Browsing by Author "Cotrufo, M. Francesca, committee member"
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Item Open Access Advancing understanding of the formation and stability of soil organic matter in a changing environment(Colorado State University. Libraries, 2015) Lavallee, Jocelyn M., author; Conant, Rich T., advisor; Paul, Eldor A., advisor; Cotrufo, M. Francesca, committee member; Borch, Thomas, committee member; Kelly, Eugene F., committee memberSoil is one of our most precious natural resources. It plays a key role in maintaining soil fertility and water quality, and represents a major reservoir in both the global carbon (C) and nitrogen (N) cycles. Soils contain more C and reactive N than the atmosphere and all vegetation combined, the majority of which is found in soil organic matter (SOM). Despite its considerable significance, little is known about the factors that control the formation of SOM, and its stability in the environment. Key questions pertain to whether environmental changes will increase the production of CO₂ during SOM formation and decomposition, forming a large positive feedback to climate change. Answering those questions required a better understanding of how various mechanisms that confer SOM stability are affected by environmental change. My dissertation research aimed to address some of these key questions, and to advance our overall understanding of SOM formation, SOM stability, and the response of stable SOM to changes in the environment. First, I conducted two soil incubation experiments using isotopically labeled (¹³C and ¹⁵N) plant material, which allowed me to track the incorporation of plant-derived C and N into SOM, and efflux of plant-derived C in CO₂. In one soil incubation, I tested the effects of plant litter quality and on the rate and efficiency of SOM formation (a measure of the amount of SOM formed versus the amount of CO₂ lost in the process) by comparing SOM formation from leaves versus roots. I found that plant litter chemistry (C/N ratio) was a reliable predictor of SOM formation after the initial stage of decomposition, with low C/N ratios resulting in more SOM formation and higher formation efficiencies overall. In the second soil incubation, I tested the effect of warming on the rate and efficiency of SOM formation, as well as the rate of destabilization of stable SOM. I found that warming generally led to lower formation efficiencies, causing greater CO₂ production per unit of SOM formed. Warming also led to higher rates of destabilization of stable SOM throughout the experiment. Next, I aimed to investigate the effect of warming on SOM in the field, using soils from two multi-factor climate change experiments. Results from that study suggested that while warming increased the rate of turnover of SOM in some cases, any resulting losses of SOM were offset by increased inputs of SOM, so that total SOM stocks were unchanged. Last, I investigated the persistence of pyrogenic SOM, which is thermally transformed by fire, in the face of land use change at three agricultural sites across the US. I found that pyrogenic SOM was present in all three soils, and had persisted to a greater extent than other SOM with land use change. Many studies of SOM dynamics do not account for pyrogenic SOM, and the results of my work suggest that this lack of accounting can preclude us from fully understanding the mechanisms behind SOM stability. Overall, my work advances our understanding of stable SOM in terms of how it is formed, and whether it will persist in the face of environmental change. Changes in plant litter quality and temperature may lead to changes fluxes of CO₂ to the atmosphere during SOM formation, and while some SOM (pyrogenic SOM) is highly stable in the environment, other SOM is susceptible to loss with warming and land use change. However, in the case of warming, increased plant inputs may offset increased rates of SOM decomposition.Item Open Access Effects of agricultural management on greenhouse gas emissions, carbon and nitrogen sequestration, and DAYCENT simulation accuracy(Colorado State University. Libraries, 2017) Toonsiri, Phasita, author; Davis, Jessica G., advisor; Cotrufo, M. Francesca, committee member; Conant, Richard T., committee member; Del Grosso, Stephen J., committee memberAgricultural activities affect greenhouse gases (GHGs) sources and sinks in terrestrial ecosystems. Organic fertilizer provides nitrogen (N) and organic carbon (C) to soil, resulting in enhanced N and C substrates for nitrification and denitrification which produce nitrous oxide (N2O) and for heterotrophic activity which generates carbon dioxide (CO2). Therefore, reduction of N and C substrates for N2O and CO2 production can reduce these emissions. Proper organic fertilizer application can regulate or reduce the loss of N2O from soil. In addition to reducing GHG production, increasing the potential of soil to sequester soil organic matter (SOM) is a key strategy for mitigating GHG emissions. Increasing organic inputs and reducing SOM turnover rate are keys for this mitigation. The persistence of SOM in agricultural soils is largely associated with the level of protection of C in stable aggregates. Therefore, applying proper practices to increase the stable aggregates can decrease the SOM decay rate, resulting in reduced loss of GHGs such as N2O and CO2 from soil. The focus of my dissertation is the study of (i) N2O and CO2 emissions from a lettuce field which received different organic fertilizer applications, (ii) SOM persistence and stable aggregates in organic and conventional farming systems, and (iii) simulation of N2O and CO2 emissions in organic lettuce using the DAYCENT model. The first study was performed in the summers of 2013 and 2014 at the Colorado State University Horticulture Research Center in Fort Collins, CO to determine the effects of environmental factors and four organic fertilizers (feather meal, blood meal, fish emulsion, and cyano-fertilizer) applied at different rates (0, 28, 56, and 112 kg N ha-1) on N2O and CO2 emissions from a lettuce field (Lactuca sativa L.). Feather meal and blood meal were applied at the full rate (single application) prior to transplanting lettuce, and fish emulsion and cyano-fertilizer were applied five times (multiple applications) after transplanting. The results showed that single application treatments significantly increased cumulative N2O emissions as compared with control, but multiple application treatments did not. However, single application treatments could be overestimated due to chamber placement over fertilizer bands. Cumulative CO2 emissions from single application and multiple application treatments in 2013 were not different, while in 2014, single application treatments presented higher CO2 emissions than multiple application treatments. The second study evaluated the effect of management on aggregate stability and SOM protection and persistence. The study was conducted by collecting soil samples from conventional and organic vegetable fields in different locations (California, Colorado, and New York) and at different soil depths (0-10, 10-20, and 20-30 cm) and analyzing their properties, microbial biomass, and aggregate size distribution. The results showed that organic farming systems have more microbial biomass, thus resulting in enhanced aggregate stability and the formation of organo-mineral bonding of microbial products, thereby storing higher C and N stocks than conventional farming systems. The last study compared N2O and CO2 emissions from field measurements with DAYCENT simulation. The data from the first study in 2014 was used to test the DAYCENT model. The result showed that DAYCENT simulated N2O and CO2 emissions from feather meal and blood meal (single application) better than for fish emulsion and cyano-fertilizer (multiple applications). In addition, the DAYCENT model had low potential to simulate soil water content and soil temperature in irrigated organic lettuce. Overall, the results of these studies show (i) multiple applications of cyano-fertilizer reduced N2O and CO2 emissions while maintaining lettuce yields, (ii) organic farming practices resulted in higher C inputs, microbial biomass, aggregate stability, and protected SOM relative to conventional farming practices, and (iii) DAYCENT reasonably simulated N2O and CO2 emissions from an irrigated organic lettuce field receiving solid organic fertilizers in single applications. These results should be used to support agricultural management decisions.Item Open Access Fire management effects on carbon flow from root litter to the soil community in a tallgrass prairie(Colorado State University. Libraries, 2013) Shaw, Elizabeth Ashley, author; Wall, Diana H., advisor; Cotrufo, M. Francesca, committee member; Kelly, Eugene F., committee memberBelowground litter decomposition is a major component of carbon cycling in grasslands, where it provides energy and nutrients for soil microbes and fauna. Fire, a historically frequent disturbance and a common management tool, removes above ground biomass and litter accumulation making belowground root litter of greater importance to decomposer food webs. While many studies use biomass measures of soil faunal groups to estimate changes in soil food web structure and energy flow, little is known about the flow of C from root litter to soil microbial and nematode communities in grasslands and if biomass measures can indicate this flow of C at a fine scale. Our greenhouse experiment first investigated how C from Andropogon gerardii (big bluestem) root litter was allocated into different soil microbial and nematode groups in frequently burned (FB) and infrequently burned (IB) tallgrass prairie soil. Incorporation of 13C into microbial fatty acids and nematode communities was determined on six occasions during decomposition in order to examine whether different groups of microorganisms and fauna were specialized on the root-litter derived C. Results showed that FB and IB soils supported microbial communities of differing community composition and abundance. IB had, generally, higher microbial abundance, more strongly dominated by bacteria than FB soil. Compound-specific stable isotope ratio analysis showed that root litter-C was more quickly incorporated into FB soil microbes. By the end of the experiment, all microbial groups were more highly 13C enriched in FB soils than in IB soils, with the exception of gram-negative bacteria for which there was no significant difference between the two soils. For nematodes, there was no significant difference in abundances; however, fungivore nematodes only incorporated root litter-C in FB soil while bacterivores, omnivores and predators derived at least some C from root litter in both treatments. Despite lower abundance of microbes in FB soil, total root litter mass loss did not differ between FB and IB soil, indicating higher microbial activity in FB soil. Our results reveal that FB prairie soil food webs are more closely coupled to root litter decomposition, where root litter is of increased importance as a C and nutrient source due to the frequent removal of standing biomass and shoot litter by fire. In the second part of our greenhouse experiment, we compared soil energy channel biomass measures with C flow into the soil food web. By coupling the energy channel biomass measurement approach with our decomposition study (using stable isotope enrichment to trace the flow of C into nematode trophic groups), we compared the quantified C flow to nematode energy channel biomass measures during decomposition of 13C-labeled big bluestem root litter. We hypothesized that biomass measures for nematode bacterial and fungal energy channels would indicate the proportion of root litter derived C incorporated into each nematode energy channel. Nematode biomasses and δ13C values were assessed initially (day 0) and after 180 days of incubation. Results showed the nematode bacterial energy channel dominated over the nematode fungal energy channel in both FB and IB grasslands. Yet, FB grassland soil had significantly higher nematode bacterial energy channel biomass than IB at time 0. In both soils, the nematode bacterial energy channel biomass increased significantly after the addition of root litter and there were no differences in the nematode bacterial channel biomass between the two soils at the final harvest (180 days). There were no differences between FB and IB soil's nematode fungal energy channel biomass at either day 0 or 180 days. 13C analysis of nematodes confirmed our hypothesis, as more root litter-C was concentrated in the dominant nematode bacterial energy channel in both FB and IB grassland soils. However, the IB soil's nematode bacterial energy channel had incorporated significantly more root litter derived C than the FB soil, despite no differences in these energy channel biomasses at the final harvest. The FB soil food web showed the opposite effect for the nematode fungal energy channel. These results indicate that while energy channel biomass measurements of nematodes give a broad overview of C flow, 13C decomposition tracer studies are more precise, and provide exact measures of C flow through soil food webs for ecosystem research. Overall, our results highlight the general view that plant litter is an important C-source in grasslands and further show that root litter-C is incorporated differently in frequently and infrequently burned soil food webs. We show that frequently burned soil food webs may be more specialized to decompose grass root litter. Our results indicate the C flow within soil food webs in differing burn management areas, and show differences between the frequently and infrequently burned tallgrass prairie.Item Open Access Modeling soil organic matter: theory, development, and applications in bioenergy cropping systems(Colorado State University. Libraries, 2015) Campbell, Eleanor Elizabeth, author; Paustian, Keith, advisor; Parton, William J., committee member; Cotrufo, M. Francesca, committee member; Reardon, Kenneth F., committee memberSoil organic matter (SOM) is a complex, dynamic, and highly variable soil constituent that is of fundamental importance to many soil functions, terrestrial ecosystem processes, and biogeochemical cycles. Its importance extends across scales, ranging from site-specific impacts on soil fertility to the global net exchange of carbon between terrestrial systems and the atmosphere. Soil organic matter is impacted by human activities, as seen most directly in agricultural systems. In this context, SOM models play an important role in integrating the understanding of complex, interacting soil processes across temporal and spatial scales, contributing to land use decision making by providing comparative evaluation of soil impacts associated with different management practices. Crop-based bioenergy feedstock productions systems are an emerging area for these types of SOM model applications. However, model evaluations are dependent on the theoretical basis of a given SOM model, as well as the quality of data used to drive the model for a given system or management scenario. This study therefore explores linkages between advances in the theoretical understanding of SOM dynamics, the development of SOM models to reflect these advances, and the application of SOM models to assess crop-based bioenergy production systems. First, five emerging areas in SOM research were reviewed in the context of SOM models, including SOM stabilization mechanisms, saturation kinetics, temperature sensitivity, dynamics in deep soils, and incorporation into earth system models. These reviews demonstrated the importance of identifying where SOM model development and applications are most limited, whether in theoretical understanding, in model implementation, or in data availability. For example, SOM saturation kinetics is theoretically well understood but remains difficult to implement in SOM models, only yielding improvements in a narrow set of ecological conditions. SOM temperature sensitivity and deep soil dynamics, however, are more limited by poor data availability in addition to poor theoretical understanding of interacting processes. A selection of shortfalls in SOM modeling were then addressed and explored with the Litter Decomposition and Leaching (LIDEL) model, a litter decomposition model that incorporates dynamic microbial carbon use efficiency (CUE) and yields dissolved organic carbon (DOC) as one of the byproducts of litter decomposition. In this analysis a hierarchical Bayesian statistical approach was used to test model performance and estimate unknown model parameters using experimental data. While this analysis showed the LIDEL model successfully integrates hypotheses for litter nitrogen and lignin controls on dynamic microbial CUE and the generation of DOC from litter decomposition, there remains a great deal of uncertainty in the rate of microbial biomass turnover as well as the proportioning of biomass from microbial turnover between solid versus soluble microbial products. Targeted experimental evaluation of the generation of DOC from microbes versus litter would support greater certainty in these model parameters and further model development for more general applications. Finally, the performance of the DAYCENT ecosystem model was evaluated in simulating US corn residue removal and Brazilian sugarcane production, two types of crop-based bioenergy feedstocks. DAYCENT is a process-based ecosystem model that integrates a soil organic carbon model to simulate carbon and nitrogen cycling processes through plant-soil interactions. The results of DAYCENT corn residue removal simulations highlighted several DAYCENT model biases, such as low corn yield estimates in dry regions and an overestimation of soil carbon loss with conventional tillage. Despite these biases, the results showed the importance of considering interactive effects between corn residue removal and other crop management practices in this type of bioenergy feedstock production system. The results suggest corn residue removal is ideally paired with management practices—such as reduced tillage—to maintain or improve soil carbon stocks. The analysis of Brazilian sugarcane management practices also highlighted management practices poorly simulated by DAYCENT, in particular identifying the need to improve DAYCENT simulations of high N₂O emission conditions observed in mechanically-harvested sugarcane, perhaps by adding simulation of DOC movement across the soil profile. However, this analysis also identified a need for more accurate and consistent daily precipitation data to drive DAYCENT simulations of N₂O emissions from Brazilian sugarcane management practices, particularly as there is interest in regionally-scaled analyses of direct greenhouse gas emissions from sugarcane production in Brazil. Taken together, the results of this study show the importance of a close connection between emerging areas in SOM theory, SOM model developments, and SOM model applications in crop-based bioenergy feedstock production systems. This connection allows for the identification of specific areas in need of further research, whether developing new modeling approaches or gathering additional data to parameterize, drive, and evaluate model simulations. This connection should remain a central emphasis as SOM models are increasingly incorporated into crop-based bioenergy policy and land management decision making.Item Open Access Revealing the controls of microbial nitrous oxide (N₂O) production and consumption using stable isotope methods(Colorado State University. Libraries, 2021) Stuchiner, Emily R., author; von Fischer, Joseph C., advisor; Baron, Jill, committee member; Cotrufo, M. Francesca, committee member; Knapp, Alan, committee memberOf the three primary anthropogenic greenhouse gases that contribute to climate change, carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O), N2O remains the most understudied. While N2O is the least abundant greenhouse gas of the three, it is also the most potent. N2O has a warming potential ~300x greater than CO2 and ~34x greater than CH4, and it is the primary stratospheric ozone depleting substance. Globally, the majority of N2O is emitted from soils through abiotic and microbial processes, but primarily through microbial metabolism. Microbes oxidize or reduce inorganic N as an energy source through different metabolic processes; they emit N2O as a byproduct of these processes. Microbes can also consume N2O by biochemically reducing it to N2, a harmless non greenhouse gas. However, the factors that regulate N2O production and consumption processes are diverse, interactive, and subject to rapid spatial and temporal changes. Drivers of N2O production and consumption include climate features, edaphic properties, and soil microbial community composition and activity. Characterizing these properties in relation to N2O flux behaviors requires a suite of measurements, and the way these factors interact to effect N2O production and consumption remain elusive. Furthermore, isotopic strategies exist to measure different N2O production processes and N2O consumption, but these strategies have been limited in their scope and capacity due to analytical constraints. Together, these challenges have limited our understanding of N2O production and consumption processes. These limitations have made it difficult to robustly disentangle the sources of N2O and understand the importance of N2O consumption in different soils. However, to curtail N2O emissions, we must be able to better understand and anticipate the drivers of N2O fluxes. In my dissertation, I seek to better understand what drives N2O production and consumption in diverse soils. In this work, I deploy innovative methods to measure different N2O production processes, and I seek to more granularly understand what controls N2O consumption. In Chapter 2 I develop a calibration algorithm for a high-throughput, novel, laser-based N2O isotopic analyzer. This allows for direct measurement of diverse microbial N2O-generating source processes. In Chapter 3 I use paired natural abundance and isotopic enrichment approaches to disentangle among N2O production processes more robustly. It will be useful for researchers to deploy paired isotopic strategies to discern more precisely which microbial process(es) are generating N2O. In Chapter 4, I shifted focus from N2O production to better understanding N2O consumption. Here, I sought to stimulate N2O consumption by amending soils with a specific blend of organic acids, and using isotope pool dilution, I learned that microbes consume more N2O when they are freed from electron donor limitation. In Chapter 5, I amended soils with different amounts of organic acids to further explore this electron donor limitation to N2O consumption. I learned that a variety of N2O flux responses can emerge from OC amendment, suggesting that perhaps our understanding of the drivers of N2O reduction are less resolved then we previously might have thought. Human activities have only exacerbated, and are poised to continue to exacerbate, N2O emissions through agricultural practices and industrial activities. There is burgeoning recognition of the importance in managing CO2 and CH4 emissions to mitigate the worst impacts of climate change, but the urgency for N2O, despite its potency and increasing atmospheric emissions, still lags. We must continue to advance understanding of the drivers of N2O production and consumption from soils, and my research makes strides to do this. This will be critical to effectively managing this highly potent greenhouse gas in a global climate that needs to make immediate, and dramatic, greenhouse gas reductions. A proposed Global Denitrification Research Network offers the potential for concerted, coordinated, and systematic N2O research to address the challenge of decreasing N2O emissions.Item Open Access Soil heterogeneity in agricultural and natural ecosystems: relationships between anaerobic activity, organic matter, nutrients, and greenhouse gases(Colorado State University. Libraries, 2017) Brewer, Paul E., author; von Fischer, Joseph, advisor; Calderón, Francisco, committee member; Conant, Richard, committee member; Cotrufo, M. Francesca, committee member; Wallenstein, Matthew, committee memberMany soil biogeochemical processes are difficult to predict, in part, due to the spatial heterogeneity of physical, chemical, and biological components of soil. Understanding how heterogeneity forms and affects biogeochemical processes is important because of the ultimate impacts on nutrient availability, carbon storage, and climate change. Oxygen and soil organic matter are two key components of soil microbial habitat, so I performed research to determine how the heterogeneity of each affect ecosystem functions. Oxygen can be absent in soil aggregates, litter patches, rhizospheres, and the guts of soil fauna, and when this occurs in unsaturated soils with oxic pore air these areas are referred to as anoxic microsites. The formation, persistence and impact of anoxic microsites are poorly characterized because these microsites are difficult to measure, especially across large areas that define ecosystem level processes. I studied what factors cause them to form and persist and how they affect C and N cycling and GHG fluxes. I performed focused, mechanistic laboratory studies of natural and agricultural soils, as well as field-scale studies of anoxic microsite effects in agricultural systems. In multiple studies, I circumvented the limitations and problems related to measuring soil oxygen or reduction-oxidation (redox) potentials at sub-millimeter scales instead by using gross CH4 production as an indicator of anoxic microsite presence and activity. I used two relatively recent methodological approaches to make gross CH4 measurements, CH4 stable isotope pool dilution for laboratory measurements and a CH4 process and transport model for field studies. I found that methanogenesis correlated with respiration, soil moisture, plant presence, and agricultural practice both in laboratory and field studies, indicating that the distribution of anoxic microsites is altered by climatic and land use factors in ways that are similar to the large-scale anoxic zones of wetlands. Methanogenesis was associated with elevated NH4+ concentrations and N2O flux, but lower NO3- concentrations. These relationships are consistent with slower nitrification and greater denitrification, so measurements of methanogenesis may be a useful proxy for other anaerobic processes. I also found evidence that consistent upland methanogenesis may stimulate methanotrophy (i.e., gross CH4 consumption) over the course of years, counterintuitively leading to an increase in net CH4 uptake. Finally, redox potential was not as strong an indicator of methanogenesis as expected, so I join others in concluding that redox potential may not be a desirable method for quantifying anoxic microsites. I also studied the effects of the spatial distribution of soil organic matter in the form of litter patches in soil. In a laboratory incubation, I manipulated the size and number of litter patches and soil moisture in a uniform mineral soil matrix. I found that dry soils with litter that was aggregated into larger patches exhibited greater rates of decomposition and nutrient availability, but that in wetter soils there were few effects of litter distribution. This complements my studies of anoxic microsites by showing that not only the presence of soil microsites, but variation in their size and distribution can also alter soil processes. In summary, my dissertation research concentrated on the causes and biogeochemical consequences of anoxic microsites and heterogeneity of organic matter in agricultural and natural ecosystems. My findings have increased our understanding of soil heterogeneity and the potential for it to cause significant changes in nutrient availability, decomposition, and greenhouse gas fluxes.Item Open Access The ecology of natural climate solutions: quantifying soil carbon and biodiversity benefits(Colorado State University. Libraries, 2021) McClelland, Shelby C., author; Schipanski, Meagan E., advisor; Cotrufo, M. Francesca, committee member; Dillon, Jasmine, committee member; Paustian, Keith, committee memberAchieving net zero greenhouse gas emission by 2050 will require simultaneous emissions reductions and carbon dioxide removal from the atmosphere. Natural climate solutions offer the most mature opportunities to remove atmospheric carbon and sequester it in woody biomass and soils but currently these options remain at low levels of adoption in the United States. To increase the uptake of these practices by growers, there needs to be greater confidence in the expected soil carbon benefits and improved understanding of potential environmental tradeoffs from these strategies across management and environmental contexts. This dissertation quantified the influence of management decisions and environmental variables on soil carbon responses under two proposed agricultural natural climate solutions: inclusion of cover crops and additions of organic amendments. The ecological and biodiversity co-benefits under these practices were also examined. Using a meta-analysis approach, the first chapter analyzed soil carbon responses to cover crop management decisions and environmental variables. Across 181 observations of 40 publications from temperate climates, inclusion of cover crops in cropping systems increased soil organic carbon stocks from 0-30 cm by twelve percent relative to a similarly managed system without cover crops. Management and environmental variables were responsible for variation in soil C responses across studies. The second chapter evaluated the application of organic amendments to improved and semi-native pastures at a semi-arid experimental site in northern Colorado. Over eight years and two applications of a high-quality organic amendment, soil organic carbon stocks as quantified by equivalent soil mass increased 0.7 Mg C ha-1 yr-1 from 0-20 cm under the organic amendment in the improved pasture relative to the control. After accounting for the additions of carbon from the two amendment applications, soil organic carbon stocks in the improved pasture increased by 0.46 Mg C ha-1 yr-1 from 0-20 cm. In contrast, there was no net change of soil carbon stocks in the semi-native pasture. The third chapter examined changes in plant and soil community composition and function after nitrogen application at the same experimental site. A single organic nitrogen addition to the improved pasture increased forage production, plant diversity, and soil microbial community composition and function. The stronger initial plant responses and the gradual change in microbial community composition and function suggests a plant-mediated response to organic nitrogen in this system, which likely impacted soil carbon cycling. Water-limited, semi-native pastures appear to be more resistant to change under one-time organic and inorganic nitrogen additions than irrigated, improved pastures. The final chapter of this dissertation compared two recommended approaches by the Food and Agriculture Organization of the United Nations for quantifying livestock production system impacts on biodiversity. The results illustrated how indicator selection and functional unit may result in discrepancies between the two methods. Together, these findings contribute to a growing body of scientific evidence in support of natural climate solutions for their climate and environmental co-benefits.Item Open Access The effect of irrigation and cropping systems on soil carbon and nitrogen stocks and organic matter aggregation in semi-arid lands(Colorado State University. Libraries, 2014) Abulobaida, Mohamed, author; Davis, Jessica G., advisor; Hansen, Neil, committee member; Cotrufo, M. Francesca, committee member; Conant, Richard T., committee member; Barbarick, Kenneth A., committee memberDemand for water is increasing as a result of population growth, economic activity and agricultural irrigation requirements. Thus, the balance between water demand and supply becomes unstable in countries suffering from water shortage. Therefore, overuse of non-rechargeable groundwater for irrigation in arid regions reduces the availability of water for other users. However, increasing drought periods, shortages of groundwater and urban competition for water have altered irrigated agriculture in Colorado. This may lead to changes in irrigated cropping practices such as alternative water conservation approaches from full irrigation to limited irrigation or dryland cropping systems to alleviate shortage. However, the risk of loss of soil C from dewatered cropland exists, because soil C levels may decline with reduced irrigation due to decreased C input into the soil. The overall goal of the study is to evaluate the impact of conversion from full irrigation to no- till limited irrigation or dryland cropping systems on soil carbon and nitrogen stocks and organic matter aggregation in semi-arid lands. This goal was achieved in the context of three studies that are included in this dissertation. First, the impact of irrigation and cropping systems management on SOC and TN stocks in a semi-arid environment was evaluated for wheat (Triticum aestivum), corn (Zea mays), and alfalfa (Medicago sativa) managed under various treatments of full irrigation, limited irrigation and dryland cropping systems. Second, the effect of different cropping systems with various irrigation levels and dryland cropping on soil aggregation and physical SOC stabilization in a semi-arid region was evaluated by measuring the aggregate size distribution, determining the C and N stocks in aggregate fractions and measuring the soil C mineralization rate in different cropping systems with various irrigation levels. Finally, the impact of conversion of irrigated farmland to limited irrigation or dryland cropping systems on SIC content was evaluated over a 3-yr period. The SOC and TN were analyzed at different depths from 0 to 60 cm depth in 2007 and 2010. Aggregate size distribution, SOC and TN contents for the aggregate size fractions [macro (M) and micro (m) aggregates, and silt & clay fractions] and for the isolated fractions from macroaggregates [coarse particulate organic matter (cPOM), microaggregate into macroaggregate (mM) and Silt&Clay-M)] were measured in soils from full irrigation alfalfa (Full-A), full irrigation corn (Full-C), limited irrigation forage alfalfa (Ltd-fA), limited irrigation forage corn (Ltd-fC), limited irrigation grain wheat (Ltd-gW), limited irrigation grain corn (Ltd-gC), dryland wheat (Dry-W) and dryland corn (Dry-C) treatments. SIC was measured in 2007 and 2010 for all treatments, and in 2013 for limited irrigation grain wheat-corn sorghum cropping system (Ltd-gWCFs). Soil pH was measured for all treatments in 2010 and for Ltd-gWCFs in 2013 in the different depths. The SOC and TN contents were significantly different among full irrigation and dryland treatments in the 0-20 cm layers of soil, but those differences were not significant below 20 cm depth. However, for all treatment comparisons, the differences remained significant throughout the soil profile in which crops rotated with alfalfa particularly limited irrigation systems (Ltd-fA and Ltd-fC) had higher SOC and TN stock compared with Ltd-gW. Our results showed the SOC and N stocks were significantly related to their concentrations not to bulk density for all depths. The SOC and TN distribution throughout the soil profile were stratified, and the SOM accumulation under the treatments almost occurred at similar C/N ratios. The amount of free microaggregates (m) under all treatments ranged from 69.4 to 75.6 % of the soil and the macroaggregates (M) comprised less than 18 % of the soil. The latter was higher under fully irrigated corn (Full-C), limited irrigation forage corn (Ltd-fC) and limited irrigation grain corn (Ltd-gC) compared to dryland corn (Dry-C). The SOC stock in the microaggregates occluded inside macroaggregates (mM) was higher under fully irrigated crops relative to dryland crops, especially in corn treatments. Conversion from full irrigation to dryland induced a reduction in macroaggregates. The Full-C treatment had higher SOC stocks in mM fraction relative to Dry-C. Our study indicates that irrigation and no-till management enhanced aggregate formation and increased C sequestration in mM fractions compared to dryland cropping systems. The SIC stock was significantly higher under limited irrigation grain wheat (Ltd-gW) treatments compared to full irrigation cropping systems (Full-C and Full-A) and limited irrigation forage cropping systems (Ltd-fC and Ltd-fA). However, there were no significant differences between Ltd-gW and other treatments (Ltd-gC, Dry-C and Dry-W). The Ltd-gW treatment gained more SIC compared to other treatments which accounted 19.4 % of total SIC sequestered under all treatments over the entire profile (0-60 cm) through the period of the study. Our results showed that the most important factor controlling the process of SIC formation in the 0-30 cm depth was soil pH which explains the high variation of SIC among treatments (R2 = 0.80, P <.01). This may be due to the effect of different cropping systems in which sunflower rotated into wheat-corn grain rotation (Ltd-gWCSf) consumed a greater amount of water than other summer crops and this may be effectively increasing soil pH in those crops rotated with sunflower.Item Open Access The influence of moisture availability on terrestrial ecosystems: effects on soil animal communities along a regional/global scale climate gradient(Colorado State University. Libraries, 2013) Sylvain, Zachary Adam, author; Wall, Diana H., advisor; Cotrufo, M. Francesca, committee member; Kelly, Eugene F., committee member; Knapp, Alan K., committee member; Seastedt, Timothy R., committee memberEarth's climate is being altered at an alarming rate, and the consequences of these changes on the planet's ecosystems are unclear. In addition to increased warming due to rising CO2 concentrations, alterations to precipitation patterns will influence soil moisture availability in terrestrial ecosystems and this will have important consequences for plant growth and the ability of soil systems to perform functions such as decomposition and nutrient cycling. The effects on soil systems are especially poorly understood, partly due to the many interactions between environmental conditions and the numerous species found within soil ecosystems, ranging from microbial organisms such as bacteria, archaea and fungi to soil animals including mites and nematodes. With chapter 2, I provide an overview of the role of soil biodiversity and the implications climate and land-use changes may have for ecosystems as a consequence of their effects on soil biodiversity. I then examine the current state of understanding for the influence of soil moisture availability on plant and soil communities of temperate ecosystems in chapter 3, and highlight challenges for future research such as the inclusion of diversity metrics and soil animal community responses in climate change experiments as well as studies that operate at scales larger than single sites in order to better capture the dynamics of ecosystem changes. My research focused on one aspect of climate change, the alteration of soil moisture availability within ecosystems due to changes in precipitation regimes, and whether it affected soil organisms, particularly soil mites and nematodes (Chapter 4 of this dissertation). These two groups were selected because of their high abundances and diversity within soil ecosystems, their dependence upon soil water availability as a consequence of life history traits and their contributions to decomposition and nutrient cycling processes. To examine the effects of changing moisture availability on communities of mites and nematodes I analyzed soil samples along a large scale regional/global climate gradient made up of four long-term ecological research (LTER) sites including Konza Prairie LTER (KNZ), Kansas, Shortgrass Steppe LTER (SGS), Colorado, Jornada Basin LTER (JRN), New Mexico and McMurdo Dry Valleys LTER (MCM), Antarctica. I established elevation transects across hill slopes to obtain landscape-scale gradients of soil moisture availability within each of these ecosystems and sampled existing experimental manipulations of moisture availability from 2009-2011. Mites and nematodes were sorted to trophic groups to determine their ecological role and how changes to their abundances may affect ecosystems. Mite and nematode abundances responded strongly to changes in moisture availability. Across the large-scale climate gradient of all four sites, a positive non-linear response was found with particularly large increases in animal abundances corresponding to incremental moisture increases at the lower limits of moisture availability. Within each of the ecosystems, however, the responses of soil animal trophic group abundances to moisture availability were very similar and were largely negative. In chapter 5 of this dissertation, I further explore the effects of soil moisture and top-down or bottom-up community dynamics on mite and nematode abundances. To do this, I constructed a structural equation model examining the direct and indirect effects of soil moisture availability and trophic interactions on soil animal trophic group abundances. Results of this model suggest that soil moisture strongly controls populations of these organisms. Additionally, predatory mite and nematode trophic groups have top-down controls on lower trophic groups, although these interactions do not appear to be due to predation and instead suggest the influence of additional, unmeasured environmental factors acting indirectly on lower-level soil animal trophic groups. With this dissertation, I demonstrate that changes to soil moisture regimes can have important effects on soil animal communities. A review of the literature (Chapter 3 of this dissertation) showed altered soil moisture availability had the clearest effects on plants, with effects on soil organisms being more idiosyncratic, likely as a result of stronger indirect than direct effects. Experimental evidence along a regional/global climate gradient of two desert and two grassland sites (Chapter 4 of this dissertation) show that increases to moisture availability have strong positive effects on mite and nematode communities, especially at low levels of moisture availability across this large, multi-site scale. At smaller scales (within individual ecosystems) this response becomes weaker and results in declines to animal groups at most sites. These results suggest that as precipitation regimes are altered as a consequence of climate change, the resultant alterations to soil moisture availability may have important feedbacks to terrestrial ecosystems. Observed changes to trophic group structuring in response to changes in moisture availability (Chapters 4 and 5 of this dissertation) show that food webs may be restructured due to future changes in moisture availability, leading to increases to root herbivory and increasing the amount of energy flowing through bacterial rather than fungal decomposition pathways. These changes to food webs can result in alterations to nutrient cycling pathways and shifts in carbon allocation within plant communities, which will further influence ecosystem dynamics.Item Open Access Tracing carbon flows through Arctic and alpine watersheds(Colorado State University. Libraries, 2018) Lynch, Laurel M., author; Wallenstein, Matthew D., advisor; Boot, Claudia M., committee member; Covino, Timothy P., committee member; Cotrufo, M. Francesca, committee memberOrganic matter turnover and mobilization links the productivity of terrestrial and fluvial ecosystems and regulates global climate. The first part of this dissertation reviews how our conceptual framework of soil organic matter (SOM) and dissolved organic matter (DOM) cycling has evolved, and emphasizes the role of microbial communities in controlling SOM stability. Chapter two investigates how fresh carbon (C) influences SOM cycling in soils underlying two dominant Arctic plant species. We amended soils colonized by Eriophorum vaginatum—a tussock-forming sedge—and Betula nana—a competitive dwarf shrub—with glucose, and employed stable isotope tracing to quantify substrate conversion to CO2, incorporation in microbial biomass, and retention in bulk soil. We measured responses during peak biomass, fall senescence, and spring thaw to assess interactive effects of glucose amendment and season. We also captured legacy responses to amendment by assessing the fate of glucose over short, intermediate, and longer-term periods. We found that glucose conversion to CO2 was twice as high in tussock soils, while stabilization in bulk soils was significantly higher in shrub soils. Our results highlight the extraordinary C storage capacity of these soils, and suggest shrub expansion could mitigate C losses even as Arctic soils warm. Chapter three evaluates the mobilization and transformation potential DOM of flowing through an Arctic hillslope. Widespread permafrost thaw is expected to increase CO2 release from soils to the atmosphere and transform the hydrological routing of water and DOM across Arctic landscapes. We traced the mobilization potential of DOM at two landscape positions (hillslope and riparian) and from two soil horizons (organic and mineral) using bromide, and characterized the chemical composition of DOM using solution state 1H-NMR and fluorescence spectroscopy. We found that compounds mobilized through the porous organic horizon were associated with plant-derived molecules, while those flowing through mineral soils had a microbial fingerprint. Landscape position also influenced the chemical diversity of DOM, which increased during downslope transport from hillslope to riparian soils. While the chemical composition of DOM varied across the landscape, the potential for rapid lateral flow across Arctic hillslopes and along the mineral-permafrost interface was uniformly high, suggesting DOM mobilization is an important mechanism of C loss from Arctic soils. Chapter four explores how geomorphic complexity and seasonal hydrology influence the cycling and transformation of DOM in alpine headwater streams. We collected surface and hyporheic water samples from two watersheds varying in channel complexity (single-thread and multi-thread) at eight time points spanning the seasonal hydrograph. We found that connectivity across the terrestrial-aquatic interface was maximized during peak discharge and decreased through the season. The chemical composition of DOM, evaluated using electron impact gas chromatography mass spectrometry and fluorescence spectroscopy, varied with watershed connectivity, with increasingly divergent DOM profiles observed with a loss of hydrologic connectivity. We suggest that widespread channel simplification, resulting from land-use and management changes, will reduce DOM processing and compromise ecosystem function.Item Embargo Tropical forest root characteristics and responses to drying across environmental gradients(Colorado State University. Libraries, 2024) Longhi Cordeiro, Amanda, author; Cusack, Daniela F., advisor; Ojima, Dennis, committee member; Cotrufo, M. Francesca, committee member; Conant, Richard, committee memberFine roots represent the interface between plants and soils, and as such regulate all major biogeochemical cycles in terrestrial ecosystems, including tropical forests. Tropical forests play a crucial role in global carbon (C) cycling, largely due to their extensive root biomass and significant soil C stocks. However, these ecosystems have been experiencing more frequent severe droughts across some regions and are predicted to continue experiencing these extreme drought events in the future. This dissertation seeks to contribute to the understanding and synthesis of tropical root responses to drying in varying environmental conditions. In chapter 1, I gave an introduction about the importance of fine roots to ecosystem function and the impacts of drying in tropical forests. In chapter 2, I characterized root biomass, morphology, nutrient content, colonization to 1.2 meters depth as well as and arbuscular mycorrhizal fungal (AMF) to 20 cm depth in 32 plots across four distinct lowland Panamanian forests which are representative of the vast variation in soil fertility and mean annual precipitation (MAP) found across tropical forests. Root characteristics measurements, such as morphology and chemistry, at soil layers deeper than 30 cm have been rarely documented and to the best of knowledge this is the first study in tropical forests. I observed that that some root traits changed with soil depth similarly across sites while others had site-specific variation. I also observed larger variation at the soil surface and that morphological traits, in addition to root biomass can affect soil C stocks. In chapter 3, the effects of experimental and seasonal drying on fine root dynamics were explored using a partial throughfall reduction experiment across the same 32 plots as in chapter 2. I found that chronic drying impacted root biomass, productivity, morphology and arbuscular mycorrhizal fungi (AMF) colonization. Root biomass and characteristics also changed across seasons with different dynamics across depths. Chapter 4 focused on the effects of drought on tropical seedling development in a controlled chamber environment. I observed that drying decreased seedling growth, but high soil fertility and AMF inoculation mitigated these effects. I also observed changes in root morphology, leached C, new C allocation patterns, and aboveground traits in response to drought, but with usually interacting effects with fertility and AMF inoculation. Chapter 5 contributes a tropical root database (TropiRoot 1.0 database) with root data extracted from scientific papers across different countries and continents. Overall, this dissertation provides novel results and insights into the variation in root characteristics among tropical forests and their responses to climatic drying with interacting effects of fertility, symbionts and soil depth effects. It brings novel measurements that have never been published in tropical forest studies. In chapter 2, I found novel results about how different tropical forests had similar patterns of root variation with depth. It indicated differences in resources acquisition at the soil surface (likely for nutrients) and at deeper soil layers (likely for water) that are usually less investigated. I also showed a large variation of roots at surface soil across different forests that may influence forest responses to global change factors. In chapter 3, I supported some results across the literature such as drying decreasing root growth at the soil surface. However, I added new results such as drying decreasing root productivity at deeper soil layers, and changing root morphology and associations with symbionts probably to compensate the lower root growth. All together I observed that drying promoted changes in acquisition strategies and also that fertile forests may respond differently to drying. In chapter 4, I showed some clear tradeoffs in plant traits providing evidence that they are constantly changing in response to the environment. Also, I provided some novel results on the mechanisms, such as nutrient retention, on how mycorrhizal and fertility mitigated some negative effects of drying on plant growth. This aligns with the field study showing some possible resilience in the fertile forests to drying. The findings highlight the complex interactions between root traits and environmental conditions, offering important implications for predicting tropical forest responses to changing moisture and nutrient availability. All these chapters together provided a good understanding on how different forests respond to environmental changes. These impacts on soil C storage, links with root function and possible larger vulnerability of some forests are great topics for future studies.Item Open Access Understanding soil treatment effectiveness in dryland restoration: ecological barriers, contexts, and baseline conditions(Colorado State University. Libraries, 2023) Kimmell, Louisa, author; Havrilla, Caroline, advisor; Cotrufo, M. Francesca, committee member; Sueltenfuss, Jeremy, committee memberLand degradation is one of the greatest environmental issues our planet faces today, with over 33% of Earth's soils currently degraded. Drylands are especially vulnerable to soil degradation given their history of intensive land use and desertification. However, dryland restoration can be very difficult, and often fails when seeding is used as a sole treatment. Soil-based restoration, which includes abiotic treatments like organic amendments and water collection pits, and biotic treatments like microbial inoculation, may be needed for ecosystem recovery in drylands. Compared to plant-based restoration, however, less is known about how and when to use active soil restoration for optimal results. To improve our understanding of how to best use active soil restoration to restore degraded drylands, we conducted two research studies: (1) a global meta-analysis of dryland soil restoration treatment effectiveness across environmental gradients (Chapter 1), and (2) a regional field study comparing microbial communities across degraded, intact, and revegetated dryland sites to understand baseline conditions and when active soil restoration (e.g., inoculation) may be needed to improve soil conditions (Chapter 2). For project 1, we generated a global database from 155 publications and 1,403 unique studies of responses of soil health variables [i.e., aggregate stability, bulk density, soil moisture, soil organic carbon, soil nitrogen, mycorrhizal colonization, and basal respiration] to soil restoration relative to untreated controls. We then used quantitative meta-analysis techniques to analyze soil restoration effect sizes. In Chapter 2, we collected soil samples from paired reference, degraded, and revegetated plots across seven different dryland sites across the southwestern United States, sequenced the 16S and ITS rRNA gene regions from extracted DNA for bacteria/archaeal and fungal communities (respectively), and analyzed differences in microbial community composition among samples. Results from the meta-analysis suggested that active soil restoration generally improves soil health and is most effective in arid, fine-textured soils. Organic amendments were most effective at increasing soil organic carbon, while fungi inoculation treatments were most effective at increasing mycorrhizal colonization. From the regional microbiome study, we found that soil microbial communities differ between paired degraded and intact sites, and that degraded sites have lower abundances of biocrust-forming bacteria and dark septate endophytic fungi, which are both indicative of reference/intact conditions, making these taxa potential targets for inoculation treatments. However, we found that microbial communities do not differ between degraded and revegetated sites, suggesting that degraded sites may require active interventions beyond revegetation, such as direct microbial inoculation, to replenish microbial communities. These findings advance understanding of the effects of dryland degradation and restoration on soil health and have actionable implications for improving restoration decision-making, and thus improve outcomes in dryland restoration.Item Open Access Unraveling key drivers of microbial community assembly and impacts on microbial function(Colorado State University. Libraries, 2015) Rocca, Jennifer Doyle, author; Wallenstein, Matthew D., advisor; Cotrufo, M. Francesca, committee member; Knapp, Alan K., committee member; Smith, Melinda D., committee memberTo view the abstract, please see the full text of the document.Item Open Access Variation in soil organic carbon across lowland tropical forest gradients: soil fertility and precipitation effects on soil carbon organic chemistry and age(Colorado State University. Libraries, 2022) Blackaby, Emily, author; Cusack, Daniela F., advisor; Boot, Claudia M., committee member; Cotrufo, M. Francesca, committee memberTropical forests hold large amounts of carbon (C) in both aboveground biomass and belowground soil organic carbon (SOC) stocks. Climate change is expected to alter tropical forests' precipitation with some forests already showing decreased rainfall. We analyzed SOC molecular composition and age in lowland tropical forests of Panama across fertility gradients, rainfall ranges, and soil order. We hypothesized that H1) rainforests with relatively greater rainfall store larger amounts of proteins (N-alkyl) and lipids (alkyl) in SOC because of greater microbial biomass and H2) subsurface SOC stocks in more strongly weathered, clay-rich soils are older (as indicated by radiocarbon) because of great sorption capacity. We found that overall, carbon decreased and became older with depth across all samples. Solid-state 13C NMR spectroscopy indicated that soil order and depth were significant predictors of C functional group abundances while phosphorus (P) was a significant predictor of alkyl, aromatic, and carboxyl C. Alkyl/O-Alkyl ratios increased with depth indicating increased degradation of the SOC. ∆14C values indicated older C with depth and varied significantly with soil order where Oxisols were the oldest and Mollisols the youngest. Soil N % and K % were significant predictors of younger soil C. Additionally, biomolecular composition of SOM from 0-10 cm was a significant predictor of ∆14C at 25-50 cm. We found that higher abundances of alkyl and O-alkyl C corresponded with younger C at depth and higher abundances of aromatic and phenolic C contained older C at depth.Item Open Access When the wells run dry: soil organic carbon dynamics during the transition from irrigated to dryland cropping systems(Colorado State University. Libraries, 2021) Núñez, Agustín, author; Schipanski, Meagan, advisor; Cotrufo, M. Francesca, committee member; Davis, Jessica, committee member; Paustian, Keith, committee memberIn many parts of the world, irrigation must decrease due to declining water availability and increased demand from other water users. The Ogallala Aquifer, one of the biggest aquifers in the world, is one example where declining groundwater levels threaten agricultural productivity and social communities across large parts of the semiarid High Plains. In this semiarid region, irrigation is not only fundamental for crop productivity, but it also has positive effects on soil organic carbon (SOC). However, little is known about the changes in SOC dynamics during the transition from irrigated to dryland cropping systems, which has important potential implications for the long-term productivity of these agricultural systems as well as the potential for the soils of the region to be a net sink or source of CO2. The general objective of my dissertation was to study how irrigation retirement affects SOC dynamics in semiarid agricultural systems of the Ogallala Aquifer Region. I used field experiments to quantify the early changes in crop productivity and C inputs, soil microbial communities, C outputs and SOC formation and turnover during the transition from irrigated to dryland cropping systems. Irrigation retirement had a stronger influence on C inputs than on C outputs because plants responded faster and to a greater magnitude than soil microorganisms to water limitations. Given intrinsic differences in growing season and water requirements, crops vary in their sensitivity to water stress, and wheat agroecosystems were less affected by irrigation retirement than maize agroecosystems. After three growing seasons, there was lower microbial activity and SOC formation in dryland (retired) than irrigated maize, but we did not find changes in the decomposition rate of old SOC. In winter wheat, low differences in soil moisture and crop productivity resulted in almost no changes in microbial activity and SOC dynamics after irrigation retirement. These short-term study results suggest that large losses of crop productivity and C inputs without changes in C outputs will decrease the formation of new SOC, thus affecting SOC storage on the longer term. I confirmed this outcome with on-farm observations of the longer-term effect of irrigation retirement on SOC stocks under different management options. After 7-10 years, sites that used to be irrigated and transitioned back to dryland systems had lower SOC than long-term irrigated sites and had the same SOC stocks as long-term dryland fields, confirming the relatively short legacy effect of irrigation. An exception to this was the transition from irrigated agriculture to perennial, ungrazed grasslands enrolled in the Conservation Reserve Program (CRP). Fields that transitioned into CRP were able to maintain intermediate SOC levels that did not differ from the currently irrigated controls. Taken together, the results of my dissertation indicate that there will be rapid and significant losses of SOC during the transition from irrigated to dryland cropping systems in the Ogallala Aquifer Region. These losses will occur mainly in response to changes in C inputs. Therefore, comparison of biomass and residue production could be used to rapidly identify crop and vegetation management strategies with higher potential to minimize the negative impact of irrigation retirement on SOC.