The use of maize (Zea mays) as a co-substrate with cattle slurry for the production of biogas was investigated in detail by running several long term digestion trials under different operational conditions in laboratory scale semi-continuous digesters. These conditions included varying the organic loading rate (OLR) from 2 to 6 g VS l-1 d-1, the proportion of cattle slurry from 25 to 100%, and the recirculating regime. Results indicated that the co-digestion of cattle slurry and maize was viable at all loading rates tested with the greatest volumetric methane yield, 1.46 l l-1 d-1, produced at a 5 g VS l-1 d-1 OLR consisting of 40% cattle slurry; this corresponded to a specific methane yield of 0.26 l g-1 VS added. Successful digestion was shown at retention times as low as 15 days where a volumetric methane yield of 1.26 l l-1 was produced. Co-digestion had a pronounced effect on the volumetric methane yield with improvements of up to 355% when compared to the digestion of cattle slurry alone. Additionally, the OLR could be doubled by the addition of an equal quantity of maize, on a VS basis, with the volumetric methane yield increasing by over 200% without a great loss of the methane potential of the maize. For each trial undertaken in this research the actual methane yield produced from co-digestion was compared to that calculated to be produced. Support for synergy was shown in the first two trials where the actual methane yield exceeded that predicted however, the method used to calculate the predicted yield was suggested to be an inaccurate determination. To address this inaccuracy a trial was designed testing the digestion of the two substrates alone and together under the same operational conditions and methodology. A comparison between the mono and co-digestion trials indicated that the addition of maize to cattle slurry produced a methane yield that more or less equalled that calculated from the sum of the cattle slurry and maize alone. This brought the early indications of synergy into doubt with suggestions that they were the result of an inaccurate determination of the predicted yield and of inhibition washout. In the final part of the research an attempt was made to improve the volumetric methane yield by introducing solids recirculation to the co-digestion process with the objective of maintaining the slowly degradable fraction of the maize and cattle slurry in the digester for longer periods. This proved not to be a viable option with the methane production showing a decline; at an OLR of 5 g VS l-1 d-1, consisting of 50% cattle slurry, a decline of 0.31 l l-1 d-1 occurred. Solids recirculation was also introduced to the mono-digestion process to determine whether the differences shown in the co-digestion trial were a result of recirculating the solids of the cattle slurry, the maize or a combination of the two. Results showed that both substrates produced unstable conditions indicating that the co-digestion trial was not the result of just one substrate failing. Liquid recirculation was also tested on the co-digestion of the substrates and while no decline was observed no improvement was produced. KEYWORDS: Anaerobic digestion, co-digestion, cattle slurry, maize, solids recirculation

Plant morphology and function are sensitive to rising atmospheric carbon dioxide (CO2) concentrations, but evidence that CO2 concentration can act as a selective pressure driving evolution is sparse. Plants originating from naturally high CO2 springs are subjected to elevated CO2 concentration over multiple generations, providing an opportunity to predict how adaptation to future atmospheres may occur, with important implications for future plant conservation and crop breeding strategies. Using Plantago lanceolata L. from such a site (the ‘spring’ site) and from an adjacent ambient CO2 site (‘control’ site), and growing the populations in ambient and elevated CO2 at 700 μmol mol-1, I have characterised, for the first time, the functional and population genomics, alongside morphology and physiology, of plant adaptation to elevated CO2 concentrations. Growing plants in elevated CO2 caused relatively modest changes in gene expression, with fewer changes evident in the spring than control plants (33 vs 131 genes differentially expressed [DE], in spring and control plants respectively). In contrast, when comparisons were made between control and spring plants grown in either ambient or elevated CO2, there were a much larger number of loci showing DE (689 in the ambient and 853 in the elevated CO2 environment). Population genomic analysis revealed that genetic differentiation between the spring and control plants was close to zero with no fixed differences, suggesting that plants are adapted to their native CO2 environment at the level of gene expression. Growth at elevated CO2 led to an unusual phenotype, with an increase in stomatal density and index in the spring, but not in control plants. Focussing on previously characterised stomatal patterning genes revealed significant DE (FDR < 0.05) between spring and control plants for three loci (YODA, CDKB1;1, and SCRM2) and between ambient and elevated CO2 for four (ER, YODA, MYB88, and BCA1). We propose that the up-regulation in spring plants of two positive regulators of stomatal numbers (SCRM2 and CDKB1;1) act here as key controllers of stomatal adaptation to elevated CO2 on an evolutionary timescale. Significant transcriptome reprogramming of the photosynthetic pathway was identified, with an overall decrease in expression across the pathway in control plants, and an increase in spring plants, in response to elevated CO2. This was followed up by physiological measurements, where a significant increase (P < 0.05) in photosynthetic capacity and regeneration rate was exhibited in spring plants, compared to control plants, at both elevated and ambient CO2 concentrations. Through this comprehensive analysis, we have identified the basis of plant adaptation to elevated CO2 likely to occur in the future.

This thesis assessed the impact of a novel low-head hydropower device, the Hydrostatic Pressure Converter (HPC), on downstream moving fish, and investigated factors that may limit both up- and down-stream fish pass efficiency. This was achieved through the use of a blade strike model (BSM) and experimental studies conducted in large open channel flumes. A BSM predicted a lower probability of strike with a HPC blade for small fish that travelled downstream faster, and when blades rotated slowly. A major pinch-point between the blade tips and the base of the flume caused severe damage to euthanized brown trout (Salmo trutta) as they passively drifted through a prototype HPC. Damage ranged from abrasive scale loss to skeletal deformation and breakage. Rainbow trout (Oncorhynchus mykiss) and European eel (Anguilla anguilla) did not exhibit avoidance behaviours when approaching the intake to a HPC located within a flume. When behavioural data (speed of downstream movement and orientation) were incorporated into BSM simulations, probability of strike increased and decreased for trout and eel, respectively, compared with an assumption of passive drift with bulk flow. Species specific behaviours influenced probability and severity of strike with a HPC blade. Management recommendations are made to ensure HPC developments meet the required environmental standards. Ensuring efficient fish passage around low-head hydropower developments presents a major ecological challenge. Behavioural data on individual fish encountering conditions ubiquitous to fish pass structures was used to investigate and identify factors that may limit passage efficiencies. Although upstream migrant adult river lamprey (Lampetra fluviatilis), a species of conservation concern in Europe, were predicted to avoid areas of elevated turbulence, little evidence in support of this was found. Instead lamprey appeared to alter their migration strategy based primarily on water velocity. Behaviours were indicative of a time conservation strategy, i.e. altering behaviour to expedite passage through energetically expensive environments. For downstream moving fish, delay due to avoidance of conditions created at bypass entrances (e.g. abrupt accelerations of velocity) can negatively impact fitness. Velocity gradients created by a constricted flume section had a clear influence over downstream moving brown trout. Avoidance behaviours occurred at a similar threshold spatial velocity gradient when dark (ca. 0.4 cm s-1 cm-1), and the addition of a light stimulus served to reduce this threshold by approximately 50%. Elevated avoidance to velocity gradients was also evident when downstream migrant juvenile salmon (Oncorhynchus tshawytscha) were able to navigate using mechanosensory and visual senses. Avoidance behaviour significantly impacted subsequent rate of passage. Information provided in this thesis significantly enhances our understanding of how fish respond to environmental stimuli, has direct application to fish passage, and the potential to improve fish survival at low-head hydropower developments.

Heavy metals in air, soil and water are a global problem and present a growing threat to the environment. These metals may have profound consequences for birds and can cause a number of sub-lethal effects, such as decreased reproductive success. The concentrations of selected heavy metals (As, Cd. Co, Cu, Fe, Pb, Mn, Ni, V, Zn) and Se in eggs and feathers from populations of black-headed gulls (Larus ridibundus L.) located on different colonies in the UK, which have different characteristics and are subject to different sources, types and degrees of pollution, were examined. Concentrations of As, Cu, Pb, Ni, Se and V measured in black-headed gull eggs were consistently high relative to those reported in previous field studies with other gull species. However, no significant effect was observed on the egg characteristics in terms of egg size and dimensions, shell thickness and index as a result of concentrations of metals measured in this study. Concentrations of Co, Fe and Ni were significantly negatively correlated with yolk:albumen ratio in the egg. The usefulness of sampling eggs to provide a reflection of local contamination has been demonstrated, with concentrations related to local sources of metal pollution and site differences reflected in sediment concentrations from previous studies. The importance of taking into account diffuse and historical pollution in addition to point source discharges has also been highlighted. As, Fe, Mn, Pb, Se, V and Zn were found at significantly higher concentrations in egg contents than egg shell, and Cd, Co and Ni concentrations were higher in shell than contents. Cu was distributed approximately equally. Within the egg contents, concentrations of As, Cu, Se and V were higher in the albumen than in the yolk, and Co, Fe, Mn, Ni, Pb and Zn concentrations were higher in the yolk than the albumen. Cd was found mainly in the shell and concentrations in egg contents were largely undetectable. Comparisons were made between a colony subject to high-level commercial egg harvesting and an un-harvested site, and between pre- and post-harvesting eggs on the harvested site. Postcollection eggs were found to be of significantly lower quality than the pre-collection eggs and the eggs from the uncollected site, as indicated by yolk:albumen ratio. Concentration of metals in eggs as a result of relaying forced by commercial harvesting has been demonstrated, with concentrations of Co, Fe and Ni significantly higher in post-collection eggs compared to precollection eggs. Average nesting density was significantly lower on the collected colony than the uncollected colony. No effect on egg size was found as a result of changes in nesting density. Concentrations of metals in black-headed gull chick down were measured and compared to egg data in order to assess the usefulness of feathers as a tool for non-destructive monitoring of metal pollution. The results suggest that feathers may be good indicators for As and Zn, and possibly also for Mn and Ni. However, the sample masses were very small and for a number of metals concentrations were largely undetectable using the analytical equipment available in this study. Future work with larger samples of down would be prudent to further examine the use of chick down to provide an indication of the level of pollution to which birds are exposed. The importance of using appropriate washing procedures to remove exogenous contamination of feathers to assess internal concentrations has been demonstrated

There has been considerable discussion in recent years about the potential of micro-algae for the production of sustainable and renewable biofuels. Unfortunately the scientific studies are accompanied by a multitude of semi-technical and commercial literature in which the claims made are difficult to substantiate or validate on the basis of theoretical considerations. To determine whether biofuel from micro-algae is a viable source of renewable energy three questions must be answered : a. How much energy can be produced by the micro-algae? b. How much energy is used in the production of micro-algae? c. Is more energy produced than used? A simple approach has been developed that allows calculation of maximum theoretical dry algal biomass and oil yields which can be used to counter some of the extreme yield values suggested in the 'grey' literature. No ready made platform was found that was capable of producing an energy balance model for micro-algal biofuel. A mechanistic energy balance model was successfully developed for the production of biogas from the anaerobic digestion of micro-algal biomass from raceways. Preliminary calculations had suggested this was the most promising approach. The energy balance model was used to consider the energetic viability of a number of production scenarios, and to identify the most critical parameters affecting net energy production. These were: a. Favourable climatic conditions. The production of micro-algal biofuel in UK would be energetically challenging at best. b. Achievement of ‘reasonable yields’ equivalent to ~3 % photosynthetic efficiency (25 g m-2 day-1) c. Low or no cost and embodied energy sources of CO2 and nutrients from flue gas and wastewater d. Mesophilic rather than thermophilic digestion e. Adequate conversion of the organic carbon to biogas (≥ 60 %) f. A low dose and low embodied energy organic flocculant that is readily digested, or micro-algal communities that settle readily g. Additional concentration after flocculation or sedimentation h. Exploitation of the heat produced from parasitic combustion of micro-algal biogas in CHP units i. Minimisation of pumping of dilute micro-algal suspension It was concluded that the production of only biodiesel from micro-algae is not economically or energetically viable using current commercial technology, however, the production of micro-algal biogas is energetically viable, but is dependent on the exploitation of the heat generated by the combustion of biogas in combined heat and power units to show a positive balance. Two novel concepts are briefly examined and proposed for further research: a. The co-production of Dunaliella in open pan salt pans. b. A 'Horizontal biorefinery' where micro-algae species and useful products vary with salt concentration driven by solar evaporation.

This project conducts an analysis of bank erosion processes on a large, monsoonaffected river, the Lower Mekong River in Laos. The methodological approach taken was to build integrated models of bank erosion processes at three study sites on the Lower Mekong River in Laos (Friendship Bridge, Ang Nyay and Pakse) to simulate processes of (i) groundwater seepage and pore water pressure evolution, (ii) the effect of this on mass-wasting (using the Geo-slope model) and, (iii) fluvial erosion (using a model adapted from Kean and Smith, 2006ab). In all cases the models were parameterised using measured bank geotechnical properties. Across the study sites, a total of 42 simulations were undertaken to represent a wide range of observed flow events. Specifically, 14 selected flow hydrographs (comprising three types: single peak, multiple peak and rapid fall) were evaluated at each of the study sites, such that the influence on bank erosion of the hydrological properties of different monsoon floods could be evaluated. The main findings indicate that although the Mekong is a big river, its dominant bank erosion process is one of slow, gradual, fluvial erosion. This research forms a partial contribution to understanding bank erosion processes operating in the Mekong. It was found that bank stability on the Mekong responses to variations in flood magnitude in ways that are similar to other rivers located within humid temperate areas. However, the Mekong has had the greater stability than these rivers due to its greater bank heights and more consolidated bank materials.

The aim of the research described in this thesis was to investigate the spatial and temporal variability of photosynthetically active radiation (PAR) over the UK, in particular, to estimate both global PAR and the fraction of diffuse PAR at spatial and temporal scales appropriate for use with plant productivity models. In the UK, the spatial and temporal variation of PAR is primarily controlled by the fractional cloud cover and the solar geometry. Diffuse flux (skylight) penetrates further into the canopy than direct flux, so knowing the diffuse PAR fraction ( ) will improve the accuracy of plant productivity models, especially for canopies with significant 3D structure, such as forest. The first part of the research investigated a novel sunshine sensor, the Delta-T Devices BF3, to test whether this simple low-cost instrument was an adequate substitute for the instruments normally used to measure the components of PAR. This was the first independent test of this instrument and it concluded that the BF3 was highly suitable for this purpose. The main study developed and tested a method to map the amount of incident PAR ( ) and the diffuse fraction ( ), based on satellite sensor data. The main systems used were the Meteosat Visible and Infrared Imager (MVIRI) on board the Meteosat First Generation (MFG) satellite and the Spinning Enhance Visible and Infrared Imager (SEVIRI) on board the Meteosat Second Generation (MSG) satellite. The resulting maps of global and diffuse PAR over the whole of the UK were validated using ground data from meteorological stations and instruments at eight FLUXNET sites around the country. It is estimated that global hourly PAR was accurate to < 50 (RMSE) and diffuse PAR fraction to <10 % (RMSE). This is the first time these variables have been mapped at moderate spatial resolution (1km) over the whole of the UK. The Forest LIGHT (FLIGHT) model (North, 1996) was used to study the influence of and on forest canopy photosynthesis. The effect of diffuse PAR fraction on gross primary productivity was clear. With the same overall level of PAR, a forest canopy under ‘direct and diffuse’ illumination had an increase in GPP around 12 % compared to one under direct illumination only. One of the major issues faced in this research was the lack of adequate ground data for validation. The research has shown that both the amount of PAR and the diffuse fraction are important factors in forest productivity, and that the Delta-T Devices BF3 instrument is well-suited as a source of validation data for a national network to monitor the gross primary productivity of forests in the UK.

Loss of habitat connectivity due to anthropogenic structures is among the greatest threats to freshwater fish populations. Re-establishing river connectivity through fish pass facilities can be an effective and cost-efficient method of enhancing local productivity, yet many are unsuccessful. A good understanding of multispecies swimming performance and behavioural response to hydraulic conditions is therefore needed to improve designs. This thesis aimed to improve knowledge in this field for non-salmonid fish species of conservation concern and economic value. Swimming performance data were collected for juvenile bighead carp (Hypophthalmichthys nobilis), a species threatened by anthropogenic barriers in China, using a range of swim chamber and open channel flume methodologies. Burst swimming performance was relatively weak, especially where multiple high velocity areas had to be passed. In addition, the availability of low velocity areas in a section of open channel flume did not improve endurance, and beyond aerobic swimming speeds these velocity refugia were rarely utilised. Management recommendations for fish pass velocities are presented based on this data. To further explore carp behavioural utilisation of low velocity regions, juvenile common carp (Cyprinus carpio) swimming performance and behaviour were evaluated under various wall roughness treatments. Fish generally maintained position close to smooth walls and small corrugations, yet often moved further from medium and large corrugations and into areas of higher velocity and lower turbulent kinetic energy. Thus, performance was not enhanced by the larger areas of low velocity created by corrugated walls. To assess the influence of accelerating flow on European eel (Anguilla anguilla) behaviour, a constricted flume created a velocity gradient representative of that found at anthropogenic structures and downstream bypass facilities. Of 138 downstream moving silver eels approaching the constriction, 46% reacted by changing orientation and/or a rapid burst of upstream swimming. Furthermore, 36% rejected the constricted channel and returned upstream, delaying downstream passage. The probability of a rejection was increased by a high abundance of the invasive parasite, Anguillicoloides crassus. These findings have potential implications for bypass efficiencies and escapement to sea. Eel swimming performance and behaviour were also evaluated during upstream passage through a culvert. Traditional corner baffles and prototype sloped baffles improved passage success compared to a bare culvert. Although the prototype created higher barrel velocities and turbulence, eel passage success was equal between the two baffle designs. Installation of the sloped baffle is recommended due to high passage efficiency and the potential to reduce the risk of debris accumulation compared to 90° baffles. The data presented in this thesis enhances our understanding of non-salmonid swimming performance and behaviour, and are used to recommend approaches to fish pass design for European eel and Asian carp.

Anabranching fluvial networks recently have become the focus of attention from environmental specialists, especially in the hydraulic field. Anabranching networks can be found in different physical environments; however, the hydraulic and geomorphological natures of such river networks are still not well known leading to on-going discussions on the definition and nature of the networks. Even though, alluvial anabranching networks generally have common features like vegetated islands, low water surface slope and stable channel planform, bedrock-confined anabranching networks also have their own characteristics inherited from the geological and structural controls imposed on the single channels that compose the network complex. This thesis focuses on the provision of a benchmark describing the bulk hydraulic characteristics of a large bedrock-confined, anabranching river network, located within southern Laos. The network can be separated into: (i) the upper river network constituted by two bifurcations and one confluence with an interpolated bathymetry based on soundings of cross-sections along the navigation channels; and, (ii) the downstream river network characterised by a complex anabranching network with five bifurcations and five confluences for which there is no bathymetric survey. The river network as whole is a ‘composite’ – partly bedrock (especially the channel-bed) and partly alluvial-filled and as such it does not accord fully with any prior description or classification of anabranching channel networks (e.g. Huang and Nanson, 1996). To understand the hydraulic nature of the river network, the energy approach in a onedimensional (1D) steady-flow hydraulic model (HEC-RAS) was applied to the network. Significant challenges arose due to the lack of boundary conditions throughout the model, namely: (i) unknown splitting discharge ratios at each bifurcation; (ii) partly non-survey bathymetry; and, (iii) ungauged downstream boundary condition of one of the channel outlets. To determine the discharge entering each channel, the splitting discharge ratio at each bifurcation was defined originally by the ratio of the cross-sectional area of the first crosssection of each downstream channel and then adjusted based on the Flow Optimization function in HEC-RAS to minimize any rise or drop of the modelled water surface around a junction. For the channels with non-surveyed bathymetry, a SPOT satellite image was processed to construct a pseudo-bathymetry showing a range of elevations, including shallow and deep portions of channels, rather than detailed bed elevations as would be obtained from a measured bathymetry. To define the boundary condition of the ungauged channel outlet, the water surface elevation was interpolated and validated according to predefined assumptions (i.e. the water surface slope along the ungauged channel was interpolated according to the available DEM and cross-sectional width extracted from a SPOT image for low discharge conditions was assumed to be similar to the gauged channels for flooding discharges). In general, the study has helped to develop methods to model the complex river network with data constraints (i.e. the boundary conditions). The findings include: (i) the developed pseudo-bathymetry based on a SPOT image is useful to model a large river network using the energy approach in a 1D hydraulic model in which the cross-sectional area is important in modelling the bulk hydraulic parameters but the influence of the cross-sectional shape is subordinate; (ii) the in-channel hydraulic roughness coefficient at each cross-section may be significantly different from neighbouring values due to the variation in the local bedrock roughness and the roughness of intervening alluvial reaches; and, (iii) the hydraulic roughness of the riparian land cover along the floodplains does not contribute noticeably to the modelled stage along the river network nor to the planform extent of flooding for overbank flooding discharges. Rather, changes in land-cover, and hence the riparian roughness, are registered as small, but measureable, changes in the local velocity over the riparian floodplain and in the average in-channel velocity. Citations: Van, P.D.T., 2009. Hydraulic modelling and flood inundation mapping in a bedrockconfined anabranching network: The Mekong River in the Siphandone wetlands, Laos. Unpublished PhD thesis submitted to the Faculty of Engineering, Science and Mathematics, University of Southampton, England.

Aerosol Optical Thickness (AOT) data have many important applications including atmospheric correction of satellite imagery and monitoring of particulate matter air pollution. Current data products are generally available at a kilometre-scale resolution, but many applications require far higher resolutions. For example, particulate matter concentrations vary on the scale of tens of metres, and thus data products at a similar scale are required to provide accurate assessments of particle densities and allow effective monitoring of air quality and analysis of local air quality effects on health. This thesis describes the development of a novel method which retrieves per-pixel AOT values from high-resolution (30m) satellite data, and this method is the main novel contribution to scientific knowledge of this PhD. This method is designed to work over a wide range of land covers including both bright and dark surfaces - and requires only standard visible bands, making it applicable to a range of data from sensors such as Landsat, DMC, SPOT and Pleiades. The method is based upon an extension of the Haze Optimized Transform (HOT), which was originally designed for estimating the haziness of each pixel in a satellite image, based upon the distance from a `Clear Line' in feature space. In this research, the HOT method is adapted and used to estimate AOT instead. Significant extensions include Monte Carlo estimation of the `Clear Line', object-based correction for land cover, and modelling of the HOT-AOT relationship using radiative transfer models. Validation against ground and satellite measurements, as well as simulated data, shows that 40-50% of the pixels have an error within ±0.1, not much lower than many presently available low-resolution products, with further work likely to improve the accuracy. Two example applications show the potential of this method for per-pixel atmospheric correction and monitoring the spatial pattern of particulate matter pollution. This novel method will enable many new applications of AOT data that were impossible with low-resolution data.