Temperature is one of the most important abiotic environmental regulators of plant growth and development. The temperature-dependent elongation of the Arabidopsis thaliana hypocotyls (seedling stems) is a well-characterised environmental response. The aim of this study was to identify allelic variants underlying Quantitative Trait Loci (QTL) responsible for the natural genetic variation of hypocotyl length in response to ambient temperatures. The Arabidopsis thaliana accessions were phenotyped for hypocotyl length at 12°C, 17°C, 22°C and 27°C ambient temperature environments and substantial genetic variation was established. This facilitated a forward genetic approach by performing a QTL analysis to identify the genetic basis of thermal sensitivity. Firstly, fine-mapped QTL were identified for hypocotyl length in response to different temperatures. SMALL AUXIN UPREGULATED RNA 38 (SAUR38) is a novel candidate gene for a QTL. Another major-effect QTL ‘Temp22.2’ was also identified which harbours the candidate gene PHYTOCHROME B (PHYB). Secondly, fine-mapped ‘Environmental QTL’ were also discovered for the genotype by environment (G x E) interaction. PHYTOCHROME D (PHYD) is a candidate for a temperature-responsiveness QTL. For QTL cloning, functional characterisation of SAUR38 and PHYB was carried out by knockout analysis and transgenic allelic complementation. The results showed that SAUR38 controlled natural variation in the Tsu-0 accession by increasing elongation. The PHYB alleles of Ct-1, Sf-2 and Col-0 accessions explain the Temp22.2 QTL. Ct-1 and Sf-2 alleles are positive regulators increasing elongation, whereas Col-0 allele is a negative regulator. Temp22.2 QTL was cloned and novel alleles were discovered revealing the molecular basis of quantitative variation in hypocotyl length in response to temperature.

Cross-stratified sandstones formed by dunes and unit bars is common in the rock record. Cross-bed architecture is controlled by the size and shape of, and processes on, the original formative bedforms, and processes that truncate, deform or bury the cross-strata. This thesis reports an investigation of cross-bedded sandstones and their internal sedimentary structures formed in fluvial environments within different depositional settings at Rillo de Gallo, (Spain) and Seaton Sluice, (Northumberland). In addition, flume experiments using well-sorted fine sand were used to investigate some of the factors controlling cross-bed architecture produced by unit bars migrating downstream in a unidirectional flow under controlled conditions over pre-existing topography. New ways of classifying cross-bedding were developed to allow analyses of patterns and relationships between set geometry, flow behaviour and stratigraphic position within sedimentary sequences. The amount and variation in divergence between scour trend and scour-fill laminae dip direction is found to be potentially diagnostic of flow pattern, and should improve palaeoenvironment interpretation. A relationship between the amount of variation in bar lee-face angle with bar height was found in the flume and may be useful for inferring bedform size in the rock record. Integration of laboratory and field observations on lee-face angle, bedform superimposition, reactivation surfaces, topography development and bottomset formation helped to mitigate the issue of preservation level when interpreting rock analogue examples and led to improved interpretations of the ancient fluvial deposits. This is an approach that should help the interpretation of other ancient fluvial sequences. The mechanisms and patterns of trough scour formation and scour filling have been to a certain extent ignored to date. Herein it is highlighted the need for further research on the understanding of scour formation and fill in association with bedform development and migration leading to improved knowledge of cross-bedded sandstones.

Marine biogeochemical processes are closely linked to phytoplankton community assemblages. Cell abundance and biomass are a measure of the successful conversion of inorganic to organic carbon. Carbon estimates are therefore often used to analyse metabolism and energy transfers within marine environments, and carbon is frequently the main parameter used in ecosystem models. Phytoplankton can be divided into functional types based on cell size: microplankton (<200 μm), nanoplankton (2-20 μm) and picoplankton (≤ 3 μm). Differences in cell volume govern variations in carbon content, nutrient uptake and influence cell fate. Reduced diameters equate to lower sedimentation rates and promote participation within the microbial loop and recycling of carbon within surface waters. Larger diameters can increase settling rates, resulting in the loss of carbon from surface waters. Current North Sea monitoring and research programmes typically only consider larger micro- and nanoplankton cells, or the bulk phytoplankton community as a whole: there is little separation by functional type. Inclusion of picoplankton and the delineation of biomass contribution by cell size are required for accurate depictions of phytoplankton productivity within this region, but this is not feasible with current water sampling protocols. Flow cytometry is a new multiparametric analysis technique offering high-speed enumeration and assessment of particles. Phytoplankton cells from 2-200 μm can be easily distinguished from debris and reproducible data on cell size and pigment content is supplied within minutes. This research uses flow cytometry to provide detailed assessments of phytoplankton community structure at a range of spatial and temporal scales. Distribution patterns are related to environmental parameters and observed patterns are used to test existing paradigm and advance current ecological theory.

Tropospheric Ozone Depletion Events (ODEs) have been known to occur during springtime in polar regions for over 20 years. During such events, ozone concentrations can fall from background amounts to below instrumental detection limits within a few minutes and remain suppressed for on the order of hours to days. The chemical destruction of ozone is driven by halogens (especially bromine radicals) that have a source associated with the sea ice zone. There is much debate over the source of bromine radicals in the atmosphere that drive polar boundary layer ODEs and few observations of speciated inorganic bromine against which to test current theory. In 2007, year round measurements were made at the British Antarctic Survey station Halley, in coastal Antarctica, using a Chemical Ionisation Mass Spectrometer (CIMS). During specific periods in the spring the CIMS was configured to measure concentrations of BrO, Br2 and BrCl. In addition, concurrent measurements of surface ozone and local meteorology were made. Presented here is an analysis of these datasets in terms of both chemistry, and the broader meteorological situation at play during the onset and termination of ODEs, in a move towards developing a generalised picture for ODEs at Halley. In order to explore halogen release, the MISTRA model is used to consider emissions from specific source regions, identified using HYSPLIT air parcel back trajectories. A new snow-photochemistry module has been developed for MISTRA which includes chemistry which takes place in the liquid like layer on frozen surfaces (MISTRA-SNOW; Thomas et al., 2011). Understanding these surface processes is of great importance to our understanding of the chemistry which initiates a bromine explosion. MISTRA-SNOW is initialised using measurements made at Halley station to explore both the chemical and meteorological conditions required to produce tropospheric ODEs in polar regions.

Increasing numbers of species are being transported beyond their natural range boundaries by humans. These non-native species can have severe negative impacts on native biodiversity. In order to guide management of these species it is important to be able predict where non-native species will spread to, and what impact they will have. This thesis aims to improve our understanding in both these areas, using the expansion of non-native birds in the Iberian Peninsula as a study system. The number of non-native passerines in the Iberian Peninsula has increased in the late 20th century, with the common waxbill Estrilda astrild, yellow-crowned bishop Euplectes afer, red avadavat Amandava amandava and black-headed weaver Ploceus melanocephalus all established as breeding species since 1960. Methods to (1) account for dispersal limitation when modelling the distribution of spreading non-native species and (2) evaluate the likely transferability of native trained species distribution models were developed. The consistency of the species-environment relationship during expansion in the non-native range was also examined. The ability of vacant niches to facilitate the spread of non-native species was tested, and a framework for detecting the early impacts of non-native species was developed. Species distribution models of the potential distribution of non-native species are improved by incorporating dispersal. Dispersal is an important constraint on the distribution of non-native species, and interacts with environmental suitability to alter the species-environment relationship between the range-margin and the range core, and over time. Despite accounting for dispersal limitation in their evaluation, the performance of native-trained species distribution models was poor when most environmental conditions that were analogous to the species native range were within the species niche. Non-native birds in the Iberian Peninsula utilised similar resources to native seed-eating birds, but small differences in resource utilisation allowed them to exploit rice fields, where resources were under-exploited by native species. Non-native birds could also interact with native reedbed nesting passerines, and indeed aggression between black-headed weavers and native Acrocephalus warblers has been recorded. However, we did not find evidence for competition between these species at current population densities of black-headed weavers. Further work on non-native species needs to extend the hybrid dispersal-species distribution models developed here, and also to conduct more assessments of the impacts of non-native species in the early stages of their invasion.

The 2010 explosive eruption (VEI 4) of Merapi volcano, Indonesia, was the volcano’s largest since 1872. In contrast, volcanism over the last century has been characterised by dome-building and gravitational dome collapse, such as in 2006 (VEI 1). The driving forces behind effusive and explosive activity, as well as factors that affect transitions in eruptive style are investigated through petrological and textural analysis, using the well-documented 2006 and 2010 eruptions as case-studies. Pre- and syn-eruptive crystallisation and degassing processes are examined via whole rock geochemical analysis, mineral compositions and thermobarometry, quantitative textural analysis of feldspar microlites and analysis of volatiles and light lithophile elements in melt inclusions. These data were gathered from a detailed set of stratigraphically controlled samples, correlated to eruptive chronology and style, which were collected during several field campaigns. Both the 2006 and 2010 eruptions produced basaltic andesite, similar in terms of major and trace element compositions. A major zone of crystallisation is proposed at between ~ 14 and 29 km depth, although crystallisation occurs throughout the crust. Magmatic temperatures are estimated to be ~920–1020 °C. Maximum H2O contents reach 3.94 wt.% in 2010 melt inclusions and up to 3.73 wt.% in those from 2006. CO2 concentrations are < 200 ppm, although they may reach up to 695 ppm in some melt inclusions from the 2010 eruption. An exsolved brine phase was present during both eruptions which “buffered” melt Cl concentrations and enriched Li at shallow depths within the conduit or edifice. Eruptive style and transitions at Merapi are linked to magma ascent rate, crystallisation and open- and closed-degassing processes, which can be influenced by magma influx. The findings of this work are crucial for understanding the full range of eruptive behaviour that Merapi is capable of producing.

This study aimed to characterise the bacterial community composition and abundance in the River Wensum in Norfolk using epifluorescence microscopy (EFM), automated ribosomal intergenic analysis (ARISA) and 454 pyrosequencing. It also aimed to determine the effects of spatial and temporal variations and environmental factors on bacterial community composition and abundance in this intensively farmed lowland catchment. The three techniques provided the same trends in bacterial community composition and abundance across the Wensum catchment. Total bacterial numbers ranged from 0.21 × 106 cells/mL to 5.34 × 106 cells/mL (mean = 1.1 × 106 cells/mL). The bacterial community composition and abundance showed significant differences between sites and times and were related to environmental parameters, with temperature and flow rate explaining most of the variation in bacterial community composition and abundance. Bacterial abundance increases as water moves downstream, while bacterial diversity decreases as water moves downstream. Some operational taxonomic units (OTUs) become commoner as the water moves downstream (3rd and 4th order streams). This presumably reflects the fact that these bacteria are actively growing in the river, and reducing the abundance of other taxa. Consequently, the community becomes less diverse moving downstream, although a small number of sites do not fit this pattern. The River Wensum is dominated by the phyla Proteobacteria, Bacteroidetes, Cyanobacteria and Actinobacteria. Members of these phyla are well known to be responsible for biogeochemical processes, such as nitrogen cycling. The commonest bacteria at upstream sites were Proteobacteria (OTUs 2 and 4), Deltaproteobacteria (OTU29), Gammaproteobacteria (OTU32), Sphingobacteria (OUT9) and Flavobacteria (OTUs 12 and 23). Most OTUs (2, 9, 17, 29 and 32) are considered to be soil bacteria, suggesting that these bacteria are terrestrial in origin and are flushed into the lower order streams. Most of the upstream bacteria showed positive relationships with total nitrogen (TN) and total carbon (TC) and the presence of arable areas. On the other hand, the commonest bacteria at downstream sites were Cyanobacteria (OTU1), Flavobacteria (OTUs 3, 10 and 19), Cytophagia (OTU14), Actinobacteria (OTUs 20, 21 and 25) and Alphaproteobacteria (OTU26). Most of the downstream bacterial OTUs showed a positive relationship with TP and the presence of urban areas. The results of this research, however, do not provide strong evidence that competition is an important process structuring these bacterial communities. In addition, the correlations between environmental parameters and bacterial composition and abundance are not strong and do not clearly distinguish the most impacted sites from others. This suggests that bacterial community composition cannot be used as an indicator of the ecological status to assess compliance with Water Framework Directive (WFD) in a moderately impacted lowland catchment like the Wensum.

River catchments are an obvious scale for soil and water resources management, since their shape and characteristics control the pathways and fluxes of water and sediment. Digital Elevation Models (DEMs) are widely used to simulate overland water paths in hydrological models. However, all DEMs are approximations to some degree and it is widely recognised that their characteristics can vary according to attributes such as spatial resolution and data sources (e.g. contours, optical or radar imagery). As a consequence, it is important to assess the ‘fitness for purpose’ of different DEMs and evaluate how uncertainty in the terrain representation may propagate into hydrological derivatives. The overall aim of this research was to assess accuracies and uncertainties associated with seven different DEMs (ASTER GDEM1, SRTM, Landform Panorama (OS 50), Landform Profile (OS 10), LandMap, NEXTMap and Bluesky DTMs) and to explore the implications of their use in hydrological analysis and catchment management applications. The research focused on the Wensum catchment in Norfolk, UK. The research initially examined the accuracy of the seven DEMs and, subsequently, a subset of these (SRTM, OS 50, OS10, NEXTMap and Bluesky) were used to evaluate different techniques for determining an appropriate flow accumulation threshold to delineate channel networks in the study catchment. These results were then used to quantitatively compare the positional accuracy of drainage networks derived from different DEMs. The final part of the thesis conducted an assessment of soil erosion and diffuse pollution risk in the study catchment using NEXTMap and OS 50 data with SCIMAP and RUSLE modelling techniques. Findings from the research demonstrate that a number of nationally available DEMs in the UK are simply not ‘fit for purpose’ as far as local catchment management is concerned. Results indicate that DEM source and resolution have considerable influence on modelling of hydrological processes, suggesting that for a lowland catchment the availability of a high resolution DEM (5m or better) is a prerequisite for any reliable assessment of the consequences of implementing particular land management measures. Several conclusions can be made from the research. (1) From the collection of DEMs used in this study the NEXTMap 5m DTM was found to be the best for representing catchment topography and is likely to prove a superior product for similar applications in other lowland catchments across the UK. (2) It is important that error modelling techniques are more routinely employed by GIS users, particularly where the fitness for purpose of a data source is not well-established. (3) GIS modelling tools that can be used to test and trial alternative management options (e.g. for reducing soil erosion) are particularly helpful in simulating the effect of possible environmental improvement measures.

The primary producers of essential omega-3 polyunsaturated fatty acids are marine microalgae, which form the base of the aquatic food web. One alternative source of our ever diminishing stocks of fish and fish oil is via the cultivation of these microorganisms. Unfortunately, these microalgae, of which diatoms are the dominant class, only accumulate oil during specific stages of their life-cycle and/or under nutritional states which are incompatible with the required high density of growth and target fatty acid profile. Additionally, the endogenous levels of desirable fatty acids such as eicospantaenoic acid (EPA; 20:5, n-3) and docosahexaenoic acid (DHA; 22:6, n-3) are usually relatively modest (in the range of 10-35% of total fatty acids) and therefore present an opportunity for enhancement. A database search carried out on the genomes of omega-3-producing unicellular photoautotrophic green alga Ostreococcus sp. RCC809 and cold-water diatom Fragilariopsis cylindrus led to the identification of four novel genes involved in omega-3 biosynthesis. These genes encoded an omega-3-specific Δ6-desaturase, a Δ4-desaturase, a Δ6-elongase and a Δ5- elongase. Overexpression of genes encoding Δ6-desaturase and Δ6-elongase activities in Thalassiosira pseudonana impacted the fatty acid and acyl-CoA profiles of this model centric diatom. Changes to chloroplast and lipid droplet phenotype were also observed. Targeted knock-down of native genes involved in the omega-3 biosynthetic pathway was carried out in T. pseudonana to further understand endogenous omega-3 fatty acid production. Cells targeted for the knock-down of Δ9-desaturase exhibited a drastically altered growth phenotype, but maintained a wild type-like fatty acid profile. This phenotype was attributed to the possibility of another, functionally redundant, protein that escaped sequence-based silencing, masking the knock-down of Δ9-desaturase. The results and observations provided in this thesis contribute new valuable information to the field of lipidomic research in microalgae, breaking new ground in metabolic engineering of lipid metabolism in diatoms.

Identification and monitoring of halocarbons in the atmosphere remains important for the purposes of regulation and prediction of stratospheric ozone depletion. Measurements of these and other compounds have created a demand for techniques that improve the number of atmospheric compounds analysable. A prototype time-of-flight gas chromatography-mass spectrometer (GCMS) was characterised for atmospheric measurements. Instrument performance was found to be at the lower end of expectations. A comparison to a quadrupole GC-MS indicated that the TOF GC-MS would be suitable for measurements in polluted environments. As part of this comparison, a number of halocarbons were analysed in London, U.K. as part of the ClearfLo campaign. HCFCs were found at higher concentration than their Northern Hemispheric (NH) baseline values. Furthermore, HFC-134a and HFC-227ea were almost double their NH baseline. CH2Cl2, C2Cl4 and C2HCl3 were encountered at high concentrations and sources of very short-lived bromomethanes (VSLB) were identified close to London. As part of the CARIBIC project, five VSLB were measured in the mid-latitude upper troposphere/ lower stratosphere and tropical troposphere. Higher mixing ratios were encountered over Southeast Asia, likely due to a locally longer CH2Br2 lifetime. Total bromine derived from these five VSLB is at the lower end of the quantity required to balance the stratospheric bromine budget. During the SAMBBA project, biomass burning and natural sources of COS, methyl halides and other halocarbons were assessed over Brazil. Methyl halide emissions from rainforest and savannah fires were quantified. The Cerrado savannah was found to be a strong source of COS. Regional biomass burning emission estimates indicate that this is an important region for emissions of these compounds. Terrestrial, natural sources of CH3Cl, CH3Br and CHCl3 were confirmed over the Amazon rainforest. Emissions from a localised source of CHCl3 were identified and wetlands or agricultural soil disturbance were hypothesised as a likely cause.