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The deep sea is a dynamic environment over various spatio-temporal scales. But, the characteristics of deep-sea natural variations and underlying processes remain poorly understood, which prevents contextualising any anthropogenic impact on this environment. Long-term observations, from which inter-annual variations can be detected, as well as detailed broad-scale spatial observations, are scarce in the deep sea. In this thesis, I examined changes in both spatial (~ 0.1-10s km scale) and temporal (inter-annual scale) domains in abyssal benthic fauna at two abyssal stations in the North East Pacific (Station M, 1991 to 2011) and in the North East Atlantic (Porcupine Abyssal Plain, PAP, 1991 to 2012) using Polychaeta as study organisms. Four main results were found. 1) At intermediate scales (0.1 to 10s km), the macrofauna and polychaete family composition were related to the sediment grain size distribution (Chapter 2). Differences in sediment grain size distribution between and among abyssal hills created habitat heterogeneity. Differences in near-bed current flows, and thus in particle size and food settling conditions, may be the primary factors influencing the sediment particle size distribution and macrofauna. Overall polychaetes and macrofauna may be more spatially variable than previously thought in abyssal areas when considering that abyssal hills might be one of the most common topographic features on Earth. 2) At inter-annual scale, polychaete families and functional groups varied in density, diversity and community structure at Sta. M and PAP (chapter 3). Sub-surface deposit feeders, such as Paraonidae, dominated the North East Pacific, whereas surface deposit feeders, such as Cirratulidae, dominated the North East Atlantic. Differences may be related to the quantity and quality of the particulate organic carbon reaching the seafloor. Overall, changes in the dominance of functional groups imply changes in abyssal ecosystem functioning. 3) At inter-annual scale, the dynamics of polychaete abundances and body sizes suggested that migration/enhanced survivorship and recruitment events occurred (chapter 4). The densities and median body sizes of the five density-dominant species at Sta. M were analysed over time to help elucidate population dynamics as population parameters such as reproduction or growth rate could not be directly measured. The results indicated that the density dynamics of Paradoneis cf. lyra may have be related to enhanced survivorship or immigration of adult individuals, while the density dynamics of Cossura cf. rostrata may have be linked to individuals shifting between growth and reproduction. 4) At inter-annual scale, Sta. M polychaete changes were detected in standing stocks, rank distributions, species and functional group composition (chapter 5). Although a change in sampling location occurred after 2005, preventing ascribing the assemblage change unequivocally to particular environmental drivers, analyses prior to 2005 showed that the polychaete assemblage composition dynamics were primary driven by food supply variation. Overall, energetic zero-sum dynamics were not clearly observed at polychaete assemblage level, but were evident in the greater macrofauna community that includes the polychaetes. Polychaete displayed stability in body size structure in space and time, following the predictions of the metabolic theory of ecology. In conclusion, this work highlighted that abyssal polychaete communities can change over spatial scales of tens of square kilometres and time scales of months or more; this work found a large but as yet underappreciated variability.

Hydrothermal circulation plays a fundamental role in the chemical transfer from deep in the Earth’s interior to the ocean crust, the oceans and the atmosphere. It is also on of the principal mechanisms for heat transfer from the mantle to the oceans, atmosphere and ultimately, outer space. This process fundamentally influences the composition of the ocean crust during formation and aging as it spreads away from the ridge axis. However, despite much research into hydrothermal alteration of oceanic crust questions still remain including: the thermal and chemical evolution of hydrothermal fluids, the geometry of hydrothermal fluid flow, and the factors that control the nature and extent of hydrothermal alteration of oceanic crust. In this study, whole rock and secondary mineral characteristics of drilled-in situ ocean crust are used to (i) Characterise hydrothermal alteration for a range of drilled, in-situ fast spread ocean crust sites (ii) assess the factors that control hydrothermal alteration within fast spread ocean crust and (iii) assess the evolution and architecture of hydrothermal fluid. Deep Sea Drilling Project, Ocean Drilling Program, and Integrated Ocean Drilling Program Sites 504, 896, 843, 1179, 1149, 1224, 1243 and 1256 represent some the most significant penetrations into the upper portion of intermediate and fast spread crust to date. Analyses of whole rock chemical changes, Sr, O. C and S isotope systematics, petrographic observations and analysis of secondary minerals indicate that all sites underwent variable degrees of cold seawater dominated hydrothermal alteration. All these sites represent variations in the composition of the upper crust, basement topography, sedimentation rates, spreading rates, capping rocks, and age. Comparisons between these factors and style and intensity of alteration for each site indicate that spreading rate and age exherts the strongest influence on hydrothermal activity. Sites 1256 and 504 are the only sites in which both low temperature and high temperature alteration are recovered, both sites now have complete chemical and isotopic records which trace the evolution of hydrothermal fluid through the crust. Chemical and isotopic analyses of anhydrite within the ocean crust and consideration of the sulfur budget at these sites imply that the majority of hydrothermal fluid is heated to moderate temperatures (~250oC) and returns to the oceans as warm diffuse fluids at unaccounted for venting sites.

Coastal lagoons are habitats of conservation importance. The characteristic fauna of lagoons includes a number of specialist species, some of which are scheduled for protection. Work on the conservation of coastal lagoons has suggested that detailed information on the ecology of lagoon specialist species is essential to ensure management strategies are relevant to the lagoonal species. This study addresses this issue by providing information about the monthly reproductive investment and energy-balance as well as interactions with parasites for the specialist lagoon amphipod, Gammarus insensibilis (Stock). For comparison information is also presented on the reproductive investment of the lagoonal isopod Idotea chelipes (Pallas). Gilkicker lagoon on the south coast of England, UK, from which the majority of samples were taken, demonstrated environmental variability characteristic of coastal lagoons. Annually, temperature varied between 2 and 28 °C and salinity fluctuated between extremes of 24 and 39. The Lymington-Keyhaven lagoons, also on the south coast of England, demonstrated similar variation. This has implications for Gammarus insensibilis, and effects on reproductive investment were evident. The amphipod was shown to employ a continuous reproductive strategy but while the overall investment, expressed as clutch volume, remained relatively stable over the course of the year, the individual components varied. In the summer, when weight-specific embryo number was at its highest with a mean of 13 embryos mg dry wt.-1 the mean size of the individual embryos was small (0.032 mm3). The opposite was true in the winter months, with mean brood sizes as low as 6 embryos mg dry wt.-1 while mean embryo volume was larger, at 0.04 mm3. Idotea chelipes demonstrated a more seasonal reproductive strategy in which winter reproductive output was low. The environmental variability also had effects on the metabolic rates of individual amphipods with temperature related increases in feeding and respiration rates in the summer months. Scope For Growth (SFG), a measure of net energy availability to the organism, was variable during the year and was unrelated to temperature and salinity. Lowest SFG occurred in spring in conjunction with peak reproductive output. This suggested that the amphipods were well adapted to the environmental variation of the lagoon and that it was reproductive investment that represented an important cost to the organism. Eighty four percent of G. insensibilis from Gilkicker were shown to be infected by microphallid trematode parasites. Reproductive investment was negatively affected, with a 36.6 % reduction in weight-specific brood size associated with higher degrees of infection. Respiration rates were also reduced in the infected organisms. The high prevalence of the parasites and the related effects on the host suggest that trematode infection should be considered, alongside the characteristic habitat variability, as an important aspect of the ecology of lagoons.

The eastern equatorial and tropical Pacific regions are areas of significant carbon fluxes from the atmosphere to the ocean interior. Changes in the function of marine biogeochemical cycles in this region potentially exert an important control on global climate. Understanding controls on and changes to ocean chemistry and circulation in this region is therefore of great importance. Redox sensitive metal distributions in hydrothermal sediments have yet to be exploited effectively as proxies of past ocean conditions. This work presents a 740 ka sediment record from an archived core collected at 14o47’S overlying 1.1 Ma crust on the western flank of the EPR. The metalliferous sedimentation is overprinted by diagenetic mobilisation arising from variations in the sediment redox status of the sediments. Amorphous ferrihydrite phases delivered to the sediment have undergone significant alteration to more stable crystalline forms. Under glacial conditions, the transformation of ferrihydrite appears to be impeded, which is inferred to be a function of a distinct change in the redox status of the sediments under glacial conditions. Oxyanions coprecipitated with Fe and Mn (hydr)oxides from the hydrothermal plume (P, V, U) are partitioned during Fe-oxide alteration. V is preferentially incorporated into goethite and residual phases, locking the plume derived V within the sediment. Sediment P/Fe ratios are lower than overlying plume values, and vary systematically with variations in ferrihydrite transformation to goethite on glacial-interglacial timescales. This transformation is inferred to lead to P loss from the particulate/sediment phase. Uranium is highly enriched in sulphide rich EPR plume particles and the sediments at 14oS. U/Fe ratios indicate there has been enhanced release of U under interglacial conditions, and preservation of plume U/Fe ratios under glacial conditions. Mo/Mn ratios are used to confirm the changes in redox status on glacial-interglacial timescales at this site. There is a general trend over Marine Isotope Stages 1-14 of a deepening of the sediment redox front through interglacial stages with a shallowing at the onset of glaciation. Enhanced sub-oxic conditions associated with glacial conditions (in particular MIS 12) are attributed to enhanced productivity (and carbon export to the seafloor) and decreased bottom water O2 (and therefore reduced ventilation of the deep water). This is consistent with paleoproductivity data from other parts of the Eastern Pacific and adds new information of past conditions in a region which has not been studied.

This study examines the geochemistry of salt marshes and intertidal sediments from the Solent estuarine system, southern England. Micro-, meso- and macro-scale studies have been carried out to assess the geochemical processes operating in these intertidal sediments and the use of radionuclides as tracers of sedimentary processes in the Solent area. Measurement of 210Pbxs, 137Cs and 60Co provides valuable information on sedimentary processes occurring in the Solent estuarine system. Subsurface maxima in activity are observed for 137Cs and 60Co (after normalisation to Al) which can be related to historical input, providing dated sediment horizons. This has enabled determination of Recent sediment accumulation rates and reconstruction of historical pollution records. Sediment accumulation rates obtained using 210PbXS/ l37Cs and 60Co in salt marsh environments provide an indication of the rate of Recent sea level rise, estimated as 4 mm y-1. This is in broad agreement with tide gauge data and when compared with longer term archaeological and radiochronological data may indicate an increase in the rate of mean sea level rise over the last 1000 years. Salt marsh areas with accumulation rates lower than 4 mm y 1 (from 137Cs and 60Co dating) are degenerating (undergoing die-back) indicating that they are failing to keep pace with the rising sea level. While local (intra-estuary) effects influence rates of sediment accumulation on a particular salt marsh the main control of sediment accretion over the whole Solent area is a rise in mean sea level. Dating of salt marsh sediment cores has allowed assessment of the historical record of anthropogenic pollutant input to the Solent (in particular for Pb and Cu). Pb isotope studies of salt marsh sediments from Southampton Water indicate increasing importance of anthropogenic Pb (from Precambrian ores) since the beginning of this century. A very prominent transient spike due to an anthropogenic Pb input is found in salt marsh sediments from the relatively unpolluted Beaulieu estuary. This may be related to military marshalling in the Beaulieu river before the Allied D-Day landings in 1944. Anthropogenic Cu is present in the Solent region mainly due to discharge from the Esso refinery at Fawley, Southampton Water. Analysis of Cu fluxes has shown that discharges peaked in ca.1970 and have significantly reduced since 1971 (due to effluent clean-up by the refinery). The reliable use of radionuclides as indicators of sediment accumulation depends on their chemical immobility (lack of redox migration). 60Co shows evidence for early diagenetic remobilisation at two salt marsh sites, and 2iopb m a v a i s o be mobile in some salt marsh areas. Remobilisation of 210Pb is apparently localised and may be aided by flooding/drainage cycles in the marsh. The use of these radionuclides as tracers of sediment accumulation in areas where significant early diagenetic remobilisation occurs is problematic. Where possible a number of chemically different radionuclides should be used to eliminate bias in calculated sediment accumulation rates due to redox mobilisation or diffusive processes. Detailed geochemical studies can assist in determining whether redox movement of radionuclides is occurring. A critical examination of the geochemical behaviour of both the stable counterparts of radionuclides and redox-sensitive elements is required if realistic sediment accumulation rates are to be obtained.

The effects of variability in the physical environment on the development of the spring phytoplankton bloom are investigated using a physically forced model of the annual plankton cycle in the ocean mixed layer. The model is optimised to fit survey data from the eastern North Atlantic, collected over a 1500 x 1500 km area between 39N and 54N, from April-June 1991, establishing the feasibility of using spatially distributed point-in-time data in model calibration. Measurements made below the seasonal pycnocline show the existence of an empirical relationship between preformed nitrate and salinity in this area, allowing salinity-based estimates of pre-bloom mixed layer nitrate concentration to be made. These estimates provide important additional constraints for the model. The observed spatio-temporal patterns, at scales between 36 km and 1500 km, in nutrients, chlorophyll and measures of bloom progression derived from these data with reference to pre-bloom nitrate are discussed, together with the corresponding patterns in seasonal stratification. During the spring bloom, when biogeochemical concentrations vary rapidly in response to the developing stratification, absence of data defining its history limits the value of comparison between point-in-time observations and model results. Predictions of variation in stratification at the seasonal time-scale from general circulation models (GCMs) can be used in place of observational data to force ecosystem models. However, the degree to which observations are used to constrain the model solutions should allow for both model error in stratification and misrepresentation of the seasonal development of stratification by the observations. The latter occurs due to sampling error associated with short-term fluctuations. It can be corrected for if a suitable contemporary sea surface temperature data set is available to define the variation of mixed layer temperature at the seasonal time-scale. It is shown that the accuracy of the GCM predictions can be improved by the application of meteorology specific to the year of observation. It is also shown that the sensitivity of the ecosystem model predictions to error in the physical forcing can be reduced by matching model and observations by a stratification measure, rather than by time, when comparing fields. The survey data show an important contribution to the stratification arising from the 'tilting' action of vertical shear on pre-existing horizontal buoyancy gradients in the winter¬ time mixed layer. This effect was severely underestimated by the GCM. The discrepancy can be accounted for by the absence of density fronts and mesoscale dynamics in the model. Ecosystem model results suggest that spatial variance in Zooplankton grazing, due to the effect of differences in the depth and duration of winter-time mixing on the over-wintering success of plankton populations, is one of the major factors controlling the spatial and temporal characteristics of the phytoplankton bloom.

The aim of this thesis was to improve our understanding of the natural iron fertilisation processes that can alleviate the High Nutrient Low Chlorophyll conditions normally associated with the Southern Ocean. The annual phytoplankton bloom occurring north of the Crozet Plateau (46°26’S - 52°18’E) provided a good opportunity to study these phenomena during CROZEX, a multidisciplinary study performed in austral summers 2004/2005 and 2005/2006. Particular emphasis has been placed on the sources of Fe to the upper water column, and on the different processes that drive the distribution of iron, such as mixing with deeper waters, advection of Fe rich waters from the islands, or particles and atmospheric inputs. A flow-injection analyser with DPD catalytic spectrophotometric detection (FIA-DPD) was first set up for the determination of total dissolved Fe (DFe, ≤ 0.2 µm) and careful assessment of data demonstrated the high quality of the information obtained in this study. Analytical measurements of DFe were performed in twenty vertical profiles from the North to the South of the islands that show evidence of a range of processes influencing the iron distributions. Most significantly, an enrichment of DFe (>1 nM) has been identified at close proximity to the islands, which suggests that the plateau and the associated sediments are a source of iron. Waters further north also appear to be affected by this input of both coastal and shelf origin, although dissolved iron concentrations decrease as a function of distance to the north of the plateau with a gradient of 0.07 nM.km-1 as a result of dispersion and mixing. This gradient was then combined with short-lived Radium isotopes profiles, allowing the determination of a horizontal advective flux of Fe. Estimates of atmosphere and vertical fluxes of Fe to surface waters were also calculated. It was then possible to estimate a pre-bloom concentration of ~ 0.44 nM, which is sufficient to drive the inferred level of the new production in the bloom area. Labile iron has been distinguished from the refractory fraction of iron in the suspended particulate matter exported from the mixed layer by developing a two-stage leaching technique. The resulting solutions were analyzed using ICP-MS. By using associated 234Th fluxes, vertical fluxes of particulate iron in both phases were determined as well as their residence times. Data clearly show that carbon export was linked to the iron residence time and enhanced in the northern region where iron inputs occur. This thesis therefore provides a comprehensive data set of DFe and particulate iron in waters surrounding the Crozet Islands. It also presents the first attempt to establish an iron budget that can be developed into a model and provides a good reference point for subsequent studies of natural iron fertilization processes that occur around these islands.

It has long been recognised that some oceanic regions have persistently low chlorophyll levels, even though inorganic nutrients are plentiful. Studies have shown that these high-nutrient, low-chlorophyll (HNLC) areas are depleted in iron, which is an essential micronutrient for phytoplankton growth. In HNLC regions biological production can be enhanced with artificial mesoscale iron fertilisation. However, the ability of artificially induced phytoplankton blooms to efficiently sequester carbon to mesopelagic depths is still an open question. SubAntarctic islands in the HNLC Southern Ocean are a natural source of iron and thus fuel the annual phytoplankton blooms observed in their proximity. One such bloom, tied to the Crozet Islands (52ºE, 46ºS), provided the opportunity to examine particulate organic carbon (POC) export during the austral summer of 2004/5. This work was imbedded into the multi-disciplinary CROZEX project thus providing a rich context for data interpretation. Based on satellite imagery, a high chlorophyll region (max = 4 µg l-1) north and downstream of the Crozet Islands was distinguished from a low chlorophyll region (typically 0.3 µg l-1) south and upstream of the islands. POC export estimates, obtained with the naturally occurring particle reactive radionuclide tracer, 234Th, were initially D15 mmol C m-2 d-1 in the high chlorophyll region, compared with D5 mmol C m-2 d-1 in the low chlorophyll region. After a moderately small increase in chlorophyll in the south (max = 0.7 µg l-1) the spatial variability in POC export was lost, resulting in equally high levels of POC export (ca. 20 mmol C m-2 d-1) throughout the study area. After comparing the daily rates of POC export with temporally integrated new production calculated from nitrate budgets, a different spatial pattern emerged. New production (NP) presented consistently higher values in the north, when compared to the south. Two hypotheses were formulated to explain this, 1) dissolved organic matter (DOM) and suspended particulate organic matter (sPOM) produced from NP was stored in the mixed layer with this effect relatively greater in the north, 2) the export event in the north was longer resulting in greater seasonal POC export. Investigation of the DOM pool revealed that DOM accounted for 46±7% of NP and was consistent across the whole study area. In contrast, sPOM accumulated at differential rates of 18±7% in the north and 0±7% in the south. This suggested that differential storage of sPOM was responsible for the lack of a latitudinal gradient in POC export after the relatively small increase in chlorophyll in the south. After investigating the second hypothesis, the daily rates of POC export were scaled to seasonal integrals using a silicon budget, which allowed the formulation of a seasonal carbon budget. This revealed that over the timescale of the study the magnitude of NP and POC export were not the same with this difference greatest within the northern high chlorophyll region. This was the result of relatively greater storage of sPOM in the north and had the effect of reducing the amount of easily exportable POC to mesopelagic depths. Thus both hypotheses contributed to better understanding carbon export in the Crozet region.

Submarine canyons are considered potential hotspots of biodiversity and abundance, which makes them an important focus for scientific investigation and for policy-makers who seek to manage their resources. This study investigates the structure and dynamics of megafaunal communities in relation to inherent environmental parameters within submarine canyons; understanding the distribution and resilience of hotspot ecosystems is important in creating ecologically-sustainable resource-management plans. Data were collected from Nazaré, Setúbal, Lisbon and Cascais Canyons (Portuguese margin) and a channel and adjacent slope on the Pakistan margin, using passively-towed camera platforms and a remotely operated vehicle. Photographic data were analysed from a range of canyon habitats; abundance and distribution of megafauna were recorded and diversity indices calculated. Environmental variables were used to interpret patterns of species distribution, abundance and diversity. Community analyses were used to assess changes in community structure within and among canyons, and the adjacent slope. Portuguese margin: The canyons were ranked in order of decreasing activity: Nazaré, Lisbon, Setúbal and Cascais Canyons. Expected species richness conformed to Connell’s intermediate disturbance hypothesis, reflecting the activity of the canyons. Megabenthic abundance did not exceed that reported in studies of nearby slope communities, suggesting that the canyons are not hotspots of megabenthic abundance. Suspension-feeders dominated all canyons though were most abundant in Nazaré Canyon, which was linked to observed higher activity. All canyons showed a higher proportion of suspension-feeders than are reported in studies from nearby slope environments. There was high variability in habitat type within and between the canyons, which was reflected in the megabenthic assemblages. Pakistan margin: Observations of turbidity and current velocity indicated that the Pakistan margin channel is relatively inactive. Megafaunal abundance was significantly lower, and diversity higher, within the channel than on the adjacent slope. Suspension-feeders dominated all sites, though were significantly more numerous on the slope. The sites were located below the base of the OMZ core, and communities displayed OMZ edge-effects with a peak in abundance at ~ 1000 m WD, high dominance and a high rate of species turnover. Community analysis suggested that the communities were more heavily influenced by the proximity to the OMZ than by the channel, which indicated that either the influence of the OMZ masks any potential channel-induced patterns, or that the channel is too small to influence megafaunal communities.