is dependent upon cycling of nutrients, such as nitrogen (N). In agricultural systems, humans have greatly altered N cycling through the application of synthetic fertilizers such that soil N in agroecosystems is lost at higher rates than N in unmanaged systems. A variety of strategies have been assessed to reduce losses of soil N through nitrous oxide (N2O) emissions and leaching, which can negatively impact climate and water quality, respectively. The application of biochar, a carbon-rich soil amendment, has shown promise for increasing N retention in agricultural systems, but field and greenhouse studies often present less dramatic and often conflicting effects, suggesting the need for greater study in these environments. Further, the effects of biochar do not occur in isolation, but rather depend on plant processes that may affect soil N dynamics. This thesis explores these ideas through: (1) a greenhouse study considering the effects of different biochar types on N cycling with and without plants and (2) a field study looking at seasonal patterns of N cycling and fixation in alfalfa as altered by strategically-placed, low rates of biochar application. Study 1 sought to determine differential effects of biochar and plants, and raw and engineered biochar, on both fertilizer and innate soil N cycling using isotopically labelled fertilizer. While biochar effects on soil-derived N were minimal, we found that engineered biochar led to significantly higher leaching losses of fertilizer N. Plants, in contrast, were found to reduce N loss and increase overall recovery of fertilizer N. Study 2 focused on the effects of low and economically feasible application rates of two different biochars on N fixation, N loss, and mineral N availability over a growing season. We found no biochar effects on any N cycling parameter and, rather, found significant temporal effects in all N pools. Seasonal dynamics suggest connections between SIN availability and N fixation and loss. Indications of increased N loss with engineered biochar in Study 1 urge the need for greater study of biochars in combination with a variety of fertilizer types in order to provide the best recommendations to farmers. Lack of effects with biochar in Study 2 indicate that low application rates of biochar may not be useful for increasing N retention, suggesting the need to find a balance between economic and effective biochar application rates. Since both studies suggest that plant processes have more substantial impacts on N cycling than biochar amendment, via reduced N loss (Study 1) or increased symbiotic N input (Study 2), it is important that plants are included in more biochar studies such that the strength of biochar effects can be more realistically evaluated.
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    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.