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ABSTRACT Soil- solution partitioning of metals determines the behaviour and toxicity of metals. Lead, copper, zinc and nickel are common pollutants, and due to historic metal deposition from the atmosphere, high levels of these metals have accumulated in upland organic soils in the UK. Atmospheric deposition of sulphur and nitrogen, and climate change, can affect soil solution pH and dissolved organic carbon (DOC) concentrations, and both pH and DOC are known to affect soil-solution partitioning of metals. In this thesis, metal concentrations were determined in archived soil and soil solution samples from a regional survey of upland sites in northern England with contrasting soils, and two experiments were undertaken to assess the effect of temperature and nitrogen deposition composition on metal concentrations in soil solution. In each case, a common objective was to assess whether variation in metal concentrations in soil solution could be explained by changes in soil solution pH and DOC concentration. Lead concentrations in soil solution were modified by heating, but not the composition of nitrogen deposition, and lead showed a strong affinity for organic matter in soils and soil solution. Zinc concentrations were affected by both heating and nitrogen deposition, with the strongest effect being through changes in pH. However, in the case of both zinc and nickel, there were also associations with DOC concentrations, indicating that the organic phase becomes more significant for partitioning of metals between soil and soil solution in organic-rich soils. For copper, there was little effect of heating or nitrogen deposition, and the strongest association was with nitrate, rather than pH or DOC, in soil solution. Future research should be focused on more comprehensive studies dealing with the relationship between DOC, pH, climate, nitrogen deposition and metal in the field, with supporting laboratory experiments.

Very short lived halogenated substances (VSLH) are of importance for the transport of reactive halogens to the troposphere and lower stratosphere, whereas molecular halogens are of specific importance to the Marine Boundary Layer (MBL). This thesis describes the field deployment of a ground based gas chromatography mass spectrometry (GC/MS) in the Canadian sub-Arctic for the determination of VSLH in seawater/sea-ice and air with a view to identify dominant sources to the MBL in the region. MBL mixing ratios of VSLH were determined from a surface site (55.28°N, 77.77°W) on the south east of Hudson Bay,(Kuujjuarapik, Canada) during the 19th -27th of February. Elevated mixing ratios of the Volatile Organic Iodine Compounds (VOIC) coincided with airmasses reaching the ground site that had previously transected regions of open water in the Bay (between 10 – 200 km away), suggesting leads/polynyas are the dominant source of VOIC within the region. This observation is supported by laboratory experiments conducted with artificial sea ice in a cold chamber (School of Earth and Environment, Leeds University) in which physico-chemical properties of the hypersaline brine, sea-ice and the underlying seawater were measured to quantify the vertical transport of a comprehensive range of volatile organic iodinated compounds (VOICs) at air temperatures of -3 and -14 oC. The results suggest that VOIC gas transfer velocities from diffusion through the sea-ice alone are at least 60 times lower at -3 ºC than gas exchange from leads and polynas during the winter (assuming a sea-ice fractional coverage of 0.1). This has significant implications for in situ VOIC losses within the brine from chlorination, hydrolysis and photolysis processes and it is unlikely that measurable concentrations of VOICs would survive vertical transport from the underlying seawater to the surface sea ice quasi-liquid layer. Further laboratory work within this thesis suggests that gaseous I2 evolution from the oxidation of iodide in the world’s oceans by atmospheric ozone is a viable source of iodine to the MBL, but its strongly constrained by the iodide and dissolved organic carbon (DOC) content of the surface ocean.

The biogeochemical cycling of nitrogen has been studied in detail at a predominantly acid grassland nature reserve, Hob Moor, just outside the city of York in the UK. Because of the risk of more frequent and/or extended summer droughts as a potential consequence of climate change, particular attention was paid to the influence of drying and rewetting upon the mobility of mineral N species. It was found that ammonification proceeds after net nitrification has ceased, and that subsequently nitrate is immobilized when the drying period is protracted. It is suggested that this is probably due to uptake by drought-tolerant microorganisms. The experimental work showed that much of the first flush of nitrate after a period of drying is therefore attributable to stored nitrate, as long as the drying out period is not excessively long. The mobility of ammonium-N in soils from Hob Moor was studied to test the hypothesis that in the heavily N-impacted soils at the site it would be more mobile than most soil scientists would predict, by measuring adsorption/desorption characteristics. The absorption isotherms confirmed that ammonium in these soils is potentially mobile, and when mobilized below the rooting depth may pass to the adjacent stream around the edge of the site. This helps explain the high ammonium-N and nitrate-N concentrations observed in this stream. A developing interest in the Gaia hypothesis prompted the author to make a brief preliminary investigation of the idea that deciduous trees have evolved naturally to provide a close match between the dynamics of N release by litter decomposition and the dynamics of plant N requirement. The experiment showed that initially the fresh litter with a high C/N ratio immobilized nitrate especially in the forest soil. Under the relatively warm conditions of the experiment decomposition was rapid, and the immobilization was not sustained as would be predicted. Further evaluation of this concept is advocated. The extent of immobilization by litter prompted a study of long-term seasonality of trends in nitrate concentration throughout the River Derwent in North Yorkshire using data obtained from the Environment Agency. It was thought that a ban on straw burning in 1993 might have reduced winter annual nitrate concentration peaks and possibly increased summer minima. The data partly supported this idea, but the timing match was not perfect, and it was thought that the foot and mouth disease impact and farmers’ responses to environmental concerns and policy and to increasing fertilizer and energy costs were probably also important. Finally a study was made of the importance of storage conditions upon extractable ammonium and nitrate concentrations in soils. Surprisingly nitrification was not sufficiently inhibited in some soils stored under refrigerated conditions overnight, and it is concluded that volumetric sampling and immediate extraction in the field may be a preferred option.

Volcanic volatile species are scavenged by silicate ash during transition through eruption plumes. Scavenging may form S, F and Cl salts and acids on ash surfaces, though the mechanisms and controlling variables remain poorly understood. A limited mechanistic understanding impedes estimation of volcanic volatile budgets and may also prevent assessment of environmental impacts resulting from volatile scavenging. Limited assessment of these impacts may have implications for local communities affected by ashfall onto vegetation, soils and into water bodies, and ashfall from very large eruptions may have global impacts. Through experimental techniques, this study examined SO2 scavenging mechanisms on silicate ash surfaces. SO2 uptake experiments were conducted on model Ca-aluminosilicate xerogels and on glasses with chemical compositions of common ash types. The materials were characterised using bulk and surface-sensitive techniques to gain insight into the mechanisms of scavenging and the reaction products formed. SO2 chemisorption onto glass surfaces may occur on non-bridging oxygens of network modifying cations (Ca), forming sulphate salts (CaSO4) and initiates diffusion mechanisms which resupplies the surface with Ca. The chemisorption-diffusion mechanism may be most efficient at high temperature, and may become significant after a few minutes of SO2 exposure. The proposed scavenging mechanism may occur during the eruption within the high temperature volcanic conduit and in the core of the plume. High temperature SO2 scavenging could deposit the soluble S salts inferred to exist on ash and may dictate its surface chemistry for later reactions during transport through the plume and dispersion in the atmosphere and/or environment. It is not yet possible to quantify this mechanism or compare it to other scavenging mechanisms (aqueous acid condensation, high temperature salt condensation), and so future studies should attempt to constrain all volatile scavenging mechanisms occurring on ash surfaces, with particular focus on high temperatures, even in the subterranean environment.

In the context of current and any future climate change, methane (CH4) is an important greenhouse gas (GHG). However, current global trends of changes in atmospheric CH4 are unpredictable and the relative contributions of individual global sources and sinks are inadequately quantified. If net CH4 emissions are to be reduced, an improved understanding of key components, including natural wetlands, is required. A study was conducted in order to construct an annual landscape estimate of CH4 flux for a typical UK blanket bog site near to Lake Vyrnwy, North Wales. Flux measurements were made following an established chamber method and sampling was maintained throughout a calendar year and was spatially stratified by vegetation to facilitate landscape extrapolation. In order to identify which environmental variables controlled CH4 fluxes from the blanket bog, regression analyses were performed using environmental variables measured at the time of flux measurement. In order to identify the longer term influence of environmental conditions, regression analyses were also conducted with running averages of measurements from periods prior to the day of flux measurement. A series of in situ experiments were undertaken to test hypotheses which examined the different controls on the observed variation in CH4 fluxes, related to temporal and spatial patterns of CH4 flux and to putative biases of sampling methods due to the limited footprint of chambers. CH4 fluxes displayed a distinct seasonal pattern with low mean fluxes from January until June, when a dramatic increase in net methane emission occurred; higher CH4 fluxes continued until November and December. The site was a net source of CH4 and the best landscape estimate of CH4 flux (± standard error of the mean) was 9.8 (±3.8) g CH4 m-2 year 1. Errors associated with the extrapolation of measurements to a landscape-scale estimate resulted in estimates that ranged from 8.6 (±3.7) to 11.1 (±3.8) g CH4 m 2 year-1. Soil temperature and water table were the environmental variables which were most consistently associated with CH4 fluxes. However, the relationship between fluxes and water table did not always control CH4 fluxes in an expected manner. At some sites CH4 emissions were lower when the water table was closer to the surface, a result which contradicted the acrotelm-catotelm model of CH4 flux, but may be explained by the hysteresis of fluxes in response to changing water table. Strong hysteresis of CH4 fluxes was also apparent in response to temperature and radiation. Hourly measurements of CH4 flux showed high variability but no significant difference between measurements during day and night. Similarly, a replicated landscape-scale experiment of water table manipulation was expected to cause changes in CH4 flux but, despite controlling for other aspects of spatial variation, the manipulation had no significant effect on CH4 fluxes. Flux estimates were made using chambers with footprints that varied by three orders of magnitude and there was no significant effect on mean CH4 fluxes. However, the variance of CH4 flux estimates strongly correlated with sample area with markedly smaller variance as chamber size increased. Overall estimates of landscape CH4 flux were in the range of previous estimates made for UK peatland sites, but virtually all estimates displayed high variability. Such variability constrained the comparison of different estimates but it is possible to use methods, such as chambers with very large footprints, to improve the results of in situ studies.

This thesis presents research at the interface of the e-Science and atmospheric chemistry disciplines. Two inter-related research topics are addressed: first, the development of computational models of the troposphere (i.e. in silico experiments); and secondly, provenance capture and representation for data produced by these computational models. The research was conducted using an ethnographic approach, seeking to develop in-depth understanding of current working practices, which then informed the research itself. The research focused on the working practices of a defined research community; the users and developers of the MCM (Master Chemical Mechanism). The MCM is a key data and information repository used by researchers, with an interest in atmospheric chemistry, across the world. A computational modelling system, the OSBM (Open Source Box Model) was successfully developed to encourage researchers to make use of the MCM, within their in silico experiments. Taking advantage of functionality provided by the OSBM, the use of in situ experimental data to constrain zero dimensional box models was explored. Limitations of current methodologies for constraining zero dimensional box models were identified, particularly associated with the use of piecewise constant interpolation and the averaging of constraint data. Improved methodologies for constraining zero dimensional box models were proposed, tested and demonstrated to offer gains in the accuracy of the model results and the efficiency of the model itself. Current data generation and provenance related working practices, within the MCM community, were mapped. An opportunity was identified to apply Semantic Web technologies to improve working practices associated with gathering and evaluating feedback from in silico experiments, to inform the ongoing development of the MCM. These envisioned working practices rely on researchers, performing in silico experiments, that make use of the MCM, capturing data and provenance using an ELN (Electronic Laboratory Notebook). A prototype ELN, employing a user-orientation approach to provenance capture and representation, was then successfully designed, implemented and evaluated. The evaluation of this prototype ELN highlighted the importance of adopting a holistic approach to the development of provenance capture tools and the difficulties of balancing researchers’ requirements for flexibility and structure their scientific processes.

In this thesis the TOMCAT chemical transport model is used to investigate the processes which control the concentrations of CO and O3 in the Arctic troposphere. Particular focus is on understanding the main sources of CO, O3 and NOy species in the Arctic, distinguishing between natural and anthropogenic sources and the current drivers of interannual variability (IAV). First results from a new version of TOMCAT, with extended hydrocarbon chemistry and heterogeneous uptake of N2O5, shows better agreement with observed CO from MOPITT, surface stations and aircraft. Changes in simulated burdens demonstrate the importance of NMHC as a source of CO, O3 and PAN in the troposphere and show that the complexity of chemical schemes may have contributed to previously reported inter-model differences. The high PAN sensitivity to additional NMHC is particularly important in the Arctic as it is the dominant source of NOx in the Arctic lower troposphere, producing up to 30% of total O3 in the summer. This thesis contains the first source contribution analysis to consider impacts of fire emissions throughout the year in comparison to anthropogenic sources. Anthropogenic emissions are found to be the largest source of Arctic CO (48%), followed by methane (25%) and fires (13%). In summer, fire and anthropogenic sources contribute equally to the total CO burden. Boreal fires are the dominant source of O3 and NOx compared to anthropogenic emissions. North America contributes the largest amount (30%) to the total anthropogenic CO burden, followed by East Asia (26%), Europe (23%) and South Asia (9%). In contrast, North America makes the largest contribution (9%) to the Arctic O3 burden, followed by Europe (7%) and then Asia (6%). Overall, CO shows that the Arctic is most sensitive to emissions changes in Europe, then North America and then Asia. Fire emissions are the dominant driver of current Arctic CO IAV, causing 84-93% of observed variability. A statistically significant correlation is found between observed CO and the El Nino 3.4 index due to a link with fires. El Nino is strongly associated with increased fire emissions in regions of North, Central and South America, Africa, and Asia. In contrast, El Nino is associated with reduced fire emissions in eastern North America, Europe, southern Asia and Australia. The temperature dependence of fires in several regions indicates that fire activity will increase in a warmer climate.