DENITRIFICATION IN SOILS: FROM GENES TO ENVIRONMENTAL OUTCOMES

Denitrification is an important process of global nitrogen cycle as it removes reactive nitrogen from the biosphere, and acts as the primary source of nitrous oxide (N2O). This thesis seeks to gain better understanding of the biogeochemistry of denitrification by investigating the process from four different aspects: genetic basis, enzymatic kinetics, environmental interactions, and environmental consequences. Laboratory and field experiments were combined with modeling efforts to unravel the complexity of denitrification process under microbiological and environmental controls. Dynamics of denitrification products observed in laboratory experiments revealed an important role of constitutive denitrification enzymes, whose presence were further confirmed with quantitative analysis of functional genes encoding nitrite reductase and nitrous oxide reductase. A metabolic model of denitrification developed with explicit denitrification enzyme kinetics and representation of constitutive enzymes successfully reproduced the dynamics of N2O and N2 accumulation observed in the incubation experiments, revealing important regulatory effect of denitrification enzyme kinetics on the accumulation of denitrification products. Field studies demonstrated complex interaction of belowground N2O production, consumption and transport, resulting in two pulse pattern in the surface flux. Coupled soil gas diffusion/denitrification model showed great potential in simulating the dynamics of N2O below ground, with explicit representation of the activity of constitutive denitrification enzymes. A complete survey of environmental variables showed distinct regulation regimes on the denitrification activity from constitutive enzymes and new synthesized enzymes. Uncertainties in N2O estimation with current biogeochemical models may be reduced as accurate simulation of the dynamics of N2O in soil and surface fluxes is possible with a coupled diffusion/denitrification model that includes explicit representation of denitrification enzyme kinetics. In conclusion, denitrification is a complex ecological function regulated at cellular level. To assess the environmental consequences of denitrification and develop useful tools to mitigate N2O emissions require a comprehensive understanding of the regulatory network of denitrification with respect to microbial physiology and environmental interactions.

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.

Spatial and temporal patterns in ungulate-ecosystem interactions

Ungulates are important components of a variety of ecosystems worldwide. This dissertation integrates aspects of ungulate and forest ecology to increase our understanding of how they work together in ways that are of interest to natural resource managers, educators, and those who are simply curious about nature. Although animal ecology and ecosystem ecology are often studied separately, one of the general goals of this dissertation is to examine how they interact across spatial and temporal scales. Forest ecosystems are heterogeneous across a range of scales. Spatial and temporal habitat use patterns of forest ungulates tend to be congregated in patches where food and/or cover are readily available. Ungulates interact with ecosystem processes by selectively foraging on plants and excreting waste products in concentrated patches. Positive feedbacks may develop where these activities increase the value of habitat through soil fertilization or the alteration of plant chemistry and architecture. Heterogeneity in ecosystem processes and plant community structure, observed at both stand and local scales, may be the integrated outcome of feedbacks between ungulate behavior and abiotic resource gradients. The first chapter of this dissertation briefly discusses pertinent background information on ungulate ecology, with a focus on white-tailed deer (Odocoileus virginianus) in the Upper Great Lakes region and moose (Alces acles) in Isle Royale National Park, Michigan, USA. The second chapter demonstrates why ecological context is important for studying ungulate ecology in forest ecosystems. Excluding deer from eastern hemlock (Tsuga canadensis) stands, which deer use primarily as winter cover, resulted in less spatial complexity in soil reactive nitrogen and greater complexity in diffuse light compared to unfenced stands. The spatial patterning of herbaceous-layer cover was more similar to nitrogen where deer were present, and was a combination of nitrogen and light within deer exclosures. This relationship depends on the seasonal timing of deer habitat use because deer fertilize the soil during winter, but leave during the growing season. The third chapter draws upon an eight-year, 39-stand data set of deer fecal pellet counts in hemlock stands to estimate the amount of nitrogen that deer are depositing in hemlock stands each winter. In stands of high winter deer use, deer-excreted nitrogen inputs consistently exceeded those of atmospheric deposition at the stand scale. At the neighborhood scale, deer-excreted nitrogen was often in excess of atmospheric deposition due to the patchy distribution of deer habitat use. Spatial patterns in habitat use were consistent over the eight-year study at both stand and neighborhood scales. The fourth chapter explores how foraging selectivity by moose interacts with an abiotic resource gradient to influence forest structure and composition. Soil depth on Isle Royale varies from east to west according to glacial history. Fir saplings growing in deeper soils on the west side are generally more palatable forage for moose (lower foliar C:N) than those growing in shallower soils on the east side. Therefore, saplings growing in better conditions are less likely to reach the canopy due to moose browsing, and fir is a smaller overstory component on the west side. Lastly, chapter five focuses on issues surrounding eastern hemlock regeneration failure, which is a habitat type that is important to many wildlife species. Increasing hemlock on the landscape is complicated by several factors including disturbance regime and climate change, in addition to the influence of deer.

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.

IMPACTS OF CLIMATE CHANGE ON SOIL MICROORGANISMS IN NORTHERN HARDWOOD FORESTS

As global climate continues to change, it becomes more important to understand possible feedbacks from soils to the climate system. This dissertation focuses on soil microbial community responses to climate change factors in northern hardwood forests. Two soil warming experiments at Harvard Forest in Massachusetts, and a climate change manipulation experiment with both elevated temperature and increased moisture inputs in Michigan were sampled. The hyphal in-growth bag method was to understand how soil fungal biomass and respiration respond to climate change factors. Our results from phospholipid fatty acid (PLFA) analyses suggest that the hyphal in-growth bag method allows relatively pure samples of fungal hyphae to be partitioned from bacteria in the soil. The contribution of fungal hyphal respiration to soil respiration was examined in climate change manipulation experiments in Massachusetts and Michigan. The Harvard Forest soil warming experiments in Massachusetts are long-term studies with 8 and 18 years of +5 °C warming treatment. Hyphal respiration and biomass production tended to decrease with soil warming at Harvard Forest. This suggests that fungal hyphae adjust to higher temperatures by decreasing the amount of carbon respired and the amount of carbon stored in biomass. The Ford Forestry Center experiment in Michigan has a 2 x 2 fully factorial design with warming (+4-5 °C) and moisture addition (+30% average ambient growing season precipitation). This experiment was used to examine hyphal growth and respiration of arbuscular mycorrhizal fungi (AMF), soil enzymatic capacity, microbial biomass and microbial community structure in the soil over two years of experimental treatment. Results from the hyphal in-growth bag study indicate that AMF hyphal growth and respiration respond negatively to drought. Soil enzyme activities tend to be higher in heated versus unheated soils. There were significant temporal variations in enzyme activity and microbial biomass estimates. When microbial biomass was estimated using chloroform fumigation extractions there were no differences between experimental treatments and the control. When PLFA analyses were used to estimate microbial biomass we found that biomass responds negatively to higher temperatures and positively to moisture addition. This pattern was present for both bacteria and fungi. More information on the quality and composition of the organic matter and nutrients in soils from climate change manipulation experiments will allow us to gain a more thorough understanding of the mechanisms driving the patterns reported here. The information presented here will improve current soil carbon and nitrogen cycling models.