Marine aggregates play an important role in the cycling of carbon, nutrients and trace metals. Within aggregates the oxygen depleted by aerobic microbial respiration may not be replaced rapidly, generating anoxic or suboxic microzones. Reduced compounds that are unstable in the oxygenated water column have been previously found associated with marine snow. Therefore, in the experiments described in this thesis, artificial aggregates were made in the laboratory from senescent phytoplankton material and incubated to investigate the role of the associated microbial populations to the biogeochemical redox cycling of iron and manganese and to the degradation of organic matter. The release of dissolved iron from artificial aggregates which did not contain any measurable (~10 μm) anoxic microzones, was demonstrated under dark conditions. The rate of release was controlled by the amount of reducible Fe(III) available, and appears to be limited by the competing oxidation of Fe(II). Moreover highly significant releases in reduced Mn were detected from aggregates incubated under a constant velocity shear, although the same aggregates did not affect the dissolution of iron. A possible reason is likely associated with the higher stability of Mn(II), compared to Fe(II) in aerobic environments. Molecular (16S rRNA gene) analyses showed the bacterial community associated with artificial aggregates to be similar to that found in natural aggregates and dominated by (predominantly uncultured) �- and �-Proteobacteria, Bacteroidetes, Planctomycetes and Cyanobacteria. It was possible to culture NO3 --, Fe(III)- and Mn(IV)-reducing bacteria from the artificial aggregates, and marine particles incubated with Fe(III) under anaerobic conditions contained a range of �- and �-Proteobacteria known to respire Fe(III) and in most cases Mn(IV). Moreover several microorganisms belonging to �-Proteobacteria were isolated from marine aggregates and strains affiliated to the genera Amphritea, Marinobacterium and Marinobacter, were demonstrated to grow through the reduction of Fe(III), with Marinobacter also capable of respiring Mn(IV). Whilst the precise mechanism of reduction is not clear, it is evident that marine aggregates can be a source of Fe(II) and dissolved Mn, in coastal waters and most probably other natural water systems. Fatty acid analyses revealed the prevalence of saturated over unsaturated fatty acids indicating that aggregates were already partially degraded when incubation started. Nonetheless, the lipids in the artificial aggregates were rapidly degraded further as indicated by a depletion in short chain (<20) saturated and monounsaturated fatty acids. In contrast, the concentrations of linear and branched, saturated long chain (>20) fatty acids fluctuated, suggesting that some of these lipids could have been produced in situ by marine microorganisms rather than deriving from II higher plant debris. In addition, a bacterial branched monounsaturated fatty acid (11- methyl-octadecenoic acid), which has not previously been found in marine particles was present in artificial aggregates. Roseobacter litoralis found among the aggregateattached bacteria contains 11-methyl-octadecenoic acid, and other bacteria present in artificial aggregates have the potential to produce long-chain saturated and polyunsaturated fatty acids. Thus, the fatty acid assemblage appears to reflect both organic matter degradation, including selective preservation, but also changes in the microbial assemblage. A range of future studies are suggested to elucidate the mechanisms for Fe(III) and Mn(IV) reduction in aggregates. These include microscale analyses of dissolved species and evaluation of the presence of metal binding ligands associated with aggregates. Moreover it is important to assess the activity of the Fe(III)- and Mn(IV)- reducing bacteria present in aggregates in situ and the production of long chain fatty acids in degrading aggregates.

This study quantitatively assesses the mesoscale spatial variability in local nitrate transport and the net nitrate flux associated with an open ocean eddy dipole, using novel data from the SUV‐6 ultra‐violet (UV) nitrate sensor integrated with SeaSoar. The innovative, combined system provides high‐resolution (2‐3 km horizontal, ~ 1 m vertical) nitrate data with 0.2 μM accuracy concomitantly with temperature, salinity and dissolved oxygen. This is the first time coincident physical data and measurements of nitrate concentration have been collected at this resolution in a three‐dimensional volume encompassing a mesoscale feature, in order to infer the net nitrate flux at specific depth levels. This approach represents a powerful new tool for quantifying the mesoscale, and potentially submesoscale, contribution to vertical nutrient flux to the euphotic layer. Data were collected during a multi‐disciplinary research cruise aboard the NERC research ship RRS Discovery to the Iceland Basin in July/August 2007. Three quasi‐synoptic spatial surveys show a southeastward flowing jet with counter‐rotating eddies on either side. The anti‐cyclonic component is a mode water eddy, characterised by a homogenous core (~ 35.5 psu and 12 °C) centred at ~ 600 m. The cyclonic eddy is characterised by a surface (10 m) temperature and salinity signature of ~ 13.5 °C and 35.21 psu, respectively, and maximum observed vertical displacement of isopycnals of over 200 m. The strong vertical velocities in the region are concentrated primarily in the central jet between the eddies, as fast flowing water is forced up over raised isopycnals associated with the large potential vorticity anomaly of the mode water eddy. Additionally, upward (downward) vertical velocity is diagnosed ahead of the cyclonic (mode water) eddy in the direction of propagation. Maximum local vertical advection of nitrate at the base of the euphotic zone due to the mesoscale is indicated to be 1.15 mol N m‐2 yr‐1. This value is an order of magnitude higher than local rates of nitrate supply due to turbulent mixing and exceeds maximum local nitrate uptake rates. However, findings indicate that estimating the net mesoscale nitrate flux into the euphotic zone associated with the eddy dipole is considerably more complex. The results obtained are heavily biased by the existence of a non‐zero mean vertical velocity for the region, arising from incomplete and/or misrepresentative sampling. The implications of this for the interpretation of the current data set, and future similar data sets, are assessed in full. A comprehensive quantitative assessment of other potential sources of error associated with the analysis is also presented.

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Using satellite imagery to achieve an early and accurate identification of oil spills will contribute towards the reduction of their impact on the marine ecosystem. Satellite imagery provided by the synthetic aperture radar (SAR) sensors are widely used for this task over the multi-temporal and multi-band visible near infra-red (VNIR) sensors. This is due to the SAR imaging capabilities through clouds, dust storms, soot and at night times, which limit the capability of VNIR sensors. However, gaps in knowledge exist regarding whether satellite ocean-colour sensors are capable of identifying unreported oil spills as true positives and whether they are able to discriminate them from lookalikes with the least uncertainty, particularly in arid land regions characterised with nearly cloud-free conditions. It was therefore, the goal of this research to develop reliable and robust methodology for data processing and interpretation of oil spills observed by VNIR sensors. The Moderate Resolution Imaging Spectroradiometer (MODIS) is a VNIR-type sensor that was selected for this project for a number of reasons: it is characterised with adequate multi-spectral features (36 spectral bands 0.405-14.385 μm) spread over three spatial resolutions (250, 500 and 1000 m); and its data is freely distributed in near-realtime. MODIS bio-geophysical products processed in this study such as sea surface temperature (SST4 and SST) and chlorophyll-a (Chlor-a) have also proven their usefulness in providing complementary data. As a result of this investigation, two methods were proposed: The spectral contrast shift (SCS) and the surface algal bloom index (SABI). The SCS identifies oil spills and classifies their thickness by using MODIS extreme (maximum and minimum) top-of-atmosphere radiance (TOA) values in the 250 m/pixel resolution bands: the red (λ1=645 nm) and the NIR (λ2 =859 nm) measured over a relatively small area selected to encompass part of an unknown class and part of the surrounding pure sea water. The method has produced consistent and highly sensitive results independent of sun-glint illuminations. Oil spills have SCS values lying within the range 0.02-0.04±0.002 varying by 0.01 corresponding to different thicknesses of oil. The SCS succeeded also in classifying surface floating blooms having SCS values greater than or equal to 0.20. The SABI is a four-band relationship, which according to MODIS 500 m/pixel resolution, is made up of the difference between the TOA radiance responses in the NIR and the red bands (aggregated from the 250 m resolution group) to the sum of the TOA radiance responses in the blue (λ3=469 nm) and green (λ4=555 nm) bands. The SABI aims to discriminate biological floating species that may appear as an oil spill look-alike without the need to perform complex corrections for atmosphere and sun-glint effects. The SABI succeeded in classifying 95% of surface blooms that had values greater than or equal to a baseline value of -0.10. Oil spills, however, always appear at values lower than the surface bloom baseline value.

Antarctic ice shelves play a key role in the global climate system, acting as important sites for the cooling of shelf waters, thereby facilitating deep and bottom water formation. Many of the processes that take place under large ice shelves can be observed more conveniently beneath smaller ice shelves such as Fimbul Ice Shelf, an ice shelf in the eastern Weddell Sea. Fimbul Ice Shelf and nearby ice shelves might also play a significant regional role: although no bottom water is produced in this area, it is thought that Fimbul Ice Shelf and nearby ice shelves precondition the shelf waters that ultimately are converted to Weddell Sea Deep Water (WSDW) in the southern Weddell Sea. Using the first data ever to be collected beneath an ice shelf from an autonomous underwater vehicle (AUV), as well as data from the vicinity of the ice shelf using traditional oceanographic methods, this thesis discusses the circulation and processes occurring beneath the ice shelf. This has been supplemented by using a coupled ice shelf/ocean model, POLAIR, to simulate the circulation, melting, and tides under Fimbul Ice Shelf and in the surrounding area. Data from the ice shelf cavity show relatively large variability in temperatures, but all within approx. 0.25 °C of the freezing point. Melt rates are found to be lower than some previous model studies, but in better agreement with observations and glaciological models. The base of the ice shelf was found to be rough in places, corresponding to `flow traces' visible in satellite imagery. This could have implications for mixing beneath the ice shelf, at least in these limited areas. The Autosub AUV was found to be a useful platform for measuring hydrography and ice shelf cavity geometry with spatial coverage and resolution not available from surface measurements.

This thesis investigates the variability of the intermediate and thermocline water mass properties in the South Atlantic, with a particular focus on salinity. These water masses form the upper branch of the Meridional Overturning Circulation in the Atlantic and have an important position in global ocean climate. Variability on various timescales is investigated: decadal changes are investigated using repeat hydrographic surveys, interannual variability is investigated using Argo float data and the two timescales are united by investigating a 40 year modern ocean model run. Salinity of thermocline water masses is shown to vary slowly on decadal timescales. Basinwide changes in salinity are evident at 24◦S over periods of 25 years. That these changes are representative of decadal changes and not merely aliasing shorter term variability is supported by analysis of the model. Increases in salinity at 24◦S from 1958 to 1983 and at 30◦S from 1993 to 2003 are linked with influence from the Indian ocean while a freshening at 24◦S from 1983 to 2009 may be linked with an intensified hydrological cycle. Antarctic Intermediate Water (AAIW) is seen to increase in salinity at 24◦S from 1958 to 1983 and in the eastern basin at 30◦S from 1993 to 2003. This is different from the Indian and Pacific Oceans where AAIW has been observed to be freshening – a change linked with the intensification of the hydrological cycle. Using the highly correlated relationship between salinity and oxygen in AAIW, these changes are linked to the influence of the Indian Ocean. Further investigation of the changes in AAIW in the South Atlantic using Argo data and model data show that the variability of this water mass is dominated by westward propagating salinity anomalies. These anomalies originate in the Agulhas influenced Cape Basin of the South Atlantic and propagate westwards with speeds similar to those predicted for second mode baroclinic Rossby waves. The techniques developed for analysis of AAIW salinity using oxygen data are expanded to the other oceans of the southern hemisphere. The conclusions drawn from this analysis put the AAIW in the South Atlantic in a global context.

Two mesoscale net sampling surveys were conducted in the south-west Atlantic between 34° and 55 °S. The first survey was in the austral spring of 1990 and used both an RMT8 net which was trawled obliquely down to 200 or 300 m and caught mainly macrozooplankton and a Bongo net which was deployed at the surface and sampled mesozooplankton. The second survey was in the austral spring of 1991 and used a Bongo net which was deployed obliquely down to 50 m and sampled mesozooplankton. This thesis considers the species composition and abundance of these samples and represents one of the first insights into the mesoscale biogeography of zooplankton communities in the south-west Atlantic. 155 species from 9 taxonomic groups were considered including euphausiids, hyperiid amphipods, chaetognaths, salps, siphonophores, and nektonic/planktonic fish. Multivariate analyses were used to highlight species assemblage distribution patterns and determine strongly correlated environmental variables. In the 1990 RMT8 samples, species assemblages showed a distribution pattern related to the location of water masses, which was reflected in a combination of water mass and latitude being the most strongly correlated environmental variables. In the 1990 Bongo samples, a combination of seasurface temperature and latitude were most strongly correlated environmental variables and different species assemblages showed a pattern of being located in exclusive temperature ranges. The two sample sets did exhibit some common distribution patterns especially in the warm, sub-tropical waters to the north and the Falkland Shelf to the south. However, there were fundamental differences in the mid-latitudes regions, possibly reflecting the reduced ability of larvae to counteract expatriating forces when compared with adults. Further comparisons made between the 1990 and 1991 Bongo sample sets highlighted some of the causal factors behind distribution patterns. For instance, the precise definition of the boundary between sub-tropical and sub-Antarctic assemblages by the 17.3°C isotherm despite the multitude of expatriating phenomena suggested that many organisms were at the edge of their physiological limits in this region. In polar waters, distribution patterns were consistent but temperatures variable suggesting that advection rather than temperature tolerance was more influential. Further data from Montu (1977) and the Discovery Investigations was examined to add a seasonal dimension to the above patterns as well as providing an insight into the importance of population ecology on community distribution. Studies were concentrated on euphausiid species from which it was apparent that size structure and species dominance changed considerably with season. Estimates of the productivity of these species showed that weight-specific rates were comparable with more sub-tropical regions despite biomass levels being proportionally low. The use of satellite thermal images for predicting faunal distribution patterns was assessed with respect to future biogeographic analysis of this region. Images were a good predictor at the sub-tropical boundary but a poor predictor in other regions highlighting the fact that in situ net sampling methods still appear to be the most effective and reliable investigative tools for biogeographic analysis.

The impacts of land reclamation and managed realignment on saltmarsh and the adjacent intertidal flats at Freiston Shore (The Wash) are investigated. The hydrodynamic and sediment dynamics over the intertidal flats and a managed realignment site are discussed, with an extensive set of hydrodynamic, sediment dynamic and geomorphological data presented. The managed realignment has improved the coastal defence of the area; the site has been colonised by vegetation, accreted sediment and experienced limited wave activity. However, the channels within the breaches in the embankment were eroded, and a creek system over the adjacent intertidal flats experienced an enhancement in its development. This has allowed the natural and enhanced development of the creek system to be described and compared. These impacts were caused by the managed realignment site being at a lower elevation than the adjacent saltmarsh, causing high tidal current speeds as water flowed into the site and prolonged drainage of the site. This resulted in sheetflow over the intertidal flats, which caused an enhancement to the natural creek development. The water and sediment interaction between this creek system and the adjacent intertidal flats are discussed; the creeks were net exporters of sediment, while the intertidal flats were importers. The most rapid period of change was in the 2 months immediately after breaching the old embankment. The ‘Regime Theory’ was used to predict the equilibrium size of the channels within the breaches, and the time for this to be attained. Some 36 months after the initiation of the scheme, the adjacent intertidal flats appear to have adjusted to a new dynamic equilibrium, related to the managed realignment. The sheetflow over the intertidal flats has stopped and, consequently, the enhanced creek development has ceased and the creeks silted up. Despite the impacts of the managed realignment scheme, no obvious changes have been identified in the pattern or strength of tidal currents and sediment transport, over the intertidal flats adjacent to the managed realignment. In contrast, the previous creation of the embankment (for land reclamation purposes) led to an increase in tidal current speeds and erosion of the intertidal flats. Hydrodynamic and suspended sediment measurements show that, over the intertidal flats, the suspended sediment concentration increases exponentially with an increase in tidal current speed; similarly, linearly with wave height. The majority of wave activity over the intertidal zone is dissipated over the saltmarsh, with the mudflats causing little wave attenuation. Based upon the results of the present study, it appears that managed realignments can provide a successful future coastal defence, as long as certain guidelines for site selection are followed.

The general thesis objective is to determine, with sufficient accuracy (i.e. using the most reliable datasets and techniques) the phytoplankton space time variability in the Mediterranean Sea (MED) using satellite data (SeaWiFS), at different timescales, and their relationship with the physical environment. A validation exercise was performed over SeaWiFS data in the context of the reliability of both oceanic and atmospheric remote sensing data, and using the most comprehensive in situ bio-optical dataset over the MED basin. This exercise led to the development of an ad hoc regional ocean colour algorithm, which has then been implemented as standard algorithm within the operational satellite data processing chain at the Group for Satellite Oceanography (GOS) at the Istituto di Scienze dell’Atmosfera e del Clima of the Italian National Research Council, Rome. Moreover, within this context, the MED basin bio-optical signature has been found to be significantly different than the global ocean, ultimately justifying the adopted approach. The derived product (i.e., chlorophyll concentration, CHL) has then been used in the rest of the thesis to answer relevant questions, such as how the phytoplankton dynamics is influenced by its physical environment, from the water column stratification to the atmospheric input of nutrients, at different space and time scales: from daily to seasonal and interannual, and from hundreds of km to the basin scale. The basin scale interannual variability of phytoplankton has been found to be very sensitive to circulation patterns in both the western and eastern sub-basins. A phytoplankton biomass decrease, at basin scale, is significantly correlated with the longterm reduction of the cyclonic circulation in the eastern basin. Similarly, the transport variability associated with the Algerian Current system has been found to play an important role in affecting the cyclonic circulation of the Ionian Sea, which in turn determines a phytoplankton decrease on a multi-year time scale in the area. Seasonally, localized to the northwestern MED and in the southern Adriatic Sea, where deep water formation processes are active during autumn-winter, the phytoplankton spring bloom dynamics is found to be significantly correlated to the surface thermal field of the previous season: a time lag of six months identifies the coupling between the preconditioning phase to deep water formation and the spring bloom. A debated and still open question concerns with the role of atmospheric dust in the regulation of the biogeochemistry of oligotrophic gyres, so that one of the challenges of this study was to investigate the impact of the atmospheric nutrient deposition on the phytoplankton dynamics of the basin, i.e. to test the Dust Fertilization Hypothesis (DFH) in a Low Nutrient Low Chlorophyll (LNLC) region. This issue has important scientific and to a non lesser extent technical implications, but the DFH is shown here to play only a minor or even negligible role in the regulation of the phytoplankton dynamics in the MED.