Marine ecosystems show natural fluctuation throughout a large range of spatial and temporal scales. Despite the large amount of study devoted to the North Atlantic Ocean, drivers of those fluctuations remain unclear. By changing global climate, polluting, introducing exotic species, expanding and intensifying land uses and overharvesting biological resources, human activities have degraded the global ecosystem and drastically accelerated species extinction rates. Consequences of this human forcing become apparent in the progressive degradation of ecosystem that are used by humans (Schroter et al. , 2005), climate change- induced shifts in species distributions toward the poles (Parmesan et al. , 1999) and higher elevations (Wilson et al. , 2005), and in rapidly changing phenology (Edwards & Richardson, 2004). Data collected by the Continuous Plankton Recorder (CPR) constitutes, by both their temporal and biogeographical extends, one of the most useful datasets to investigate further major marine management issues as the distinction between anthropogenic, climatically forced and natural ecosystems fluctuations. The present work is a contribution to environmental change biology focused on copepods Calanus species as key structural species characteristic of the North Atlantic Ocean and adjacent seas. The purpose is to (1) identify environmental factors leading to the large-scale distribution patterns of Calanus that occurred in the North Atlantic Ocean, and (2) to propose and investigate new methods to assess both fundamental and realised niches of a dominant species in these basins. Most current approaches using Hutchinson concept of ecological niches to model species distribution belong to correlative or mechanistic models. A correlative approach has been developed to assess statistical relationships between the observed spatial distributions of two congeneric species and a set of environmental variables characteristic of the studied area. The method is designed to show the seasonal dynamics of environmental restriction driving observed distributions. Both Calanus finmarchicus and C. helgolandicus environmental preferences and optimum have been defined for 11 environmental parameters. A principal component analysis (PCA) has been used (1) to quantify the importance on the spatial distribution of each environmental parameter and (2) to identify the ecological niche. A numerical analysis based on Multiple Response Permutation Procedures (MRPP) was utilised to assess the breath of each niche and to compare them. The egg production rate of Calanus finmarchicus has been defined to investigate the link between physiology, macroecological patterns and ecological niches. It typically assesses the fundamental niche as in opposition to the correlative approach, the model based on a fundamental biological process is more focused on the potential response of C. finmarchicus to environmental conditions. The simplicity of the method which used only Sea Surface Temperature (SST) allows us to use IPCC scenarios and predict a shift in distribution over the 21st century.

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The integrated model is finally applied to simulate the hydro-environmental processes in the Loughor Estuary to find out the contribution of different pollution sources on the receiving water nutrient concentration levels, and the influences of pollutant discharging schemes and temperature. The results show that the refined model is accurate and provides a valuable state-of-the-art novel tool for predicting improved nutrient concentration distributions in estuarine and coastal waters.

Studying and understanding the hydro-environmental characteristics of the Arabian Gulf has received growing interest over the past few decades. This is mainly attributed to the strategic importance of the area, since it has been utilised to transport most of the oil production from the Gulf states. Over the last five decades, rapid industrial coastal development also has taken place around the Gulf. Development has brought desalination, power and petroleum refining plants. Coastal developments and industrial and domestic sewage discharges have contributed to the total nutrient levels in the Gulf, which have enhanced unwanted algal growth in various coastal areas. More recently, climate change has brought flooding to the Gulf states and frequent dust storms, which have increased various environmental issues, such as sediment transport and nutrient sorption processes, also in the shallow regions of the Gulf. In the current study the geographic dispersion of numerical tracers and flushing characteristics, in terms of residence time, of the Gulf have been investigated. The study has revealed that dispersion of numerical tracers is chiefly controlled by tides in the Gulf, while winds had limited effects. The residence time in the Gulf was predicted to be almost 3 years using ELCOM. Kuwait Bay was also investigated in terms of the governing hydrodynamics using ELCOM. Similar to the Gulf, the study revealed that the Bay was chiefly driven by tides and to a lesser extent by winds. Detailed studies of temperature, using the same model, showed that temperatures varied seasonally in the Bay. In terms of salinity, investigations have shown that the Shatt Al Arab has an apparent effect on the Bay's salinity, particularly in the northern areas. The maximum residence time of the Bay was calculated to be 57 days near al Jahra using ELCOM. The main model refinements were conducted on including the phosphorus source terms in TRIVAST, based on experimental investigations in a hydraulics flume channel. The refinements included the addition of new source terms accounting for the adsorption of phosphorus to suspended sediments and bed sediments. Model investigations have shown that the model refinements improved the model predictions of phosphorus levels, with phosphorus being the limiting nutrient during high suspended sediment events in Kuwait Bay. In general, good water quality predictions in Kuwait Bay were achieved using both ELCOM-CAEDYM and TRIVAST. Predictions have shown that the Shatt Al-Arab waterway has significant effects of the water quality of the Bay. Better hydrodynamic predictions were achieved using ELCOM than TRIVAST for the Gulf and the Bay. This was due to the additional mathematical terms included in ELCOM, including, in particular, the terms representing tidal forces that were calculated from the gravitational potential.

High resolution multi-proxy analysis was undertaken on core MD02-2589 (41 26.03'S, 25 15.30'E, 2660 m water depth) from the Agulhas Plateau, Indian to Atlantic throughflow region, for the past 170 ka in order to provide a detailed record of both deep and surface ocean-climate interactions in the region. Particular focus was on Terminations I and II and Marine Isotope Stage (MIS) 5a-4 transition. Planktonic foraminifera assemblage counts and inferred sea surface temperature calculations combined with planktonic stable carbon and oxygen isotopes and ice rafted debris counts were used to show that towards the end of glacial periods MIS 6 and 2 there was a pooling of heat and salt in the throughflow region, transported to the area by the Agulhas Current. These waters were unable to be transported into the Atlantic Ocean due to the northwards position of the frontal systems associated with the Antarctic Circumpolar Current (ACC). Wider Southern Ocean warming towards the end of MIS 6, during maximum global ice volume, also shown by the benthic proxies, is seen to release a pulse of the pooled waters through the Agulhas throughflow region, some 6 ka before a Southern Ocean wide cold reversal linked to the resumption of North Atlantic Deep Water (NADW) convection to interglacial levels. This is significantly longer than ages suggested through modelling for the resumption of the thermohaline circulation interglacial mode following the recommencement of Agulhas leakage. Additional planktonic carbon isotope data from core MD02-2588 (41 19.90'S, 25 49.40'E, 2907 m water depth) show the development of a Carbon Isotope Minima Event during Terminations I and II, probably linked to the breakdown of stratification of the water column following glacial periods. Benthic stable carbon and oxygen isotope measurements combined with the sortable silt mean grain size sedimentological proxy are used to show the phasing of bottom water changes over terminations, with changes in chemical ventilation being largely decoupled from near-bottom physical flow speeds. Flow speeds record Southern Ocean variability and the chemical ventilation Northern Component Water variability. The results suggest the persistent presence of a high 5,3C water mass, similar to present day NADW, during glacial periods, with a rapid shoaling of NADW in the water column and replacement by Southern Component Water (SCW) over the MIS5a-4 transition. The benthic 8,3C record of MD02-2589, combined with that of MD95-2042 (Shackleton et al., 2000) from the Iberian Margin, show 8 periods in the past 150 ka where the mid-depth South Atlantic was bathed by a better ventilated water mass than the mid-depth North Atlantic, corresponding with glacial stages, substages and Heinrich events. The high 8,3C water mass present at MD02-2589 must have originated from outside the North Atlantic. Productivity and air-sea gas exchange overprints on both records cannot explain the full offsets seen with the most likely mechanism being the formation of a separate high 8I3C SCW mass, different to Antarctic Intermediate Water (AAIW) during glacial periods. It is possible that increased depth penetration of AAIW can explain the offset during Heinrich events. A suite of cores forming a latitudinal and depth transect over the modern day position of the Polar, Subantarctic and Subtropical Fronts (PF, SAF, STF) are investigated for MIS 2, with a chemocline, seen by Hodell et al. (2003), being identified. This study however shows the presence of a mid-depth divide north and south of the SAF, with very depleted values south and enriched values north, with deep depths (>3750 m water depth) both north and south of the SAF showing depleted values. This is used to suggest that the high 8,3C SCW mass seen during glacial periods is forming around the SAF in the southeastern Atlantic Ocean due to air-sea gas exchange and upwelling linked to wind forcing and sea ice extent. This study suggests that previous work using benthic 8 C data looking at the extent of glacial water masses in the world's oceans may have been over-reconstructing the extent of glacial Northern Component Water as it is likely to have a very similar 8 C and 8I3Ca$ signature as this SCW mass forming around the SAF and migrating northwards.

This study consists of three parts: (i) Field work and data collection from the Loughor and Severn Estuaries. P adsorption increased with decreasing median sediment size in both estuaries. A positive correlation was found between the P adsorption in sediment and salinity in the Loughor Estuary, whereas a negative correlation was found in the Severn Estuary. Some factors, such as particle grain size, salinity, pH, organic matter, suspended sediment concentration and P concentration were found to control the exchangeable or loosely sorbed P (adsorbed P) in both estuaries. (ii) Laboratory experiments were conducted on P adsorption/desorption on different types on sediment, including Kaolinite, Silica, mud, silt, sand and suspended sediment. P adsorbed to the mud fraction than to the sand fraction. The adsorption coefficient (K_d) and Maximum P adsorption (PS_Max) for the mud fraction were 0.0091/g and 0.39 mg/g for the silt 0.007 l/g and 0.30 mg/g and the sand 0.001 l/g and 0.05 mg/g. (iii) Flume experiments were conducted in the hydraulic laboratory at Cardiff University, U.K. The main findings revealed that the velocity and the P concentrations in the water were important factors controlling the amount of P adsorbed processes on the sediment. The results from the field work and the laboratory experiments were similar to flume channel findings. These findings were used to develop new source term equations and these equations were added to the QUAL2E water quality model to improve the capability of the model to predict the P adsorption processes in a 2D computer model. These new equations were then used to simulate P concentrations in the estuarine environment using DIVAST.

Marine sediments harbour vast and diverse prokaryotic communities. With ongoing burial and ageing of respective sediment layers, however, available organic matter becomes more recalcitrant. Thus, sedimentary microorganisms face starvation and ultimately death. Nonetheless, live and active cells are present in old and deeply buried sediments, up to 111 Ma (Roussel et al., 2008). During IODP Leg 307 an organic-matter poor, cold-water, buried coral carbonate mound was sampled. Nineteen isolates, mainly Proteobacteria, were obtained from the mound and surrounding sediments. Additionally, one putative new species belonging to the genus Ornithinimicrobium (Actinobacteria) was isolated. Strains were subsequently phylogenetically and phenotypically characterised. Selected isolates and other sedimentary bacteria were subsequently subjected to anaerobic starvation-survival experiments and their responses to substrate limitation were compared to those of near-surface relatives. All strains survived long periods of starvation (incubated up to 3 years). This was confirmed by constant total cell counts and only slowly increasing proportions of dead cells (20% after one year). Culturability and FISH detectability decreased with time but radiotracer experiments conducted after starvation confirmed viability and potential metabolic activity of many strains. No significant correlations between FISH detectability and other viability measures occurred. Instead starvation time was significantly positively correlated with percentages of dead cells and inversely with culturability. Pure culture starvation experiments were complemented by a study on an estuarine, surface-sediment microbial community, which was stressed in sediment slurry sequential heating experiments. This mimicked burial and resulted in decreasing total counts, culturability, and FISH detcctability but these were still present even after heating to 90 °C. Temperatures above 42 °C were significantly correlated with the reduction of total cells and FISH detectability This project showed that marine sedimentary microbes maintain high levels of viability and culturability during long-term anaerobic starvation and during sequential heating to mimic burial this is consistent with the large cell population in sub-seafloor sediments.

Recent estimates of global sea level rise indicate mean values around 3.1 mm yr"1. As a result, many coastlines face an increasing risk of coastal erosion, and the threat of flooding is becoming a major concern. Unfortunately, coastal defences can be very costly with recent estimates as high as £5000 per metre length of seawall in the UK. There is a need to consider more economically feasible options, and by accounting for the ability of saltmarshes to absorb wave energy, reduce flow velocities and stabilise sediments, the costs of coastal defence structures may be significantly reduced. But first, an improved understanding of the implications of saltmarsh vegetation on hydrodynamics is fundamental to their inclusion in the design of coastal protection schemes. This includes the influence of saltmarsh vegetation on velocity and turbulence structures and the drag forces that arise due to the obstruction to the flow created by the vegetation. Two contrasting areas of coastal saltmarsh were selected for the location of a field survey to identify typical field conditions, such as bed gradients, submergence levels, vegetation types and densities. The two sites differ in that the first was non- grazed, while the second was heavily grazed to assess the impact of sheep farming on vegetation characteristics. The vegetation species, stem densities and submergence levels observed during the field survey were used as a guideline for designing a series of laboratory experiments to investigate the impact of saltmarsh vegetation on hydrodynamics. Uniform cylinder models are widely used to simulate vegetation canopies in hydrodynamic studies, yet the cylinder model can lead to an oversimplification of vegetation morphology. A comparison was made by conducting experiments under uniform flow conditions where uniform cylinder arrays and vegetation canopies were installed onto a flume bed at stem densities of 800, 1160 and 1850 stems m*2. There were differences in velocity and turbulence structures through the two types of canopy. For the same stem density, the proportion of the total flow passing through the canopy region was approximately 10% greater for the uniform cylinder arrays. The foliage found in the upper part of vegetation canopies resulted in a considerably higher level of obstruction and contributed towards reducing velocities and Reynolds stresses within the canopy. Reynolds stress penetration depths were up to 15 times greater for the uniform cylinder arrays compared to the vegetation canopies. Computational fluid dynamics models can be a useful tool for predicting the impact of saltmarsh vegetation on hydrodynamics for coastal management. Applying such models to vegetated flows requires knowledge of the drag coefficient to determine the drag term in the Navier-Stokes equations. However, in the absence of measured data, such models are often applied with the assumption that the drag coefficient is constant in value, and commonly used values include '1.0' and '1.2'. Such assumptions may be easily linked to the uniform cylinder model. However, drag coefficients calculated for Common Cordgrass ranged between 0.4 and 1.7. Values were dependent on numerous parameters, including the Reynolds number, the submergence level, the stem density and the maturity of the vegetation. Instead of the traditional drag-force approach for determining canopy hydrodynamics, a method for predicting velocity and turbulence structures based on the projected area of the vegetation was proposed. For the emergent canopy, the mean velocity was estimated by relating to a reference canopy of known projected area and mean velocity. For the submerged canopy, the surface flow layer velocity was determined effectively using the Manning's roughness approach and the depth- averaged canopy velocity was a function of the surface layer velocity and the canopy density. Velocity profile shapes for both canopies were obtained by linking the mean canopy velocity to the projected area profile. Reynolds stresses for the emergent canopy and lower part of the submerged canopy were negligible and a function of depth-averaged canopy velocity. For the upper part of a submerged canopy, Reynolds stresses were a function of the depth-averaged surface layer and canopy velocities. The proportion of the submerged canopy region experiencing higher Reynolds stresses is also a function of the vegetation density.

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