RESPONSE OF ECTOMYCORRHIZAL FUNGI TO INORGANIC AND ORGANIC FORMS OF NITROGEN AND PHOSPHORUS

The nutrient uptake response of ectomycorrhizal fungi (ECM) to different nutrient substrates is a driving force in ecosystem nutrient cycling. We hypothesized that taxa from low nitrogen (N) soils would be more likely to use organic N compared to taxa from high N soils, and that taxa from high N would be more likely to use organic phosphorus (P) sources when compared to the ECM dominant in low N soils. This study focuses on the growth response of ECM species collected over a N gradient to different forms of N and P nutrient substrates and whether ECM growth in a particular nutrient source can be related to how the ECM fungi have responded to elevated N in the field. This study found a mixed ECM response to organic and inorganic N and P treatments. High affinity N taxa expected to respond positively to inorganic N produced the phosphatase enzyme to take up organic phosphorus, but not all low affinity N taxa expected to negatively respond to organic P produced the protease enzyme to take up organic N. Interspecific variability was displayed by some high and low affinity N taxa responded and ECM intraspecific variability in response to N and P treatments was also noted. Future analysis of may show more evident ECM response patterns to inorganic and organic forms of N and P.

Nitrogen Oxides in the North Atlantic Troposphere: Impacts of Boreal Wildfire and Anthropogenic Emissions

Nitrogen oxides play a crucial role in the budget of tropospheric ozone (O sub(3)) and the formation of the hydroxyl radical. Anthropogenic activities and boreal wildfires are large sources of emissions in the atmosphere. However, the influence of the transport of these emissions on nitrogen oxides and O sub(3) levels at hemispheric scales is not well understood, in particular due to a lack of nitrogen oxides measurements in remote regions. In order to address these deficiencies, measurements of NO, NO sub(2) and NO sub(y) (total reactive nitrogen oxides) were made in the lower free troposphere (FT) over the central North Atlantic region (Pico Mountain station, 38 degree N 28 degree W, 2.3 km asl) from July 2002 to August 2005. These measurements reveal a well-defined seasonal cycle of nitrogen oxides (NO sub(x) = NO+NO sub(2) and NO sub(y)) in the background central North Atlantic lower FT, with higher mixing ratios during the summertime. Observed NO sub(x) and NO sub(y) levels are consistent with long-range transport of emissions, but with significant removal en-route to the measurement site. Reactive nitrogen largely exists in the form of PAN and HNO sub(3) ( similar to 80-90% of NO sub(y)) all year round. A shift in the composition of NO sub(y) from dominance of PAN to dominance of HNO sub(3) occurs from winter-spring to summer-fall, as a result of changes in temperature and photochemistry over the region. Analysis of the long-range transport of boreal wildfire emissions on nitrogen oxides provides evidence of the very large-scale impacts of boreal wildfires on the tropospheric NO sub(x) and O sub(3) budgets. Boreal wildfire emissions are responsible for significant shifts in the nitrogen oxides distributions toward higher levels during the summer, with medians of NO sub(y) (117-175 pptv) and NO sub(x) (9-30 pptv) greater in the presence of boreal wildfire emissions. Extreme levels of NO sub(x) (up to 150 pptv) and NO sub(y) (up to 1100 pptv) observed in boreal wildfire plumes suggest that decomposition of PAN to NO sub(x) is a significant source of NO sub(x), and imply that O sub(3) formation occurs during transport. Ozone levels are also significantly enhanced in boreal wildfire plumes. However, a complex behavior of O sub(3) is observed in the plumes, which varies from significant to lower O sub(3) production to O sub(3) destruction. Long-range transport of anthropogenic emissions from North America also has a significant influence on the regional NO sub(x) and O sub(3) budgets. Transport of pollution from North America causes significant enhancements on nitrogen oxides year-round. Enhancements of CO, NO sub(y) and NO sub(x) indicate that, consistent with previous studies, more than 95% of the NO sub(x) emitted over the U.S. is removed before and during export out of the U.S. boundary layer. However, about 30% of the NO sub(x) emissions exported out of the U.S. boundary layer remain in the airmasses. Since the lifetime of NO sub(x) is shorter than the transport timescale, PAN decomposition and potentially photolysis of HNO sub(3) provide a supply of NO sub(x) over the central North Atlantic lower FT. Observed Delta O sub(3)/ Delta NO sub(y) and large NO sub(y) levels remaining in the North American plumes suggest potential O sub(3) formation well downwind from North America. Finally, a comparison of the nitrogen oxides measurements with results from the global chemical transport (GCT) model GEOS-Chem identifies differences between the observations and the model. GEOS-Chem reproduces the seasonal variation of nitrogen oxides over the central North Atlantic lower FT, but does not capture the magnitude of the cycles. Improvements in our understanding of nitrogen oxides chemistry in the remote FT and emission sources are necessary for the current GCT models to adequately estimate the impacts of emissions on tropospheric NO sub(x) and the resulting impacts on the O sub(3) budget.

MODELING DYNAMICS OF OZONE AND NITROGEN OXIDES AT SUMMIT, GREENLAND WITH A 1-D PROCESS-SCALE MODEL

This work presents a 1-D process scale model used to investigate the chemical dynamics and temporal variability of nitrogen oxides (NOx) and ozone (O3) within and above snowpack at Summit, Greenland for March-May 2009 and estimates surface exchange of NOx between the snowpack and surface layer in April-May 2009. The model assumes the surface of snowflakes have a Liquid Like Layer (LLL) where aqueous chemistry occurs and interacts with the interstitial air of the snowpack. Model parameters and initialization are physically and chemically representative of snowpack at Summit, Greenland and model results are compared to measurements of NOx and O3 collected by our group at Summit, Greenland from 2008-2010. The model paired with measurements confirmed the main hypothesis in literature that photolysis of nitrate on the surface of snowflakes is responsible for nitrogen dioxide (NO2) production in the top ~50 cm of the snowpack at solar noon for March – May time periods in 2009. Nighttime peaks of NO2 in the snowpack for April and May were reproduced with aqueous formation of peroxynitric acid (HNO4) in the top ~50 cm of the snowpack with subsequent mass transfer to the gas phase, decomposition to form NO2 at nighttime, and transportation of the NO2 to depths of 2 meters. Modeled production of HNO4 was hindered in March 2009 due to the low production of its precursor, hydroperoxy radical, resulting in underestimation of nighttime NO2 in the snowpack for March 2009. The aqueous reaction of O3 with formic acid was the major sync of O3 in the snowpack for March-May, 2009. Nitrogen monoxide (NO) production in the top ~50 cm of the snowpack is related to the photolysis of NO2, which underrepresents NO in May of 2009. Modeled surface exchange of NOx in April and May are on the order of 1011 molecules m-2 s-1. Removal of measured downward fluxes of NO and NO2 in measured fluxes resulted in agreement between measured NOx fluxes and modeled surface exchange in April and an order of magnitude deviation in May. Modeled transport of NOx above the snowpack in May shows an order of magnitude increase of NOx fluxes in the first 50 cm of the snowpack and is attributed to the production of NO2 during the day from the thermal decomposition and photolysis of peroxynitric acid with minor contributions of NO from HONO photolysis in the early morning.

Screening, optimization and extraction of polyhydroxyalkanoates and peptidoglycan from Bacillus megaterium

Bioplastics are polymers (such as polyesters) produced from bacterial fermentations that are biodegradable and nonhazardous. They are produced by a wide variety of bacteria and are made only when stress conditions allow, such as when nutrient levels are low, more specifically levels of nitrogen and oxygen. These stress conditions cause certain bacteria to build up excess carbon deposits as energy reserves in the form of polyhydroxyalkanoates (PHAs). PHAs can be extracted and formed into actual plastic with the same strength of conventional, synthetic-based plastics without the need to rely on foreign petroleum. The overall goal of this project was to select for a bacteria that could grow on sugars found in the lignocellulosic biomass, and get the bacteria to produce PHAs and peptidoglycan. Once this was accomplished the goal was to extract PHAs and peptidoglycan in order to make a stronger more rigid plastic, by combing them into a co-polymer. The individual goals of this project were to: (1) Select and screen bacteria that are capable of producing PHAs by utilizing the carbon/energy sources found in lignocellulosic biomass; (2) Maximize the utilization of those sugars present in woody biomass in order to produce optimal levels of PHAs. (3) Use room temperature ionic liquids (RTILs) in order to separate the cell membrane and peptidoglycan, allowing for better extraction of PHAs and more intact peptidoglycan. B. megaterium a Gram-positive PHA-producing bacterium was selected for study in this project. It was grown on a variety of different substrates in order to maximize both its growth and production of PHAs. The optimal conditions were found to be 30°C, pH 6.0 and sugar concentration of either 30g/L glucose or xylose. After optimal growth was obtained, both RTILs and enzymatic treatments were used to break the cell wall, in order to extract the PHAs, and peptidoglycan. PHAs and peptidoglycan were successfully extracted from the cell, and will be used in the future to create a new stronger co-polymer. Peptidoglycan recovery yield was 16% of the cells’ dry weight.

Structural characterization of water-soluble atmospheric organic matter by ultrahigh-resolution mass spectrometry

Isolated water-soluble analytes extracted from fog water collected during a radiation fog event near Fresno, CA were analyzed using collision induced dissociation and ultrahigh-resolution mass spectrometry. Tandem mass analysis was performed on scan ranges between 100-400 u to characterize the structures of nitrogen and/or sulfur containing species. CHNO, CHOS, and CHNOS compounds were targeted specifically because of the high number of oxygen atoms contained in their molecular formulas. The presence of 22 neutral losses corresponding to fragment ions was evaluated for each of the 1308 precursors. Priority neutral losses represent specific polar functional groups (H2O, CO2, CH3OH, HNO3, SO3, etc., and several combinations of these). Additional neutral losses represent non-specific functional groups (CO, CH2O, C3H8, etc.) Five distinct monoterpene derived organonitrates, organosulfates, and nitroxy-organosulfates were observed in this study, including C10H16O7S, C10H17NO7S, C10H17 NO8S, C10H17NO9S, and C10H17NO10S. Nitrophenols and linear alkyl benzene sulfonates were present in high abundance. Liquid chromatography/mass spectrometery methodology was developed to isolate and quantify nitrophenols based on their fragmentation behavior.

Spin-strain coupling in a 3-D transition metal oxides

ab-initio Hartree Fock (HF), density functional theory (DFT) and hybrid potentials were employed to compute the optimized lattice parameters and elastic properties of perovskite 3-d transition metal oxides. The optimized lattice parameters and elastic properties are interdependent in these materials. An interaction is observed between the electronic charge, spin and lattice degrees of freedom in 3-d transition metal oxides. The coupling between the electronic charge, spin and lattice structures originates due to localization of d-atomic orbitals. The coupling between the electronic charge, spin and crystalline lattice also contributes in the ferroelectric and ferromagnetic properties in perovskites. The cubic and tetragonal crystalline structures of perovskite transition metal oxides of ABO3 are studied. The electronic structure and the physics of 3-d perovskite materials is complex and less well considered. Moreover, the novelty of the electronic structure and properties of these perovskites transition metal oxides exceeds the challenge offered by their complex crystalline structures. To achieve the objective of understanding the structure and property relationship of these materials the first-principle computational method is employed. CRYSTAL09 code is employed for computing crystalline structure, elastic, ferromagnetic and other electronic properties. Second-order elastic constants (SOEC) and bulk moduli (B) are computed in an automated process by employing ELASTCON (elastic constants) and EOS (equation of state) programs in CRYSTAL09 code. ELASTCON, EOS and other computational algorithms are utilized to determine the elastic properties of tetragonal BaTiO3, rutile TiO2, cubic and tetragonal BaFeO3 and the ferromagentic properties of 3-d transition metal oxides. Multiple methods are employed to crosscheck the consistency of our computational results. Computational results have motivated us to explore the ferromagnetic properties of 3-d transition metal oxides. Billyscript and CRYSTAL09 code are employed to compute the optimized geometry of the cubic and tetragonal crystalline structure of transition metal oxides of Sc to Cu. Cubic crystalline structure is initially chosen to determine the effect of lattice strains on ferromagnetism due to the spin angular momentum of an electron. The 3-d transition metals and their oxides are challenging as the basis functions and potentials are not fully developed to address the complex physics of the transition metals. Moreover, perovskite crystalline structures are extremely challenging with respect to the quality of computations as the latter requires the well established methods. Ferroelectric and ferromagnetic properties of bulk, surfaces and interfaces are explored by employing CRYSTAL09 code. In our computations done on cubic TMOs of Sc-Fe it is observed that there is a coupling between the crystalline structure and FM/AFM spin polarization. Strained crystalline structures of 3-d transition metal oxides are subjected to changes in the electromagnetic and electronic properties. The electronic structure and properties of bulk, composites, surfaces of 3-d transition metal oxides are computed successfully.

Systemic analysis of microarray data sets towards identifying genes regulating root development

Nitrogen and water are essential for plant growth and development. In this study, we designed experiments to produce gene expression data of poplar roots under nitrogen starvation and water deprivation conditions. We found low concentration of nitrogen led first to increased root elongation followed by lateral root proliferation and eventually increased root biomass. To identify genes regulating root growth and development under nitrogen starvation and water deprivation, we designed a series of data analysis procedures, through which, we have successfully identified biologically important genes. Differentially Expressed Genes (DEGs) analysis identified the genes that are differentially expressed under nitrogen starvation or drought. Protein domain enrichment analysis identified enriched themes (in same domains) that are highly interactive during the treatment. Gene Ontology (GO) enrichment analysis allowed us to identify biological process changed during nitrogen starvation. Based on the above analyses, we examined the local Gene Regulatory Network (GRN) and identified a number of transcription factors. After testing, one of them is a high hierarchically ranked transcription factor that affects root growth under nitrogen starvation. It is very tedious and time-consuming to analyze gene expression data. To avoid doing analysis manually, we attempt to automate a computational pipeline that now can be used for identification of DEGs and protein domain analysis in a single run. It is implemented in scripts of Perl and R.

Boreal forest fire impacts on lower troposphere carbon monoxide and ozone levels at the regional to hemispheric scales

Tropospheric ozone (O3) and carbon monoxide (CO) pollution in the Northern Hemisphere is commonly thought to be of anthropogenic origin. While this is true in most cases, copious quantities of pollutants are emitted by fires in boreal regions, and the impact of these fires on CO has been shown to significantly exceed the impact of urban and industrial sources during large fire years. The impact of boreal fires on ozone is still poorly quantified, and large uncertainties exist in the estimates of the fire-released nitrogen oxides (NO x ), a critical factor in ozone production. As boreal fire activity is predicted to increase in the future due to its strong dependence on weather conditions, it is necessary to understand how these fires affect atmospheric composition. To determine the scale of boreal fire impacts on ozone and its precursors, this work combined statistical analysis of ground-based measurements downwind of fires, satellite data analysis, transport modeling and the results of chemical model simulations. The first part of this work focused on determining boreal fire impact on ozone levels downwind of fires, using analysis of observations in several-days-old fire plumes intercepted at the Pico Mountain station (Azores). The results of this study revealed that fires significantly increase midlatitude summertime ozone background during high fire years, implying that predicted future increases in boreal wildfires may affect ozone levels over large regions in the Northern Hemisphere. To improve current estimates of NOx emissions from boreal fires, we further analyzed ΔNOy /ΔCO enhancement ratios in the observed fire plumes together with transport modeling of fire emission estimates. The results of this analysis revealed the presence of a considerable seasonal trend in the fire NOx /CO emission ratio due to the late-summer changes in burning properties. This finding implies that the constant NOx /CO emission ratio currently used in atmospheric modeling is unrealistic, and is likely to introduce a significant bias in the estimated ozone production. Finally, satellite observations were used to determine the impact of fires on atmospheric burdens of nitrogen dioxide (NO2 ) and formaldehyde (HCHO) in the North American boreal region. This analysis demonstrated that fires dominated the HCHO burden over the fires and in plumes up to two days old. This finding provides insights into the magnitude of secondary HCHO production and further enhances scientific understanding of the atmospheric impacts of boreal fires.