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Item Open Access A population model of folate-mediated one-carbon metabolism.(Nutrients, 2013-07-05) Duncan, Tanya M; Reed, Michael C; Nijhout, H FrederikBACKGROUND: Previous mathematical models for hepatic and tissue one-carbon metabolism have been combined and extended to include a blood plasma compartment. We use this model to study how the concentrations of metabolites that can be measured in the plasma are related to their respective intracellular concentrations. METHODS: The model consists of a set of ordinary differential equations, one for each metabolite in each compartment, and kinetic equations for metabolism and for transport between compartments. The model was validated by comparison to a variety of experimental data such as the methionine load test and variation in folate intake. We further extended this model by introducing random and systematic variation in enzyme activity. OUTCOMES AND CONCLUSIONS: A database of 10,000 virtual individuals was generated, each with a quantitatively different one-carbon metabolism. Our population has distributions of folate and homocysteine in the plasma and tissues that are similar to those found in the NHANES data. The model reproduces many other sets of clinical data. We show that tissue and plasma folate is highly correlated, but liver and plasma folate much less so. Oxidative stress increases the plasma S-adenosylmethionine/S-adenosylhomocysteine (SAM/SAH) ratio. We show that many relationships among variables are nonlinear and in many cases we provide explanations. Sampling of subpopulations produces dramatically different apparent associations among variables. The model can be used to simulate populations with polymorphisms in genes for folate metabolism and variations in dietary input.Item Open Access ACE Basin National Wildlife Refuge Forest Inventory and Carbon Stock Analysis(2021-12-08) Murphy, Mary CarltonThe ACE Basin National Wildlife Refuge (NWR) is 11,815 acres of critical wildlife habitat in South Carolina’s Lowcountry region. The Refuge contains a mosaic of forest types, including upland pine and hardwood, bottomland hardwood, and cypress-tupelo swamps. Periodic forest inventories serve to update Refuge managers on current forest conditions and identify areas outside of desired forest conditions. Desired Forest Conditions (DFC) are defined forest composition and structure metrics representing critical wildlife habitat. Active forest management, including thinning and prescribed fire, is often used on NWRs to meet DFC metrics, and thereby promote and enhance wildlife habitat. This project consisted of a 10-week forest inventory field assessment of ACE Basin NWR to evaluate current forest conditions in relation to DFC metrics. A subsequent analysis quantified how potential forest management activities to achieve DFC metrics would affect carbon stocks. Project findings suggest that most Refuge forests are outside of desired conditions and require a suite of management activities to achieve optimal wildlife habitat. These activities, however, will reduce forest carbon stocks and this project suggests forest management practices that may address these tradeoffs.Item Open Access Analyzing site selectivity in Rh2(esp)2-catalyzed intermolecular C-H amination reactions.(J Am Chem Soc, 2014-04-16) Bess, Elizabeth N; DeLuca, Ryan J; Tindall, Daniel J; Oderinde, Martins S; Roizen, Jennifer L; Du Bois, J; Sigman, Matthew SPredicting site selectivity in C-H bond oxidation reactions involving heteroatom transfer is challenged by the small energetic differences between disparate bond types and the subtle interplay of steric and electronic effects that influence reactivity. Herein, the factors governing selective Rh2(esp)2-catalyzed C-H amination of isoamylbenzene derivatives are investigated, where modification to both the nitrogen source, a sulfamate ester, and substrate are shown to impact isomeric product ratios. Linear regression mathematical modeling is used to define a relationship that equates both IR stretching parameters and Hammett σ(+) values to the differential free energy of benzylic versus tertiary C-H amination. This model has informed the development of a novel sulfamate ester, which affords the highest benzylic-to-tertiary site selectivity (9.5:1) observed for this system.Item Open Access Carbon Considerations and Pricing in Global Asset Classes(2023-04-28) Tran, Ben; Nair, Nidhi; Schofield, Hannah; McCarthy, Sean; Verma, SnehalAngeleno Group (AG) is a venture capital and growth equity firm interested in pricing carbon costs into their asset class valuations. AG hopes to understand the financial impacts of carbon because companies with higher levels of carbon exposure are expected to be riskier, which should be reflected in higher returns. In this analysis of a portfolio of the S&P 500 from 2013 to 2022, performance is evaluated by considering how a hypothetical carbon cost based on the constituents’ absolute emissions and carbon intensity changes the portfolio’s volatility, returns, and Sharpe ratio. The carbon impacts are analyzed from the perspective of AG and institutions such as endowments and foundations.Item Open Access Comparisons of Carbon and Water Fluxes of Pine Forests in Boreal and Temperate Climatic Zones(2015) Torngern, PantanaQuantifying carbon fluxes and pools of forest ecosystems is an active research area in global climate study, particularly in the currently and projected increasing atmospheric carbon dioxide concentration environment. Forest carbon dynamics are closely linked to the water cycle through plant stomata which are regulated by environmental conditions associated with atmospheric and soil humidity, air temperature and light. Thus, it is imperative to study both carbon and water fluxes of a forest ecosystem to be able to assess the impact of environmental changes, including those resulting from climate change, on global carbon and hydrologic cycles. However, challenges hampering such global study lie in the spatial heterogeneity of and the temporal variability of fluxes in forests around the globe. Moreover, continuous, long-term monitoring and measurements of fluxes are not feasible at global forest scale. Therefore, the need to quantify carbon and water fluxes and to identify key variables controlling them at multiple stands and time scales is growing. Such analyses will benefit the upscaling of stand-level observations to large- or global-scale modelling approaches.
I performed a series of studies investigating carbon and water fluxes in pine forests of various site characteristics, conditions and latitudinal locations. The common techniques used in these studies largely involved sap flux sensors to measure tree-level water flow which is scaled up to stand-level transpiration and a process-based model which calculates canopy light absorption and carbon assimilation constrained by the sap-flux beased canopy stomatal conductance (called Canopy Conductance Constrained Carbon Assimilation or 4C-A model). I collected and analyzed sap flux data from pine forests of two major species: Pinus taeda in temperate (36 °N) and Pinus sylvestris in boreal (64 °N) climatic zones. These forests were of different stage-related canopy leaf area and some were under treatments for elevated atmospheric CO2 concentration or fertilization.
I found that (Chapter 2) the 17-year long free-air CO2 enrichment (FACE) had little effect on canopy transpiration of a mixed forest with the dominant P. taeda and other broadleaved species as the understory in North Carolina, USA (Duke FACE). The result was due to the compensation of elevated [CO2]-induced increase of canopy leaf area for the reduction of mean canopy stomatal conductance. My next theoretical study (Chapter 3), comparing P. taeda (native at 36 °N in North Carolina), P. sylvestris (native at 64 °N in norther Sweden) and Pinus contorta (native at 58 °N in British Columbia, Canada) canopies, revealed that the interaction between crown architecture and solar elevation associated with site latitude of pine canopies affected the distribution and total amount of canopy light absorption and potentially photosynthesis such that the latitudinally prescribed needle organization of a pine canopy is optimal for light interception and survival in its native location. Then, I quantified and analyzed water fluxes in four pine forests: one composed of P. taeda in North Carolina and three containing P. sylvestris in northern Sweden (Chapter 4). The latter forests consisted of various stage-related canopy leaf area and nutrient status. Combining my estimates with other published results from forests of various types and latitudinal locations, I derived an approach to estimate daily canopy transpiration during the growing season based on a few environmental variables including atmospheric and soil humidity and canopy leaf area. Moreover, based on a water budget analysis, I discovered that the intra-annual variation of precipitation in a forest has a small effect on evapotranspiration and primarily affecting outflow; however, variation of precipitation across latitudes proportionally influences anuual evapotranspiration and outflow. Furthermore, the hydrologic analyses implied the `disequilibrium' of forest water cycling during the growing season when forests may use less and more water in dry and wet regions, respectively, than the incoming precipitation. Nevertherless, at annual timescale, most forests became in `equilibrium' by using similar proportion of incoming precipitation. Finally, (Chapter 5) I estimated and analyzed the temporal and spatial variabilities of carbon fluxes of the same four forests measured in Chapter 4 using the 4C-A computational approach and analyzed their resource-use efficiencies. I concluded that, based on my results and others as available, despite the differences in species clumping and latitudes which influence growing season length and solar elevation, the gross primary productivity can be conservatively linearly related to the canopy light absorption. However, based on previous findings from a global study, different allocation of the acquired carbon to the above- and belowground is regulated by soil nutrient status.
Overall, the findings in this dissertation offer new insights into the impacts of environmental changes on carbon and water dynamics in forests across multiple sites and temporal scales which will be useful for larger-scale analyses such as those pertaining to global climate projection.
Item Open Access Connectivity Drives Function: Carbon and Nitrogen Dynamics in a Floodplain-Aquifer Ecosystem(2012) Appling, Alison PaigeRivers interact with their valleys from headwaters to mouth, but nowhere as dynamically as in their floodplains. Rivers deliver water, sediments, and solutes onto the floodplain land surface, and the land in turn supplies solutes, leaves, and woody debris to the channel. These reciprocal exchanges maintain both aquatic and terrestrial biodiversity and productivity. In this dissertation I examine river-floodplain exchanges on the well-studied Nyack Floodplain, a dynamic, gravel-bedded floodplain along the Middle Fork Flathead River in the mountains of northwest Montana. I quantify exchanges at multiple timescales, from moments to centuries, to better understand how connectivity between aquatic and terrestrial habitats shapes their ecology.
I first address connectivity in the context of a long-standing question in ecosystem ecology: What determines the rate of ecosystem development during primary succession? Rivers have an immediate effect on floodplains when scouring floods remove vegetation and nutrients such as nitrogen (N) and leave only barren soils, but they might also affect the ensuing primary succession through the gradual delivery of N and other materials to floodplain soils. I quantify N inputs to successional floodplain forest soils of the Nyack Floodplain and find that sediment deposition by river flood water is the dominant source of N to soils, with lesser contributions from dissolved N in the river, biological N fixation, and atmospheric deposition. I also synthesize published rates of soil N accumulation in floodplain and non-floodplain primary-successional systems around the world, and I find that western floodplains often accumulate soil N faster than non-floodplain primary successional systems. My results collectively point to the importance of riverine N inputs in accelerating ecosystem development during floodplain primary succession.
I next investigate the role of river-floodplain exchanges in shaping the spatial distribution of a suite of soil properties. Even after flood waters have receded, dissolved N, carbon (C), and moisture could be delivered from the river to floodplain soils via belowground water flow. Alternatively, C inputs and N withdrawals by floodplain vegetation might be a dominant influence on soil properties. To test these hypotheses, I excavated and sampled soil pits from the soil surface to the water table (50-270 cm) under forests, meadows, and gravel bars of the Nyack Floodplain. Near-surface soils had C and N pools and N flux rates that varied predictably with vegetation cover, but soil properties below ~50 cm reflected influence by neither vegetation cover nor aquifer delivery. Instead, soil properties at these depths appear to relate to soil texture, which in turn is structured by the river's erosional and depositional activities. This finding suggests the revised hypothesis that soil properties in gravel-bedded alluvial floodplains may depend more on the decadal-scale geomorphic influences of floods than on short-term vertical interactions with floodplain vegetation or aquifer water.
Lastly, I explore the potential sources of organic C to the diverse and active community of aquatic organisms in the floodplain aquifer, where the lack of light prohibits in-situ organic C production by photosynthesis. I quantify floodplain carbon pools and the fluxes of organic carbon connecting the aquifer, river, and overlying forest. Spring flood waters infiltrating the soil are responsible for the largest dissolved carbon flux into the aquifer, while very large floods are essential for the other major C input, the burial of woody carbon in the aquifer. These findings emphasize the importance of a dynamic river hydrograph - in particular, annual floods and extreme annual floods - in delivering organic C to the aquifer community.
Overall, this dissertation draws our attention not just to the current exchanges of C, N, water, and sediment but to the episodic nature of those exchanges. To fully understand floodplain ecosystems, we have to consider not just present-day interactions but also the legacies of past floods and their roles in delivering solutes, eroding forests, depositing sediments, and physically shaping the floodplain environment.
Item Open Access Cytocidal amino acid starvation of Saccharomyces cerevisiae and Candida albicans acetolactate synthase (ilv2{Delta}) mutants is influenced by the carbon source and rapamycin.(Microbiology, 2010-03) Kingsbury, Joanne M; McCusker, John HThe isoleucine and valine biosynthetic enzyme acetolactate synthase (Ilv2p) is an attractive antifungal drug target, since the isoleucine and valine biosynthetic pathway is not present in mammals, Saccharomyces cerevisiae ilv2Delta mutants do not survive in vivo, Cryptococcus neoformans ilv2 mutants are avirulent, and both S. cerevisiae and Cr. neoformans ilv2 mutants die upon isoleucine and valine starvation. To further explore the potential of Ilv2p as an antifungal drug target, we disrupted Candida albicans ILV2, and demonstrated that Ca. albicans ilv2Delta mutants were significantly attenuated in virulence, and were also profoundly starvation-cidal, with a greater than 100-fold reduction in viability after only 4 h of isoleucine and valine starvation. As fungicidal starvation would be advantageous for drug design, we explored the basis of the starvation-cidal phenotype in both S. cerevisiae and Ca. albicans ilv2Delta mutants. Since the mutation of ILV1, required for the first step of isoleucine biosynthesis, did not suppress the ilv2Delta starvation-cidal defects in either species, the cidal phenotype was not due to alpha-ketobutyrate accumulation. We found that starvation for isoleucine alone was more deleterious in Ca. albicans than in S. cerevisiae, and starvation for valine was more deleterious than for isoleucine in both species. Interestingly, while the target of rapamycin (TOR) pathway inhibitor rapamycin further reduced S. cerevisiae ilv2Delta starvation viability, it increased Ca. albicans ilv1Delta and ilv2Delta viability. Furthermore, the recovery from starvation was dependent on the carbon source present during recovery for S. cerevisiae ilv2Delta mutants, reminiscent of isoleucine and valine starvation inducing a viable but non-culturable-like state in this species, while Ca. albicans ilv1Delta and ilv2 Delta viability was influenced by the carbon source present during starvation, supporting a role for glucose wasting in the Ca. albicans cidal phenotype.Item Open Access Deadwood stocks increase with selective logging and large tree frequency in Gabon.(Glob Chang Biol, 2017-04) Carlson, Ben S; Koerner, Sally E; Medjibe, Vincent P; White, Lee JT; Poulsen, John RDeadwood is a major component of aboveground biomass (AGB) in tropical forests and is important as habitat and for nutrient cycling and carbon storage. With deforestation and degradation taking place throughout the tropics, improved understanding of the magnitude and spatial variation in deadwood is vital for the development of regional and global carbon budgets. However, this potentially important carbon pool is poorly quantified in Afrotropical forests and the regional drivers of deadwood stocks are unknown. In the first large-scale study of deadwood in Central Africa, we quantified stocks in 47 forest sites across Gabon and evaluated the effects of disturbance (logging), forest structure variables (live AGB, wood density, abundance of large trees), and abiotic variables (temperature, precipitation, seasonality). Average deadwood stocks (measured as necromass, the biomass of deadwood) were 65 Mg ha-1 or 23% of live AGB. Deadwood stocks varied spatially with disturbance and forest structure, but not abiotic variables. Deadwood stocks increased significantly with logging (+38 Mg ha-1 ) and the abundance of large trees (+2.4 Mg ha-1 for every tree >60 cm dbh). Gabon holds 0.74 Pg C, or 21% of total aboveground carbon in deadwood, a threefold increase over previous estimates. Importantly, deadwood densities in Gabon are comparable to those in the Neotropics and respond similarly to logging, but represent a lower proportion of live AGB (median of 18% in Gabon compared to 26% in the Neotropics). In forest carbon accounting, necromass is often assumed to be a constant proportion (9%) of biomass, but in humid tropical forests this ratio varies from 2% in undisturbed forest to 300% in logged forest. Because logging significantly increases the deadwood carbon pool, estimates of tropical forest carbon should at a minimum use different ratios for logged (mean of 30%) and unlogged forests (mean of 18%).Item Open Access Development of a System for Real-Time Measurements of Metabolite Transport in Plants Using Short-Lived Positron-Emitting Radiotracers(2008-07-29) Kiser, Matthew RyanOver the past 200 years, the Earth's atmospheric carbon dioxide (CO2) concentration has increased by more than 35%, and climate experts predict that CO2 levels may double by the end of this century. Understanding the mechanisms of resource management in plants is fundamental for predicting how plants will respond to the increase in atmospheric CO2. Plant productivity sustains life on Earth and is a principal component of the planet's system that regulates atmospheric CO2 concentration. As such, one of the central goals of plant science is to understand the regulatory mechanisms of plant growth in a changing environment. Short-lived positron-emitting radiotracer techniques provide time-dependent data that are critical for developing models of metabolite transport and resource distribution in plants and their microenvironments. To better understand the effects of environmental changes on resource transport and allocation in plants, we have developed a system for real-time measurements of metabolite transport in plants using short-lived positron-emitting radiotracers. This thesis project includes the design, construction, and demonstration of the capabilities of this system for performing real-time measurements of metabolite transport in plants.
The short-lived radiotracer system described in this dissertation takes advantage of the combined capabilities and close proximity of two research facilities at Duke University: the Triangle Universities Nuclear Laboratory (TUNL) and the Duke University Phytotron, which are separated by approximately 100 meters. The short-lived positron-emitting radioisotopes are generated using the 10-MV tandem Van de Graaff accelerator located in the main TUNL building, which provides the capability of producing short-lived positron-emitting isotopes such as carbon-11 (11C; 20 minute half-life), nitrogen-13 (13N; 10 minute half-life), fluorine-18 (18F; 110 minute half-life), and oxygen-15 (15O; 2 minute half-life). The radioisotopes may be introduced to plants as biologically active molecules such as 11CO2, 13NO3-, 18F--[H2O], and H215<\sup>O. Plants for these studies are grown in controlled-environment chambers at the Phytotron. The chambers offer an array of control for temperature, humidity, atmospheric CO2 concentration, and light intensity. Additionally, the Phytotron houses one large reach-in growth chamber that is dedicated to this project for radioisotope labeling measurements.
There are several important properties of short-lived positron-emitting radiotracers that make them well suited for use in investigating metabolite transport in plants. First, because the molecular mass of a radioisotope-tagged compound is only minutely different from the corresponding stable compound, radiotracer substances should be metabolized and transported in plants the same as their non-radioactive counterparts. Second, because the relatively high energy gamma rays emitted from electron-positron annihilation are attenuated very little by plant tissue, the real-time distribution of a radiotracer can be measured in vivo in plants. Finally, the short radioactive half-lives of these isotopes allow for repeat measurements on the same plant in a short period of time. For example, in studies of short-term environmental changes on plant metabolite dynamics, a single plant can be labeled multiple times to measure its responses to different environmental conditions. Also, different short-lived radiotracers can be applied to the same plant over a short period of time to investigate the transport and allocation of various metabolites.
This newly developed system provides the capabilities for production of 11CO2 at TUNL, transfer of the 11CO2 gas from the target area at TUNL to a radiation-shielded cryogenic trap at the Phytotron, labeling of photoassimilates with 11C, and in vivo gamma-ray detection for real-time measurements of the radiotracer distribution in small plants. The experimental techniques and instrumentation that enabled the quantitative biological studies reported in this thesis were developed through a series of experiments made at TUNL and the Phytotron. Collimated single detectors and coincidence counting techniques were used to monitor the radiotracer distribution on a coarse spatial scale. Additionally, a prototype Versatile Imager for Positron Emitting Radiotracers (VIPER) was built to provide the capability of measuring radiotracer distributions in plants with high spatial resolution (~2.5 mm). This device enables detailed quantification of real-time metabolite dynamics on fine spatial scales.
The full capabilities of this radiotracer system were utilized in an investigation of the effects of elevated atmospheric CO2 concentration and root nutrient availability on the transport and allocation of recently fixed carbon, including that released from the roots via exudation or respiration, in two grass species. The 11CO2 gas was introduced to a leaf on the plants grown at either ambient or elevated atmospheric CO2. Two sequential measurements were performed per day on each plant: a control nutrient solution labeling immediately followed by labeling with a 10-fold increase or decrease in nutrient concentration. The real-time distribution of 11C-labeled photoassimilate was measured in vivo throughout the plant and root environment. This measurement resulted in the first observation of a rapid plant response to short-term changes in nutrient availability via correlated changes in the photoassimilate allocation to root exudates. Our data indicated that root exudation was consistently enhanced at lower nutrient concentrations. Also, we found that elevated atmospheric CO2 increased the velocity of photoassimilate transport throughout the plant, enhanced root exudation in an annual crop grass, and reduced root exudation in a perennial native grass.
Item Open Access Differential nutrient limitation of soil microbial biomass and metabolic quotients (qCO2): is there a biological stoichiometry of soil microbes?(PLoS One, 2013) Hartman, Wyatt H; Richardson, Curtis JBACKGROUND: Variation in microbial metabolism poses one of the greatest current uncertainties in models of global carbon cycling, and is particularly poorly understood in soils. Biological Stoichiometry theory describes biochemical mechanisms linking metabolic rates with variation in the elemental composition of cells and organisms, and has been widely observed in animals, plants, and plankton. However, this theory has not been widely tested in microbes, which are considered to have fixed ratios of major elements in soils. METHODOLOGY/ PRINCIPAL FINDINGS: To determine whether Biological Stoichiometry underlies patterns of soil microbial metabolism, we compiled published data on microbial biomass carbon (C), nitrogen (N), and phosphorus (P) pools in soils spanning the global range of climate, vegetation, and land use types. We compared element ratios in microbial biomass pools to the metabolic quotient qCO2 (respiration per unit biomass), where soil C mineralization was simultaneously measured in controlled incubations. Although microbial C, N, and P stoichiometry appeared to follow somewhat constrained allometric relationships at the global scale, we found significant variation in the C∶N∶P ratios of soil microbes across land use and habitat types, and size-dependent scaling of microbial C∶N and C∶P (but not N∶P) ratios. Microbial stoichiometry and metabolic quotients were also weakly correlated as suggested by Biological Stoichiometry theory. Importantly, we found that while soil microbial biomass appeared constrained by soil N availability, microbial metabolic rates (qCO2) were most strongly associated with inorganic P availability. CONCLUSIONS/ SIGNIFICANCE: Our findings appear consistent with the model of cellular metabolism described by Biological Stoichiometry theory, where biomass is limited by N needed to build proteins, but rates of protein synthesis are limited by the high P demands of ribosomes. Incorporation of these physiological processes may improve models of carbon cycling and understanding of the effects of nutrient availability on soil C turnover across terrestrial and wetland habitats.Item Open Access Duke Forest Carbon(2011-12-09) Downing, Eric; Fulton, Erin; Strauss, JoshuaDuke University is dedicated to achieving climate neutrality by 2024. With over 7000 acres of sustainably managed forest land, the Duke Forest has great potential for generating “in house” carbon offsets to help reach this goal. In this project we quantified the carbon represented in Duke’s forest holdings and analyzed the potential for generating emissions-reducing offsets based on Climate Action Reserve (CAR) and American Carbon Registry (ACR) protocols. Throughout the process we focused on three varieties of forest offsets: Avoided Conversion, Improved Forest Management, and Afforestation/Reforestation, comparing the relative advantages and disadvantages of each under CAR and ACR carbon accounting systems. After completing these carbon calculations we conducted a financial analysis of our results in order to make recommendations to the Duke Carbon Offsets Initiative concerning how they might apply these forest offsets toward the university’s carbon neutrality goal. Ultimately we concluded that the Duke Forest has the potential to produce significant amounts of high quality carbon offsets at a cost considerably below that of purchasing them on the voluntary market. The generation of Improved Forest Management offsets under CAR protocols proved particularly compatible with current Duke Forest management practices, yielding substantial carbon and financial benefits with minimal project development investment. Based on the results of our carbon and financial models we determined that the Duke Forest could generate 358,109 offset credits over the next 50 years, saving the university over $1.5 million.Item Open Access Ecosystem recovery from acid precipitation: Carbon and nitrogen cycling in the soil-stream continuum(2018) Marinos, RichardWhile the problem of acid precipitation has been greatly reduced across the developed world, acid-impaired ecosystems still bear important legacies of historic acid deposition, and these ecosystems are only slowly beginning to recover. Early evidence suggests that this recovery may have multiple unexpected, substantial impacts on ecosystem carbon (C) and nitrogen (N) cycling, including large reductions in soil organic C and N pools and greatly increased export of dissolved organic C to aquatic ecosystems. These losses of soil C and N, driven by ecosystem recovery from acid precipitation, have the potential to dwarf any gains in biomass pools due to enhanced forest growth. The mechanisms driving these changes remain poorly understood, however. In this work, I ask the following questions: a) How does ecosystem recovery from acid precipitation alter soil C and N cycling, and b) what are the consequences of these changes for ecosystem N retention?
A watershed acid remediation experiment, performed at Hubbard Brook, White Mountains National Forest, New Hampshire, offers an opportunity to study now processes of ecosystem recovery from acid precipitation that will take decades to centuries to occur naturally. In this experiment, researchers applied calcium (Ca) silicate to a watershed to restore soil Ca fertility and raise soil pH. This treatment caused a rapid, substantial decrease in soil organic C, and greatly increased streamwater export of inorganic nitrogen. My dissertation examines my research questions through the lens of this experiment.
In the first part of my dissertation (Chapter 2), I examined how changes to soil pH and Ca fertility, individually and together, drive changes in the solubility and respiration of soil C, and how vegetation mediates these effects. I examined this topic through a soil mesocosm experiment in which I modified soil pH and soil Ca status individually and in combination. I found that there was a strong interactive effect between increases in soil pH and the presence of vegetation. Increasing soil pH increased soil respiration and soil C solubility, but only in the presence of sugar maple (Acer saccharum) roots. I also found that Ca fertilization stimulated plant growth, but had no effect on soil C dynamics. This suggests that vegetation and soil microbiota may respond to different aspects of ecosystem recovery from acid precipitation, with vegetation sensitive to changes in soil Ca content and microbiota sensitive to changes in soil pH.
In the second part of my dissertation (Chapter 3), I performed a field-based study to examine how the acid remediation treatment altered soil N cycling. I found that the acid remediation treatment increased both gross N mineralization and N uptake in the leaf litter, causing an accelerated N cycle. This accelerated N cycling resulted in larger inorganic N pools throughout the soil profile. These observed changes in N cycling contrast with earlier studies showing no treatment effect on N cycling rates, and this lag may be coupled to changes in plant community structure.
In the last part of my dissertation (Chapter 4), I examined how these changes in soil N cycling resulted in changes to ecosystem N export, using a combination of re-analysis of long term data sets and intensive stream monitoring. I found that, as a result of the Ca treatment, flushing of inorganic N during storms became a substantially more important mechanism of ecosystem N loss. I found evidence that the flushing of N during stormflow was the result of the mobilization of distal, hydrologically disconnected pools of soil N. This suggests that changes in forest floor N cycling, observed in Chapter 3, were responsible for this response. Finally, I found that in-stream uptake of N was significantly enhanced during baseflow conditions in the Ca-enriched watershed, reducing N export during baseflow.
This dissertation adds new mechanistic insight into the drivers by which ecosystem recovery from acid precipitation will affect C and N cycling. It demonstrates that, while acid precipitation has abated in the developed world, its legacy effects will remain with us for a long while. The changes to ecosystem C and N cycling studied here are concerning from the perspectives of climate change and loading of nutrients to aquatic ecosystems. This suggests the need for further work that couples vegetation dynamics, changes to geochemical properties of soils, and watershed hydrology.
Item Open Access Emissions Trading: EU ETS, US Voluntary Market & Carbon Credit Projects As Offsets(2008-04-25T17:40:38Z) Hansen, MorganThis project examines the Kyoto Protocol-based European Union Emissions Trading Scheme (EU ETS), the current US voluntary carbon market, and the role of carbon credit projects as offsets within emissions trading programs. The objectives of this paper are twofold: (1) to ascertain the risk factors associated with a carbon credit generating renewable energy projects that have the greatest impact on the rate of return for an investor, and (2) to identify factors of trading programs that have been or will be particularly successful, as well as factors that have/will lead to inefficiencies when implemented in the trading market. The methods used include a quantitative analysis of a carbon credit generating project, as well as a qualitative policy discussion of the existing and proposed emissions trading program designs. The quantitative method attempts to analyze the impact of different risk factors (i.e. project timing risk, credit delivery risk, price risk, etc.) on the rate of return of investment in a hypothetical carbon credit project.Item Open Access Environmental and genetic determinants of colony morphology in yeast.(PLoS Genet, 2010-01-22) Granek, JA; Magwene, PMNutrient stresses trigger a variety of developmental switches in the budding yeast Saccharomyces cerevisiae. One of the least understood of such responses is the development of complex colony morphology, characterized by intricate, organized, and strain-specific patterns of colony growth and architecture. The genetic bases of this phenotype and the key environmental signals involved in its induction have heretofore remained poorly understood. By surveying multiple strain backgrounds and a large number of growth conditions, we show that limitation for fermentable carbon sources coupled with a rich nitrogen source is the primary trigger for the colony morphology response in budding yeast. Using knockout mutants and transposon-mediated mutagenesis, we demonstrate that two key signaling networks regulating this response are the filamentous growth MAP kinase cascade and the Ras-cAMP-PKA pathway. We further show synergistic epistasis between Rim15, a kinase involved in integration of nutrient signals, and other genes in these pathways. Ploidy, mating-type, and genotype-by-environment interactions also appear to play a role in the controlling colony morphology. Our study highlights the high degree of network reuse in this model eukaryote; yeast use the same core signaling pathways in multiple contexts to integrate information about environmental and physiological states and generate diverse developmental outputs.Item Open Access Environmental Impacts of the Coal Ash Spill in Kingston, Tennessee: An 18-Month Survey(2010) Ruhl; L; Vengosh, A; Dwyer; G, S; Hsu-Kim; H; DeonarineAn 18 month investigation of the environmental impacts of the Tennessee Valley Authority (TVA) coal ash spill in Kingston, Tennessee combined with leaching experiments on the spilled TVA coal ash have revealed that leachable coal ash contaminants (LCACs), particularly arsenic, selenium, boron, strontium, and barium, have different effects on the quality of impacted environments. While LCACs levels in the downstream river water are relatively low and below the EPA drinking water and ecological thresholds, elevated levels were found in surface water with restricted water exchange and in pore water extracted from the river sediments downstream from the spill. The high concentration of arsenic (up to 2000 mu g/L) is associated with some degree of anoxic conditions and predominance of the reduced arsenic species (arsenite) in the pore waters. Laboratory leaching simulations show that the pH and ash/water ratio control the LCACs' abundance and geochemical composition of the impacted water. These results have important implications for the prediction of the fate and migration of LCACs in the environment, particularly for the storage of coal combustion residues (CCRs) in holding ponds and landfills, and any potential CCRs effluents leakage into lakes, rivers, and other aquatic systems.Item Open Access Evaluation of 11 terrestrial carbon-nitrogen cycle models against observations from two temperate Free-Air CO2 Enrichment studies.(The New phytologist, 2014-05) Zaehle, Sönke; Medlyn, Belinda E; De Kauwe, Martin G; Walker, Anthony P; Dietze, Michael C; Hickler, Thomas; Luo, Yiqi; Wang, Ying-Ping; El-Masri, Bassil; Thornton, Peter; Jain, Atul; Wang, Shusen; Warlind, David; Weng, Ensheng; Parton, William; Iversen, Colleen M; Gallet-Budynek, Anne; McCarthy, Heather; Finzi, Adrien; Hanson, Paul J; Prentice, I Colin; Oren, Ram; Norby, Richard JWe analysed the responses of 11 ecosystem models to elevated atmospheric [CO2 ] (eCO2 ) at two temperate forest ecosystems (Duke and Oak Ridge National Laboratory (ORNL) Free-Air CO2 Enrichment (FACE) experiments) to test alternative representations of carbon (C)-nitrogen (N) cycle processes. We decomposed the model responses into component processes affecting the response to eCO2 and confronted these with observations from the FACE experiments. Most of the models reproduced the observed initial enhancement of net primary production (NPP) at both sites, but none was able to simulate both the sustained 10-yr enhancement at Duke and the declining response at ORNL: models generally showed signs of progressive N limitation as a result of lower than observed plant N uptake. Nonetheless, many models showed qualitative agreement with observed component processes. The results suggest that improved representation of above-ground-below-ground interactions and better constraints on plant stoichiometry are important for a predictive understanding of eCO2 effects. Improved accuracy of soil organic matter inventories is pivotal to reduce uncertainty in the observed C-N budgets. The two FACE experiments are insufficient to fully constrain terrestrial responses to eCO2 , given the complexity of factors leading to the observed diverging trends, and the consequential inability of the models to explain these trends. Nevertheless, the ecosystem models were able to capture important features of the experiments, lending some support to their projections.Item Open Access Examine Agricultural Land Use Practices and Their Effects on Carbon Storage and Flux in the United States(2022-04-22) Wang, Hongyi; Luo, ZhixianThe terrestrial ecosystem has provided a net carbon sink, equal to 20% of total greenhouse gas (GHG) emission from industrial activities in the past three decades, yet many land use activities, mainly agriculture, can drastically change natural land carbon flux. We worked with Resources for the Future (RFF) on the Carbon and Land Use Model (CALM) that helps with evaluating the effects of policy decisions on land use and relevant carbon flux changes. To evaluate potential approaches for estimating accurate carbon fluxes from agricultural land use practices, our team first conducted literature review to ascertain carbon flux from different land use changes along with detailed examination of the EPA GHG Emission inventory report 2021 and the 2006 IPCC Guidelines for National Greenhouse Gas Inventories. Then, we identified and assessed data knowledge gaps in existing methods of emission estimation and carbon fluxes modeling. Finally, recommendations were provided to RFF on how the CALM model can be further developed and utilized.Item Open Access Extending Forest Rotation Age for Carbon Sequestration: A Cross-Protocol Comparison of Carbon Offsets of North American Forests(2009-04-22T18:12:55Z) Foley, TimothyAs the issue of climate change rises in prominence, growing attention is being paid to the ability of forests to mitigate rising atmospheric concentrations of CO2. Through carbon offset programs, forest owners can be offered financial incentives to enhance the uptake and storage of carbon on their lands. This project presents a modeling framework within which the creditable carbon potential can be quantified from extending the rotation age of multiple forest stands. The differences in creditable carbon potential from rotation extensions across several North American forest types are explored. Additionally, the model enables the comparison of project creditable carbon amongst three accounting methodologies: the Department of Energy 1605b Registry, the Chicago Climate Exchange Protocol, and the Voluntary Carbon Standard Protocol. There are important methodological differences between these carbon accounting schemes which have implications to both forest owners and policymakers alike. It is shown here that the inclusion of methodologies to account for such issues as leakage, permanence, additionality and baseline-establishment, while increasing the overall legitimacy of any forest carbon offset program, can reduce creditable carbon to the forest owner by up to 70%. Regardless of the protocol used, Pacific Northwest forest types emerge as the most effective at sequestering carbon on a per area basis.Item Open Access Gabon’s Overlooked Carbon: A tropical forest study of coarse woody debris(2013-04-26) Carlson, BenLarge dead trees and other large forest detritus (collectively known as coarse woody debris, or CWD) play an important role in the global carbon cycle. In tropical systems, CWD stocks (necromass) have been found to constitute 5% to 33% of total biomass. Despite harboring the second largest rain forest on earth, in Central Africa there have been virtually no studies of coarse woody debris. In this study 15 plots were established in 5 forest zones in Gabon, Africa to measure CWD stocks and potential environmental and land-use determinants of CWD. Necromass of CWD was found to be positively correlated with precipitation and was higher in logged forests than in primary forests. Extrapolated to the entire country, Gabon is estimated to contain carbon CWD content of between 0.34 Pg C to 0.72 Pg C (14 Mg C ha-1 to 30.1 Mg C ha-1). The results of this study will help improve tropical forest carbon flux estimates.Item Open Access Human Dimensions of Blue Carbon - Resource Portal(2023-04-28) Lo Presti, Marta; Liyanagamage, Sandunie; Pertuz Molina, María CeciliaBlue carbon is defined as the carbon stored in ocean ecosystems, and there is increased interest (among governments, non-government organizations, businesses, and philanthropies) in preserving, restoring, or enhancing blue carbon ecosystems. Categorized as a natural climate solution (NCS), blue carbon interventions are among the tools countries can mobilize to combat climate change. The Environmental Defense Fund (EDF) has formed an EDF-Bezos Earth Fund Blue Carbon Pathways Working Group to explore which blue carbon solutions would serve as high-quality carbon credits in three broad ecosystems: near shore (e.g., mangrove, seagrass, salt marsh), macroalgae, and off-shore (e.g., mesopelagic, and pelagic fish, great whales, the seabed). The criteria presented in the “Carbon Credit Guidance for Buyers,” a joint study by EDF, WWF, and Oeko-Institut, can be used to assess whether a carbon credit is of high-quality (World Wildlife Fund (WWF) et al., 2020). EDF wanted a better understanding of the existing knowledge around the socioeconomic aspects of implementing blue carbon interventions that could contribute significantly towards meeting country-specific decarbonization goals. Therefore, during the summer of 2022, our team conducted an extensive review of the social, economic, institutional, and governance aspects of blue carbon interventions. This research identified a gap in the multiple blue carbon resources and tools available to the public. Though there are multiple resources that discuss different aspects of blue carbon ecosystems (e.g., methodologies to calculate carbon sequestration), we found limited information about the human dimensions of blue carbon interventions. As blue carbon ecosystems are explored for their carbon sequestration potential and source of high-quality carbon credits by multiple stakeholders, it is vital that the human dimensions of blue carbon and blue carbon intervention are considered because of equity concerns and the project’s impacts on livelihoods. Therefore, our master’s Project focuses on developing a database, ‘Human Dimensions of Blue Carbon – Resource Portal’, to identify key findings on social, economic, management, finance, equity, and community participation aspects associated with blue carbon initiatives. We collected and analyzed 60 resources developed in the 2011-2023 timeframe. We focus on the nearshore, macroalgal, and offshore blue carbon ecosystems to align with EDF’s ecosystems of interest. These resources are in various forms, including reports, news articles, websites, case studies, and guidelines. We focus specifically on the gray literature, produced, or commissioned by the various government, non-government and private sector actors working on blue carbon, with goals similar to EDF: to identify the conditions under which blue carbon initiatives are likely to succeed, ideally delivering co-benefits for carbon sequestration, biodiversity, and people. The database serves as a structure for our overall analysis and contains general bibliographic information for each resource (e.g., reference type, author type, year published, partners list) followed by an indication of which, if any, of the human dimensions are addressed. The database can thus serve as a resource for EDF and others, directing them to specific resources that address particular topics (e.g., users interested in learning more about equity in blue carbon can identify resources that include it). It also serves as the base of an analysis of the current state of human dimensions coverage in the gray literature presented in this report. Our findings suggest that a majority of blue carbon projects are not taking human dimensions into consideration. This database and our analysis would help project developers and carbon credit buyers understand the social context associated with implementing a blue carbon project. This database should also provide insights into understanding the gaps in the knowledge on socioeconomic and equity views. Based on our 60-resource sample, it is clear that the different categories of equity are not deeply explored within the blue carbon space. Our database should be used by project developers evaluating a blue carbon initiative as a tool to identify gaps in human dimensions. We expect to provide this database to EDF to be housed within their website and shared with the broader blue carbon community. Our analysis is based on 60 resources, but further resources can be added to support more comprehensive analyses. Although our analysis may answer some important questions and provide insights into blue carbon interventions, we want to highlight the importance and need for continuous updates to the database to keep track of the most recent findings in that space.