This work addresses the retrieval of the three water quality parameters chlorophyll-a, yellow substance and suspended particulate matter from spectra of remote sensing reflectance in European coastal waters. We study the suitability of a semi-analytical algorithm for the retrieval of these parameters in coastal waters to investigate the validity of radiative transfer theory and bio-optical models that have been developed primarily for open ocean waters. To obtain water quality parameters from reflectance measurements we employ a non-linear inversion method (Gauss-Newton). Algorithm parameters are established to ensure convergence of the method and reduce trapping by local minima. The developed algorithm is then evaluated with the help of a case-specific sensitivity analysis that reveals strengths and weaknesses with respect to measurement errors and inaccuracies of the bio-optical models on which the algorithm is based. In order to establish the validity of the results, a second sensitivity analysis is carried out based on the analysis of normalised partial derivatives of the algorithm's central equation. The algorithm is then applied to an extensive in situ data set consisting of 447 high-resolution spectra of remote sensing reflectance and water quality parameters from a range of European coastal waters, acquired in the framework of three different projects. Given the different measurement techniques within the various projects, it is not surprising that the algorithm performs poorly for the complete data set. Studying the regional subsets individually yields improved results in some cases, suggesting potential for developing regionally specific algorithms on the basis of dedicated tuning. The complete failure of the algorithm in other regions displays the shortcomings of the methodology. It is shown that, in some cases, the forward model fails to describe the optical characteristics encountered producing a pronounced mismatch between calculated and measured reflectance spectra in both spectral shape and magnitude. In other regions the spectral shape is largely reproduced by the model but a mismatch in magnitude results in failure of the inversion procedure. However, the most fundamental problem encountered is the non-uniqueness of the reflectance inversion process for some spectra. Improved bio-optical models and dedicated measurement campaigns in coastal waters are a crucial requirement to resolve this problem for future regional applications of semi-analytical algorithms. We point out the optical characteristics of favourable and unfavourable conditions for the retrieval of water quality parameters and provide some guidelines to future measurements of optical properties of coastal waters.

We describe a generalization of the Bernoulli inverse method, which produces an estimate of Sea Surface Height (SSH) across the region of interest rather than simply at station positions. Real-time ‘float’ observations and satellite altimetry measurements are used to map a ‘sea surface elevation’ to study the large-scale ocean circulation in the North Atlantic. The inverse has been applied to simulated Argo floats and satellite altimetry tracks in the Ocean Circulation and climate model (OCCAM). The Bernoulli inverse method predicts the SSH by finding geostrophic streamlines along which the Bernoulli function is conserved. These streamlines are defined where modified potential temperature and salinity are conserved. This predicted SSH is combined with that measured by the satellite altimetry. The revised method uses linear regression to give a surface solution for the region rather than solving the function at fixed positions, hence increasing the resolution of the problem by combining the altimetry measurements for the region. We will present results of a comparison study where real-time Argo and satellite altimetry have been used in combination with OCCAM using the same method to see how robust the solutions are for the NorthAtlantic.

The Atlantic Meridional Overturning Circulation (AMOC) represents a key component of the climate system. Previous studies indicate the present-day configuration of the circulation is highly sensitive to freshwater forcing, and appears able to exhibit bistability whereby contrasting states of circulation can exist under the same freshwater forcing, the choice of which is determined by the system’s history. This thesis presents an investigation into the dynamics and bistability of the AMOC in the context of the intermediate complexity Earth System Model, GENIE. Investigation of the dynamics of the AMOC is performed using diagnostic code implemented into the GENIE framework which allows decomposition of the dynamic and kinematic budgets of the ocean, in terms of density, pressure-gradient, velocity and overturning tendencies. Analysis of decomposition results from an optimal initial steady state demonstrates the complex and spatially heterogeneous nature of the underlying physical balances. Typically, simple dynamical balances are not representative, and a full compliment of advective, diffusive, convective and surface forcing components act to maintain a steady state. Implementation of a stratification dependent vertical diffusivity parameterisation into the GENIE framework allows assessment of the effect of mixing scheme complexity. A novel experimental approach based on factorial sampling of parameter space in combination with multi-objective optimisation techniques, provides a large database of AMOC stability metrics, which are analysed using general linear modelling techniques. The statistical conclusions suggest that whilst the stratification dependent diffusivity parameterisation can modify the initial strength of the AMOC, consequences for apparent bistability are minimal. The existence of hysteresis behaviour and apparent bistability is confirmed in a fully dynamic coupled model environment. However, experimental examination of the effect of rate of change of freshwater forcing on the apparent bistability using a simpler model configuration, indicates the magnitude of apparent bistability is strongly dependent on the rate of change of forcing. Decomposition of a quasi-equilibrium freshwater hosing experiment presents a complex picture of dynamic and kinematic changes which act to produce the overall hysteresis response. An initial analysis of these results indicates the importance of the role of convection for maintaining a deep zonal pressure gradient which is partly responsible for sustaining the AMOC.

A quiet revolution is taking place in ocean observations: in the last decade new multiplatform ocean observatories have been progressively implemented in forward looking countries with ocean borders of economic and strategic importance. These developments are designed to fill significant gaps in our knowledge of ocean state and ocean variability through long-term science and society led monitoring. These new ocean observatories are now delivering results, not only the headline results of single issue experiments, but careful and systematic improvements in our knowledge of ocean variability, and thereby, increasing ocean forecast skill, the ability to link physical process to ecosystem response and to detect the impact of future climatic change. This PhD has used data from a recently initiated glider monitoring program to characterise variability in key components of the Mediterranean circulation that act through the Ibiza Channel. The Ibiza Channel is a key ‘choke’ point in the Mediterranean basin scale circulation and governs an important north/south exchange of different water mass that is known to impact regional ecosystems, in a zone of high biodiversity. The quasi-continuous glider sampling at this critical location has enabled important sub-seasonal to seasonal variability to be captured, and models to be developed to characterise the previously described ‘complex’ pattern of exchange. For the first time, glider monitoring revealed high frequency variability in the transport of water mass, of the same magnitude as the previously characterised seasonal cycle, but occurring over timescales of days to weeks. Although previous ship surveys had noted high cruise-to-cruise variability, they were insufficient to show that in fact water volumes exchanged through the Ibiza Channel vary on ‘weather’ timescales. Using the glider data in combination with an 18-year record of ship missions, long-term seasonal cycles in the north/south exchange were characterised. New month-by-month patterns were defined for the southward transport, while generally held views regarding the seasonality of the northward transport were revised. The pattern of the exchange was further characterised by 4 proposed seasonal ‘modes’, which reflect an annual interplay between vigorous mesoscale and basin scale dynamics. Restricted ‘choke’ points between our ocean basins are critical locations to monitor water transport variability, as they constrain the inter-basin exchange of heat, salt and nutrients. The Ibiza Channel is one such location. In addition to characterising key components of the regional circulation, this PhD also provides insight into use of glider monitoring at such critical locations, which can be used to inform multi-platform ocean observation strategy. This study is part of the quiet revolution.

In the northern Adriatic and north western Black Sea, relatively high concentrations of nutrients inducing eutrophication, have been observed. The biodegradation of organic matter, which occurred below the thermocline or at the sediment-water interface, influence the reduction-oxidation potential in the water column. Fluctuation of the reduction-oxidation potential in the water column influence the distribution of metals which are redox sensitive elements (Mn, Fe and Co). Dissolved Mn and Fe concentrations were high in some cases mainly due to the reduction of Mn- and Fe- oxides which occurred in microenvironments in the dominantly oxic medium at the thermocline or in low O2 zones near the bottom. The distributions were also influenced by riverine inputs. Dissolved Mn, Fe and Co concentrations were generally higher in the north-western Black Sea than in the Adriatic Sea suggesting that diagenetic reactions involving the destruction of organic carbon are more intense in the north-western Black Sea than in the Adriatic Sea. Total particulate concentrations of Mn and Fe were high, due to reprecipitation of Mn2+ and Fe2+ in presence of oxygen, riverine inputs and advective transport. Trace metal distributions (Co, Pb, Cd, Zn, Cu, Ni) were influenced by the Mn and Fe cycling and by riverine inputs. Relatively high dissolved and leachable or total particulate concentrations were generally found in surface waters at stations directly influenced by the River Po and the River Danube. High dissolved metal concentrations were found at the thermocline or near the sediment-water interface where dissolution of Mn- and Fe- oxides, on which metals were adsorbed, occurs under suboxic or anoxic conditions. Dissolved concentrations of Pb, Cd, Cu, Ni and Zn are generally similar in the northern Adriatic Sea and in the north-western Black Sea. Particulate Fe, Pb, Ni, Cd and Zn concentrations were higher in the northern Adriatic Sea than in the north-western Black Sea reflecting the strong influence of riverine inputs on the shallow northern part of the Adriatic where the depth hardly ever exceeds 40 m.

This work presents a study of the mesoscale surface processes occurring in the Southwestern Atlantic Ocean. Two regions in this ocean, the Brazil-Malvinas (Falkland) Confluence (BMC) Zone and the South Brazilian Continental Shelf (SBCS) are studied by means of a 14 year long series of low-resolution Multi-Channel Sea Surface Temperature (MCSST) images of the Advanced Very High Resolution Radiometer (AVHRR) together with high-resolution data from the same sensor and Lagrangian (buoy) data for the period between March 1993 and July 1994. The AVHRR and buoy data were available from the project COROAS (Oceanic Circulation in the Western Region of the South Atlantic), the Brazilian contribution to the World Ocean Circulation Experiment (WOCE). The variability of the sea surface temperature (SST) fields in the South Atlantic is investigated for the period between January 1982 and December 1995 utilising Principal Component analysis techniques on the MCSST data set. The distribution and oscillation of the SST fields of the South Atlantic are compared to those present in the BMC and SBCS regions, as described by the high-resolution AVHRR and buoy data. The oceanographic surface frontal systems observed in the AVHRR images and buoy trajectories are also studied for the BMC and SBCS regions during 1993 and 1994. Direct measurements of currents taken by the buoys are utilised to describe the characteristics of the Brazil Current (BC), the South Atlantic Current (SAC) and the Brazilian Coastal Current (BCC). These currents are described by their mean surface velocities, kinetic energies, temperature statistics and oscillations. The BCC is a newly described current, very poorly understood in the past and very important for fisheries and, possibly, for the weather of the southern region of Brazil. The surface component of the BCC is described in this thesis as a coastal, northeasterly current flowing in opposition to the BC main flow and with a seasonal behaviour off the South American coast. The eddy field present in the BMC and SBCS regions during 1993 and 1994 is investigated in this work as well. Distinct behaviour and driving mechanisms are reported for the eddies present in these two areas of the Southwestern Atlantic. For the first time in the known literature, small scale and shelfbreak eddies are described for the SBCS region. The nature of these small scale eddies is discussed in relation to that of the mesoscale, geostrophically balanced BMC eddies already known to occur in the study area. The importance of the shear instabilities in the oceanographic front between the BC and the BCC for the eddy generation and mixture processes is emphasised here. Comparing AVHRR and buoy data, empirical relationships are obtained for linking eddy sizes to their rotational periods and tangential velocities. The relationships are useful for monitoring the effects of the eddies in the ocean by remote sensing techniques when in situ data are lacking. The question of whether the high-resolution satellite images utilised in this work are truly representing the SST of the ocean is also addressed here. Moreover, with the support of extra satellite data from the Along-Track Scanning Radiometer (ATSR) and in situ data from ships of opportunity, we investigate the nature of the temperature differences (deltaT) between 'skin' and 'bulk' SSTs in the study area. 'Match-ups' between satellite and in situ SSTs demonstrated the presence of a bias in the satellite estimates of SST. DeltaT images also indicated that, owing to the highly dynamic nature of the BMC and BC/BCC fronts, large errors can arise when matching-up buoy with satellite data in these areas.

The Atlantic Meridional Overturning Circulation (AMOC) and its variability has received considerable attention, motivated by its major role in the global climate system. Observations of AMOC strength at 26�N made by Rapid-WATCH (Rapid climate change - Will the Atlantic Thermohaline Circulation Halt) provide our best current estimate of the state of the AMOC. This study aims to improve understanding of ongoing measurements of AMOC variability made by Rapid-WATCH, and provide context for the 5-year timeseries presently available. The Rapid-WATCH system combines Gulf Stream transport, zonally integrated Ekman transport and mid-ocean transport observations at 26�N to assess AMOC strength. The Gulf Stream is found to possess a smooth annual cycle set by regional meridional wind stress, which is obscured on a year to year basis by internal ocean variability. Ekman transport possesses no dominant annual or semi-annual periodicity, and the seasonal cycle is obscured on a year to year basis by internal atmospheric variability largely related to fluctuations of the Azores high and the North Atlantic Oscillation. Sverdrup transport shows a dominant semi-annual periodicity which is strongly persistent from year to year but not seen in Rapid-WATCH measurements due to barotropic adjustment at these timescales. At interannual timescales, Sverdrup transport variability estimated from wind stress climatologies is found to exceed that of Gulf Stream variability, suggesting AMOC fluctuations of several Sverdrups have occurred over the past 30 years, partly related to the North Atlantic Oscillation. At decadal timescales, six hydrographic sections spread over half a century show that high latitude deep water mass changes have consistently spread to 24�N, with the DWBC their principal conduit into the 24�N section. Decadal changes in deep water transport of several Sverdrups are balanced by dynamic height changes close to the western boundary whilst water mass changes are largely density compensated.

This analysis indicates that the Southern Ocean provides a trong sink, yet low storage, for atmospheric CO2. The South Atlantic Ocean, in particular, facilitates major interbasin exchange through the interaction of the Antarctic Circumpolar Current (ACC), Atlantic Meridional Overturning Circulation (AMOC), Agulhas Current and Weddell Gyre systems. Hydrographic occupations from Drake Passage (WOCE section SR1) in 1990 and 2009, along 30�E from the African continent to Antarctica (WOCE section I6S) in 1996 and 2008 and across 24�S in the Atlantic in 2009 create a ‘box’ and enable comparison between repeat occupations on each box boundary. Calibration factors from GLODAP and CARINA cross-calibration projects were applied for salinity, oxygen and nutrients to 1990 and 1996 occupations.

Observations of interannual variability in 18 Water (Talley and Raymer 1982) and Gulf Stream transport (Worthington 1977) motivate an ocean model sensitivity study. The North Atlantic circulation is simulated with a three-dimensional isopycniccoordinate GCM. Idealized anomalous buoyancy-forcing fields (associated with outbreaks of cold, dry continental air over the Gulf Stream/Sargasso Sea region) are constructed. In a series of sensitivity experiments, wintertime buoyancy loss over the Gulf Stream and Sargasso Sea is thus increased to varying degrees, with anomalous ocean-to-atmosphere buoyancy fluxes of up to double climatological values. Under excess buoyancy loss, winter mixed layer depths increase, and a greater volume of model 18 Water is formed. End-of-winter mixed layer density also increases, leading to the formation of a denser variety of 18 Water. The anomalous 18 Water recirculates around the Sargasso Sea as a signal of low potential vorticity, which spreads out and weakens on a decadal timescale. Strengthened horizontal pressure gradients in the vicinity of the anomalous 18 Water drive intensified baroclinic transports at the "immediate" end of winter (in March), after which a full-depth barotropic intensification of the Gulf Stream develops. Strongest intensification occurs in May, when the Gulf Stream barotropic transport is increased locally by up to 10 Sv. The anomalous transports which account for barotropic intensification are confined to deep and abyssal layers of the model. Where the associated anomalous bottom currents traverse isobaths, "extra" bottom pressure torque (BPT) is invoked. An anomalous BPT term in the barotropic vorticity balance may therefore account for the intensification. Computed from the model fields of density and sea surface height, such a term does appear to produce the extra negative vorticity associated with anticyclogenic intensification. It is concluded that wintertime excess buoyancy loss drives a springtime barotropic response of the subtropical gyre, through BPT, due to "JEBAR" (the Joint Effect of Baroclinicity And Relief). The Gulf Stream intensification decreases after May as lateral eddy mixing weakens anomalous cross-stream pressure gradients. This eddy mixing is parameterized in the model by a layer thickness diffusion velocity, ud, nominally chosen to be 1.0 cm s'1. Further experiments establish the sensitivity of intensification strength to the choice of ud. With ud = 0.1 cm s"1 (weak thickness diffusion), the intensification is increased by ~50%, while, for ud - 10 cm s"1 (strong thickness diffusion), the intensification is roughly halved. These further sensitivity experiments also reveal the varying degrees to which the model subtropical gyre can be dominated by diffusive eddy mixing (Rhines and Young 1982a, 1982b) or adiabatic (nondiffusive) ventilation of the thermocline (Luyten, Pedlosky and Stommel 1983). Recent (1980-97) interannual variability in the formation and recirculation of 18 Water, and other water masses, is deduced from observed surface heat and freshwater fluxes. Interannual variations in the strength of 18 Water renewal (thus deduced) and a wintertime index of the North Atlantic Oscillation (NAO) are found to be strongly anticorrelated (with a correlation coefficient of -0.70, statistically significant at a 99% confidence level). A further sensitivity experiment establishes that anomalous wind forcing, characteristic of a minimum phase in the NAO, does not intensify the Gulf Stream in the manner of excess cooling. It is concluded that 18 Water is more strongly renewed, with accompanying Gulf Stream intensification, under NAO-minimum buoyancy forcing.

Studies of the effects of trace metal perturbation on microbial communities have, to date, concentrated on contaminated environments, single phylotypes or single metals. The effects of trace metals on bacterial communities in estuarine and marine environments have been largely overlooked. The aim of this research was to advance the scientific knowledge in this area by the implementation of incubation experiments. Experiments were designed to determine the effects of trace metal enrichment and aggregate formation on the structure and function of bacterial communities. Environmental samples included bacterioplankton from a pristine estuary (Erme, Devon), a moderately contaminated estuary (Tamar, Devon), a contaminated estuary (Fal, Cornwall), a coastal station (M1) and a truly marine station off the continental shelf (M2). Key factors influencing the response of bacterial communities to trace metal enrichment were identified. In marine communities the most influential factors were; environmental parameters, such as type and concentration of organic matter; initial community composition and ambient concentration of zinc. The addition of trace metals resulted in a decrease in diversity in the bacterial community from the Tamar Estuary, however, bacterial association with aggregates appeared to reduce this effect. Community dynamics of bacteria from a pristine estuary (Erme) demonstrated remarkable bacterial resilience under trace metal stress, particularly in samples dominated by bacteria from the Rhodobacteraceae. Some metals were shown to have a more profound effect on community dynamics than others, resulting in the division of trace metals into Type 1 and Type 2 categories as a function of bacterial response. RNA derived community fingerprints were more different between incubation conditions than DNA derived fingerprints, and were thus a more sensitive indication of response to trace metal enrichment. The wider implications of the effects of trace metals on bacterial communities in estuarine and marine environments are discussed, along with possible future research directions. Recommendations are made for future investigations of the effects of metal contamination in light of the results presented here.