Browsing by Author "Wallenstein, Matthew, committee member"
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Item Open Access A microbiome approach to cultivation and management of sugar beet(Colorado State University. Libraries, 2024) Gaylord, Margaret, author; Trivedi, Pankaj, advisor; Charkowski, Amy, committee member; Wallenstein, Matthew, committee memberThe world's population is projected to reach 9.8 billion by 2050, while the urgent threat of climate change is expected to impact crop physiology and pest dynamics. Understanding, preserving and leveraging the plant-associated microbiome can result in enhanced agroecosystem functioning and disease resistance for agricultural crops, thus improving food security. Sugar beet, an economically important sugar producer in the northern hemisphere, offers insights into plant-microbiome dynamics due to its susceptibility to pathogenic microbes and its association with disease suppressive soils. Cultural and chemical management practices of sugar beet are a persistent debate due to the potential negative effects on the essential microbiome and the emergence of resistant populations. To investigate the impact of weed control strategies on the soil microbiome, we conducted a long-term field study at two locations. Using next-generation sequencing and in vitro assays, we assessed the effects of glyphosate, a mix of selective herbicides and tillage treatments on the structure and function of the soil microbiome. Furthermore, we isolated 136 bacteria from the sugar beet agroecosystem and evaluated their antagonistic abilities against key diseases of sugar beet. Through in vitro and greenhouse assays, we identified effective microbial consortia for disease reduction. Additionally, we investigated the interactions between a single antagonistic isolate and an important fungal disease of sugar beet using transcriptomic analysis to reveal underlying mechanisms for biological control and pathogen response. This comprehensive understanding of the impact of various management strategies on the microbiome provides crucial insights for future crop management and highlights the potential for exploiting beneficial microbes to enhance disease control.Item Open Access Biochar effects on soil microbial communities and resistance of enzymes to stress(Colorado State University. Libraries, 2013) Elzobair, Khalid, author; Stromberger, Mary, advisor; Ippolito, James, committee member; Barbarick, Kenneth, committee member; Wallenstein, Matthew, committee memberBiochar, a product of the pyrolysis of organic material, has received wide attention as a means to improve soil fertility and crop productivity, absorb pollutants in soil, and sequester carbon to mitigate climate change. Little information exists on the short- and longer-term effects of biochar on soil microbial communities and enzyme activities, relative to other organic amendments such as manure. Therefore, the objectives of this study were to determine the short and longer terms effects of biochar amendment on soil microbial communities, arbuscular mycorrhizal (AM) fungi, and enzyme activities in a semi-arid soil. Secondly, due to the porosity and surface area of biochar, enzyme stabilization on biochar was assessed to determine if biochar could prohibit the loss of extracellular enzyme activity following a denaturing stress. In a field study, a fast pyrolysis biochar (CQuest) derived from oak and hickory hardwood was applied to calcareous soil of replicate field plots in fall 2008 at a rate of 22.4 Mg ha-1 (dry wt.). Other plots received dairy manure (42 Mg ha-1 dry wt), a combination of biochar and manure at the aforementioned rates, or no amendment (control). Plots were annually cropped to corn (Zea maize L.). Surface soils (0-30 cm) were sampled directly under corn plants in late June 2009 and early August 2012, one and four years after treatment application, and assayed for microbial community fatty acid profiles and six extracellular enzyme activities involved in C, N, and P cycling in soil. In addition, AM fungal colonization was assayed in corn roots in 2012. Relative to the manure treatment, biochar had no effect on microbial community biomass, community structure, extracellular enzyme activities, or root colonization of corn by AM fungi. Manure amendment increased microbial biomass in 2009, when total FAME concentration was 2.3-fold and 2.6-fold greater in manure and biochar plus manure treatments, respectively, compared to non-amended soil. The concentration of the AM fungal FAME biomarker (16:1ω5c) was significantly reduced by the manure treatments in 2009 (P=0.014) but not in 2012. In 2009, principle components analysis (PCA) revealed shifts in the FAME structure of the soil microbial community in response to the manure treatments. However, the effects of manure on microbial biomass and community structure were short-lived, as no effects were observed in 2012. A laboratory incubation study was conducted to determine whether biochar would stabilize extracellular enzymes in soil and prohibit the loss of potential enzyme activity following a denaturing stress such as microwaving. Soil was incubated in the presence of biochar (0, 1, 2, 5, or 10% by weight) and exposed to increasing levels of microwave stress. Results showed that extracellular enzymes responded differently to biochar rate, stress level and their interactions. The main effect of stress level was highly significant (P<0.0001) on the potential activities of β-glucosidase, β-D-cellobiosidase, N-acetyl-β-glucosaminidase, and phosphatase enzymes. Potential activity of leucine aminopeptidase was significantly affected by biochar rate (P=0.016), stress level (P<0.0001), and their interaction (P=0.0008). In addition, potential activity of β-xylosidase was marginally affected by biochar's interaction with stress level (P=0.066). The potential activity of these two enzymes were reduced after a 36-day incubation in the presence of biochar. For β-xylosidase, intermediate application rates (1 and 5 %) of biochar prevented a complete loss of this enzyme's potential activity after soil was exposed to 400 (1% biochar treatment) or 1600 (5% biochar treatment) J microwave energy g-1 soil. In conclusion, this study demonstrated that land application of biochar may not affect microbial community biomass, potential activities of soil enzymes, or AM fungal biomass in soil, or alter community structure, presumably because of the type of biochar employed in this study. Both biochar and manure added carbon to soil, but microorganisms were responsive to manure rather than biochar. While biochar had no effect on potential activity of soil enzymes in the field study, the laboratory incubation study revealed that biochar has the potential to stabilize extracellular enzymes and prohibit the loss of potential enzyme activity in soil when exposed to a denaturing stress.Item Open Access Crop protection in industrial algae farming: detecting weedy algae and characterizing bacterial communities(Colorado State University. Libraries, 2015) Fulbright, Scott Paul, author; Reardon, Kenneth F., advisor; Reddy, Anireddy, committee member; Laybourn, Paul, committee member; Wallenstein, Matthew, committee member; Tisserat, Ned, committee memberMicroalgae are a promising source of feedstock for biofuel and bioproducts. Algae have higher rates of biomass production than terrestrial crops, and therefore can use less land for producing equivalent energy compared to other biofuels. Elite algae strains are chosen based on traits such as fast and robust growth, and rapid production of desired biochemical products, including fatty acids and other high-energy compounds. Monocultures of elite strains are grown in large algae production systems. A major challenge algae growers face is consistently growing robust cultures of elite algae. This is due to unwanted organisms invading cultures such as weedy algae that contain less desirable biochemical products, and bacteria that can detract from algae growth, thereby reducing overall system productivity. Historically, algae have not been grown at scales required for biofuels and bioproducts, and thus there is a lack of fundamental pest management knowledge and developed tools. In this work, we developed three polymerase chain reaction (PCR)-based tools for detecting and quantifying weedy and elite algae. We developed a simple and inexpensive CAPS (cleaved amplified polymorphic sequence) assay that can determine the presence of dominant algae species in cultures. Also, we developed and validated qPCR primers were able to detect one weedy algae cell in 108 cells in a culture. Compared to flow cytometry, the qPCR primers were 104 times more sensitive for detecting weedy algae. We validated tools by monitoring industrial algae systems, and exhibited their utility for assisting in culture management decisions. Bacteria are also prevalent in industrial algae cultures yet little is understood about their dynamics or role in the ecosystem of elite algae cultures. We sampled small, medium and large cultures from an industrial algae system growing elite algae Nannochloropsis salina, and sequenced the 16S rDNA gene and used QIIME bioinformatics program to analyze data. In this study, we characterized bacterial communities diversity, richness, and composition in industrial algae bioreactors during the scale-up process, through time and during various algae growth rates. We demonstrate that bacterial diversity richness increases as the size of the algae production system increases in the scale-up process. Therefore, larger cultures are comprised of more complex communities than smaller cultures, thus increasing the probability of detrimental algae-bacteria interactions. We identified a single core bacterium Saprospiraceae that was present in 100% of samples, and was on average the most abundant bacterium in all systems. Further, we identified a Deltaproteobacterium that was detected at abnormally high relative abundances in poorly growing algae cultures. Identifying pest bacteria that can detract from elite algae growth is an important step in developing crop protection strategies. We isolated bacteria from a poorly performing algae system and determined their influence on algae growth. We identified a single isolate, S7 as a growth inhibiting bacteria that was capable of completely inhibiting Nannochloropsis gaditana and N. salina growth. The bacterium was characterized as Bacillus pumilus. Additionally, we identified nutrients and cell concentrations required for inhibition of N. gaditana and N. salina. B. pumilus inhibition effect is species-specific as it did not inhibit weedy algae, Chlorella vulgaris and Tetraselmis striata. Due to this, B. pumilus is capable of manipulating algae population composition and reducing productivity. Contaminating organisms such as bacteria will often be prevalent in algae systems and understanding their influence on culture productivity is essential for successful large-scale cultivation of algae. In summary, we 1) developed molecular tools to monitor weedy algae that can be used by growers, 2) characterized bacterial communities in industrial algae system cultures, and 3) identified a novel pest for elite algae, N. gaditana and N. salina.Item Open Access Exploring the role of planned and unplanned biodiversity in the soil health of agroecosystems(Colorado State University. Libraries, 2021) Kelly, Courtland, author; Fonte, Steven J., advisor; Schipanski, Meagan E., committee member; Wallenstein, Matthew, committee member; Hall, Ed, committee memberTo view the abstract, please see the full text of the document.Item Open Access Greenhouse gases in arctic and alpine streams: patterns, drivers, and responses to disturbance(Colorado State University. Libraries, 2016) Dunn, Samuel T., author; von Fischer, Joseph, advisor; Baron, Jill, committee member; Gooseff, Michael, committee member; Wallenstein, Matthew, committee memberStreams have recently received attention as previously unaccounted for sources of greenhouse gases (GHG; CH4,CO2, and N2O) to the atmosphere. While progress has been made at incorporating streams into global estimates of GHG flux, many spatial gaps remain, especially in remote regions of the Siberian Arctic and high elevation ecosystems worldwide. To address a critical gap in regional estimates of emissions and better understand the sources of variability of those emissions, we quantified the vertical flux of CH4, N2O, and CO2 and examined the sources of variability and spatial-temporal patterns of those fluxes in Siberian streams and high elevation streams. Emissions to the atmosphere from Siberian streams were smaller than expected with mean fluxes of CH4 (12.4 µmol CH4 m-2 d-1) and CO2 (2.6 mmol m-2 d-1). In contrast, downstream export of dissolved gas is three orders of magnitude larger than emissions to the atmosphere and the fate of this dissolved gas is ultimately unknown. Water column transit time, dissolved oxygen concentration, and specific conductivity explained the majority of variability in the emissions of both gases, but variability in CO2 emission was equally influenced by biological and physical processes whereas variability in CH4 emission is mainly influenced by biological variability. High elevation streams were, on average, net sources of CH4, CO2, and N2O to the atmosphere over the course of the observations period. However, instances of net uptake of these gases from the atmosphere by streams were also recorded during this time. Variability in mountainous gas emissions is strongly influenced by variability in the concentration gradient and less so by the reaeration coefficient. However, some site characteristics, namely elevation and silt fraction of sediments, were also contributing factors to overall emission variability. We observed a concurrent increase in N2O emission and stream dissolved organic carbon (DOC) during an algae bloom in an upstream lake which explained a large part of the seasonal variability and average emission rate. Stream sediments from these contrasting sites, some of which were adjacent to other aquatic systems, showed a range of responses to alterations of their chemical environment not unlike what occurred during the algal bloom. From these data we were able to observe that enhanced N2O production was only possible under aerobic conditions, suggesting that inefficient nitrification, as opposed to enhanced denitrification, was the source of the increase in N2O emissions.Item Open Access 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 memberLeaf 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.Item Open Access Prions in the environment: from the host to the environment and back again(Colorado State University. Libraries, 2013) Wyckoff, A. Christy, author; Zabel, Mark, advisor; VerCauteren, Kurt, advisor; Spraker, Terry, committee member; Wallenstein, Matthew, committee memberTo view the abstract, please see the full text of the document.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 Soil organic matter as a nitrogen source for Brassica napus(Colorado State University. Libraries, 2020) Carter, Candace, author; Schipanski, Meagan, advisor; Fletcher, Richard, committee member; Vivanco, Jorge, committee member; Wallenstein, Matthew, committee memberDecreasing nitrogen (N) fertilizer losses from agricultural systems is a major focus in sustainable agriculture research. Most research to date has focused on reducing and managing N fertilizer additions in time and space. However, approximately half of the N taken up by most field crops is not from that season's fertilizer but is derived from the mineralization of soil organic matter (SOM). Despite its importance, intentionally managing crop utilization of background SOM as a source of N has received little attention. Our study explored N uptake patterns of rapeseed or canola (Brassica napus) in a greenhouse pot study and in a field setting. In the greenhouse pot study, we explored the effects of rapeseed genotypic diversity on N uptake from organic and inorganic N sources. We used dual 15N labeled ammonium-nitrate fertilizer to examine N uptake patterns of rapeseed in different N environments. Using a full factorial experiment, 10 varieties were grown under four treatments that included combinations of high and low N fertilizer and SOM. While we found limited varietal differences in N uptake dynamics, SOM was an important N source across all varieties even as N fertilizer availability increased. Our High SOM/High Fertilizer treatment obtained 64% of N from SOM, while the High SOM/Low Fertilizer obtained 89% of total N from SOM. Nitrogen source uptake was dependent on the treatment level N availability. We found evidence of enhanced SOM mineralization in higher N treatments, where high N fertilizer additions increased overall plant N uptake from SOM by 42% relative to low N fertilizer treatments. Although overall plant N uptake from SOM increased in high fertilizer treatments, microbial enzyme activity related to nutrient mineralization processes was suppressed in the high N fertilizer treatments relative to low fertilizer treatments in similar SOM environments by 16-58%. This result suggests high N fertilizer additions change microbial nutrient cycling dynamics. Based on the general results from our greenhouse study that N from SOM had an additive effect to fertilizer additions on rapeseed biomass production, we estimated the potential yield contributions of SOM increases with the adoption of conservation tillage practices in Canada. We used yield data provided by a literature search and the Canola Council of Canada to examine how the adoption of conservation tillage practices over the last 25 years has contributed to crop yield improvements in the Canadian prairies. We found that on average canola yields increase by 54.9 kg/ha per year, with 13% of annual yields attributed to agronomic practices. We estimated that the adoption of conservation tillage has increased soil N by 320 kg N/ha per year. Although N mineralization is highly variable and dependent on many factors, we estimated that 2% of total soil N is available annually for plant uptake. This translated to an additional 6.4 kg N/ha per year available for plant nutrition. We estimated that 91 to 164 kg/ha of the annual canola yield increases could be contributed to an increase in soil N availability. It is important to acknowledge the complex nature of N mineralization and plant N uptake patterns. This complexity likely leads to an underestimation of the contribution of SOM as an N source in cropping systems. Because of the dynamic and complex nature of agricultural systems, an integrated approach to N management where both N fertilizer and SOM are considered in crop breeding and system management is an important step in improving agricultural sustainability.Item Open Access Temperature sensitivity as a microbial trait(Colorado State University. Libraries, 2017) Alster, Charlotte J., author; von Fischer, Joseph, advisor; Cotrufo, Francesca, committee member; Smith, Melinda, committee member; Wallenstein, Matthew, committee memberReaction rates in biological systems are strongly controlled by temperature, yet the degree to which temperature sensitivity varies for different enzymes and microorganisms is being largely reformulated. The Arrhenius equation is the most commonly used model over the last century that predicts reaction rate response with temperature. However, the Arrhenius equation does not account for large heat capacities associated with enzymes in biological reactions, thus creating significant deviations from predicted reaction rates. A relatively new model, Macromolecular Rate Theory (MMRT), modifies the Arrhenius equation by accounting for the temperature dependence of these large heat capacities found in biological reactions. Using the MMRT model I have developed a novel framework to assess temperature sensitivity as a biological trait through a series of experiments. This work provides evidence that microbes and enzymes can have distinct heat capacities, and thus distinct temperature sensitivities, independent of their external environment. I first assessed temperature sensitivity of soil CO2 production from different soil microbial communities and then worked with pure cultures to examine temperature sensitivity of enzyme activities from soil microbial isolates. From these experiments I determined that temperature sensitivity varies based on genetic variation of the microbe and substrate type as well as examined the importance of using MMRT over the Arrhenius equation. Finally, I used a meta-analysis to analyze the distribution of temperature sensitivity traits to look across a variety of biological systems (e.g., the food industry, wastewater treatment, soils). I found that temperature sensitivity traits vary with organism type, environment, process type, and biodiversity. Exploring temperature sensitivity as a trait allows for new insights of soil microbes from an ecological perspective as well has the potential to inform ecosystem climate models.Item Open Access The effects of temperature and moisture on alpine microbial processes across a gradient of soil development(Colorado State University. Libraries, 2012) Osborne, Brooke Bossert, author; Baron, Jill, advisor; Cotrufo, Francesca, committee member; von Fischer, Joseph, committee member; Wallenstein, Matthew, committee memberAlpine ecosystems are being transformed by global change. Climate change and atmospheric nitrogen deposition are exposing soils to novel temperature regimes, melting alpine glaciers, altering precipitation patterns, and directly introducing bioavailable nutrients. Because microbial communities are important drivers of nutrient cycling and ecosystem function in the alpine, and because temperature, moisture and nutrient availability are primary controls of microbial abundance and activity, it is likely that microbial linkages exist between global change and ecosystem-level consequences of global change in alpine regions. Deglaciation in high-elevation regions incrementally exposes soils to primary succession, which creates a wide range of soil environments. Yet, little is understood about these unusual environments' respective microbial communities or how they respond to the influence of global change. This research studied the effects of changing temperature and moisture controls on microbial carbon and nitrate (NO3-) processing in a range of alpine soils. The soils were collected from a watershed that exhibits characteristics of nitrogen saturation as a result of atmospheric nitrogen deposition. Glacial outwash, talus, and meadow soils were characterized by physical, chemical and biological properties. Soil temperature regimes were highly variable in the field, with some soils experiencing great diurnal fluctuations, while others remained consistently cold. The response of microbial community size, structure, activity and behavior to warming and changing soil moisture was addressed with laboratory incubations. Microbial community size and nutrient availability increased with increasing soil organic carbon. Microbial activity in all soils increased with temperature and moisture, as evidenced by total and microbial biomass-specific rates of respiration. However changes in microbial biomass carbon and parameters of community structure and behavior differed among the soils. This indicated that the soils responded using individual mechanisms to changing microclimate conditions during the incubations. The net production of NO3- occurred in all soils under all experimental conditions, however the rate at which NO3- was produced responded differently to temperature and moisture treatments. This suggests that global change may affect biological controls of NO3- availability in the alpine.Item Open Access What happens during soil incubations? Exploring microbial biomass, carbon availability and temperature constraints on soil respiration(Colorado State University. Libraries, 2013) Birgé, Hannah E., author; Conant, Richard, advisor; Paul, Eldor, committee member; Wallenstein, Matthew, committee member; Stromberger, Mary, committee memberDecomposition of soil organic matter (SOM) is one of earth's most important and dynamic biogeochemical cycles. Much research is devoted to separating and studying individual controls on SOM decomposition. A commonly-used approach is to incubate soils under controlled conditions to understand the drivers of SOM decomposition. In chapter 1, I explore the use of soil incubations to investigate SOM-temperature dynamics, and emphasize the importance of testing the assumptions of laboratory soil incubations. In chapter 2, I describe how I tested whether depletion of available SOM, soil microbial biomass, or extra-cellular enzyme pools drive the decline in soil respiration over the course of a long-term incubation in soils from two sites (a cultivated plot and a forested plot at Kellogg Biological Station, Hickory Corners, MI USA). I found that the availability of SOM was the key determinant of respiration, and the loss of microbial biomass and extra-cellular enzymes over the course of a long-term incubation did not limit the ability of the remaining microbial biomass to respire available SOM. I observed a sharp increase in respiration when the soils were mixed, which support availability as a key driver of soil respiration. My results support a paradigm in which physico-chemical drivers are the primary determinant of soil respiration over the course of a long-term incubation. In chapter 3, I describe how I investigated the validity of using constant temperatures - a departure from diurnal temperature oscillations soils experience in situ - in laboratory soil incubations. The effect of oscillating versus constant temperature in incubation experiments designed to measure soil organic matter (SOM) decomposition response to temperature is not well studied in the laboratory. I investigated the impact of oscillating versus constant temperature incubation regimes on soils from the two sites listed above with varying levels of available SOM, microbial biomass and extra-cellular enzymes. Over 42 days of incubation I measured changes in soil respiration, changes in the existing microbial biomass and extra-cellular enzyme pools, and shifts in the thermal optima of four common soil extra-cellular enzymes in response to oscillating (shifting between 25°C and 35°C every 12 hours) and constant (30°C) temperature treatments. I found that none of these soil pools were significantly affected by incubation temperature oscillations. My results justify the use of soils depleted of microbial biomass and a constant temperature regime to investigate SOM decomposition in laboratory soil incubations.