Marine phytoplankton growth is controlled by non-linear processes, such as the photosynthetic and photoacclimative response to irradiance. Traditional Eulerian models calculate rates of primary production using the assumption that phytoplankton have identical properties, whereas Lagrangian models simulate phytoplankton as individual particles, tracking their trajectories through the light field. It might therefore be expected that photoacclimation in Lagrangian models would have an impact on seasonal cycles. In this thesis, I construct a Lagrangian ecosystem model, applying it to two questions: whether the individual responses of phytoplankton to their local irradiance affects the overall rates of primary production, and whether Lagrangian models are necessary for the study of the mechanisms surrounding the spring bloom, due to their representation of phytoplankton growth in response to mixing. The study begins by addressing some of the fundamental assumptions underpinning Lagrangian models, and provides novel solutions for some of the difficulties. The model was set up for Ocean Weather Station India (OWSI) in the North Atlantic, and the predicted seasonal cycles of primary production were shown to not differ from those predicted by an Eulerian equivalent, due to the phytoplankton being mixed too fast to have time to acclimate to local irradiances. Additionally, the results suggested a closer relationship between the timescales of growth and mixing, demonstrating that vertical profiles of phytoplankton could form within a well-mixed layer, resulting in changes to the overall rates of primary production. The model was next used to investigate the controls of the spring bloom at OWSI, by investigating the critical depth, critical turbulence and disturbance-recovery hypotheses. Although the use of Lagrangian model did highlight a possible source of inaccuracy when calculating critical depth with an Eulerian model, overall an Eulerian model could have performed the experiments with the same results, given information about the vertical profile of phytoplankton in the mixed layer. However, the study successfully reconciled the three hypotheses, showing how each describes a mechanism that can affect the critical depth.

The activity of photosynthetic cyanobacteria capable of nitrogen (N2) fixation (diazotrophs) strongly influences oceanic primary production and global biogeochemical cycles. The niche of these organisms extends mainly across low latitude oligotrophic oceans, largely deficient in nitrate, where they introduce ‘new’ nitrogen (N) to the system. In these regions the abundant marine cyanobacterium Trichodesmium spp. accounts for a significant proportion of the fixed N flux. Despite fixation of N, the availability of phosphorus (P) and iron (Fe) remain a constraint to the activity and biogeography of diazotrophs. The genome of Trichodesmium has therefore been shaped to provide intricate adaptive strategies optimising growth under both P and Fe depletion. Characterisation of these strategies can provide information that will enhance the understanding of the organism’s biogeography in the contemporary and future ocean. In this work, molecular and physiological techniques are employed to study nutrient uptake pathways, and the metabolic response of Trichodesmium erythraeum IMS101 (Trichodesmium hereafter) to nutrient limitation. The current lack of an established system for genetic manipulation of this organism inhibits direct functional characterisation of proteins. To circumvent this, the model cyanobacteria Synechocystis sp. PCC 6803 (Synechocystis hereafter) is used as a vehicle for the heterologous expression of Trichodesmium genes. Using this technique, the suggested contribution of Trichodesmium to an emerging oceanic P redox cycle is first explored. A four-gene cluster (ptxABCD), that encodes a putative ABC transporter (ptxABC) and NAD-dependent dehydrogenase (ptxD), is demonstrated to be responsible for the organism’s ability to utilise the reduced inorganic compound phosphite. The presence and expression of this gene cluster is also confirmed in diverse field metagenomic and metatranscriptomic datasets further confirming its role in Trichodesmium species. Pathways of Fe utilisation are also investigated. Through heterologous expression the function of a currently employed Fe stress biomarker, protein Tery_3377 (IdiA), which is homologous to both Fe3+ transporters (FutA2-like) and intracellular proteins with protective function under Fe stress (FutA1-like), is elucidated. Fusing the signal sequence of this protein to GFP revealed its periplasmic localisation, and its expression in Synechocystis mutants of both futA1 and futA2 paralogues further supported involvement in Fe3+ uptake, providing evidence for its function as an Fe transporter in Trichodesmium. Finally, a physiological experiment was performed to determine the significance of direct physical contact with Saharan desert dust for acquisition of Fe by Trichodesmium. It is demonstrated that cell surface processes are fundamental in dust-Fe utilisation by this organism and transcriptomic analysis identifies a number of unique genes regulated under different Fe and dust regimes including putative cell-surface proteins not previously studied in Trichodesmium. Combined, these studies have revealed a diverse array of molecular and physiological strategies potentially employed by Trichodesmium to survive and thrive on the ephemeral supplies of nutrients encountered in oligotrophic oceans, an attribute that facilitates its significant contribution to biogeochemical cycles.

It is widely held that as the ocean becomes more intensely stratified with anthropogenic-driven climate change, marine primary productivity (PP) will decline within mid-to-low latitude nutrient-limited waters, and increase within higher latitude light-limited waters. This is consistent with projections from Earth-system models, which predict a decline in global PP over the next century for ‘business-as-usual’ and high-mitigation warming scenarios. However, interannual and longer-term relationships between stratification and PP are more ambiguous in observational studies. Underlying the projected changes in PP are assumptions as to the response of phytoplankton to changes in stratification and vertical mixing at these time scales. This thesis focuses upon the identification and analysis of interannual relationships between phytoplankton biomass and vertical mixing in the North Atlantic. Satellite-derived chlorophyll (Chl) data are divided into regions of similar variability in order to assess the spatial dependence of interannual relationships with vertical mixing. A large-scale bimodal pattern represents the Chl response to the tri-pole pattern of climatic variability associated with the NAO in the North Atlantic. This Chl pattern is related to similar patterns in satellite-derived sea surface temperature (SST), wind speed, and Argo float-derived mixed layer depth (MLD) and stratification. Relationships with these proxies for vertical mixing are found to be spatially heterogeneous. However, it is general to this analysis that relationships are also spatial-scale dependent: localised variability may dominate the local-scale, but tends to cancel-out within regions of similar Chl response to reveal larger-scale relationships that dominate overall variability. Thus, while observational data tend to be noisier at the local-scale, they are consistent with Earth-system models in revealing an overall dependence of phytoplankton upon vertical mixing at larger scales. These large-scale patterns and relationships are in good agreement with output from a hindcast biogeochemical model (NEMO MEDUSA), which is analysed to determine how indirect-relationships with vertical mixing are mediated. Interannual Chl variability is shown to depend upon nutrient-availability throughout the mid-to-low latitude North Atlantic; relationships within the subpolar North Atlantic are undetermined, presumably due to a seasonal-dependence of relationships that are poorly represented by yearly-averaged/yearly-metric time series at these latitudes. Lastly, the bimodal pattern of Chl variability is assessed for stability and continuity of relationships against climate warming. In the projected output of NEMO MEDUSA, under a relative concentration pathway (RCP) 8.5 ‘business-as-usual’ warming scenario, this bimodal pattern in Chl variability is shown to weaken over the next century. While relationships with vertical mixing appear to continue unabated, the dominance of this bimodal pattern upon Chl, SST and MLD variability in the North Atlantic appears to decline over this time.

The Indian Ocean Dipole (IOD) is a coupled ocean-atmosphere phenomenon in the equatorial Indian Ocean, with a positive mode characterized by anomalous warming of sea surface temperatures in the west and anomalous cooling in the east. The IOD has been shown to affect inter-annual variability of the Indian monsoon. There is also evidence that the IOD may affect the formation, strength and duration of monsoon-related oceanic features in the North West Indian Ocean (NWIO), including fronts and eddies, the Somali upwelling and the ‘Great Whirl’ system. However, the mechanism by which the IOD develops and details of its connection with monsoon-related oceanic phenomena in the NWIO remain unclear. Satellite datasets of sea surface temperature anomalies (SSTA) and sea surface height anomalies (SSHA) over the past two decades have been examined, mainly to investigate the relationship between the IOD and large-scale climate modes like the Indian monsoon, El Niño Southern Oscillation (ENSO) and Rossby/Kelvin Waves. Early results show SSHA in NWIO; is more correlated with the IOD than with the ENSO. Also the results indicate an impact of Rossby wave patterns on the Somali Current system. Satellite datasets of sea surface temperature anomalies (SSTA) and sea surface height anomalies (SSHA) over the past two decades have been examined, mainly to investigate the relationship between the IOD and large-scale climate modes like the Indian monsoon, El Niño Southern Oscillation (ENSO) and Rossby/Kelvin Waves. Early results show SSHA in NWIO; is more correlated with the IOD than with the ENSO. Also the results indicate an impact of Rossby wave patterns on the Somali Current system. Satellite datasets of sea surface temperature anomalies (SSTA) and sea surface height anomalies (SSHA) over the past two decades have been examined, mainly to investigate the relationship between the IOD and large-scale climate modes like the Indian monsoon, El Niño Southern Oscillation (ENSO) and Rossby/Kelvin Waves. Early results show SSHA in NWIO; is more correlated with the IOD than with the ENSO. Also the results indicate an impact of Rossby wave patterns on the Somali Current system.

In-situ marine biogeochemical sensing allows measurement at high frequency to investigate short and long-term variability in processes in ocean waters. In trace analyses, not only the low concentrations of analytes but also possible interferences from the matrix and other elements must be considered, therefore a pre-concentration step prior to the determination of trace metals needs to be implemented. The way forward for improved in-situ analyses of manganese in seawater was to build on the existing technology of the Sensors Group at NOC, Southampton and develop a pre-concentration system for coupling to spectrophotometric Lab on a Chip (LOAC) technologies. This thesis describes the development and optimisation of LOAC analyser for manganese determination in aquatic environments, integrated with pre-concentration. Optimised conditions for the extraction of manganese from seawater with a Toyopearl iminodiacetate resin column were developed using Mn-54 tracer. Conditions evaluated were optimal pH for manganese removal, optimal flow rate required for full recovery of manganese, and the concentration and the volume of the acid solution needed for quantitative elution of manganese from the resin. The LOAC system used the colorimetric 1-(2-Pyridylazo)-2-naphthol (PAN) method for Mn determinations. The modified method was used for manganese determinations, when sodium dodecyl sulfate (SDS) was used as surfactant, with calibration curves constructed and precision (in the range 1.08 - 3.81 % RSD) and the LOD of the method assessed (3SD, typically 14 nM with 10 cm cell). Results of the adaptation of the modified PAN method on the chip and its coupling to a resin column for collection of manganese proves the concept of on-chip pre-concentration. The design and production method of the microfluidic chips and the operation procedure of the bench-top LOAC manganese determination system with the resin column implemented on the chip are described. The LOAC system coupled with the resin column and PAN chemistry was used for manganese determination with calibration curve constructed and precision of the method determined (0.86-2.69 % RSD).

As the largest portion of the Earth's surface, the deep-sea contains various ecosystems and harbours among the highest biodiversity on the planet. Complex deep-sea environments such as submarine canyons are some of the true ecosystem hotspots harbouring extensive species diversity owing to their high terrain variability. However, their complexity and limited accessibility has left many unanswered questions concerning their spatial structure and ecology. Recently, there has been an increasing amount of interest to understand the ecosystem function of this challenging environment, which has led to the development of technology to enable accessibility for research and exploration. Along with this, evidence of anthropogenic impacts has been uncovered, and this calls for more effective management in this complex type of deep-sea environment. Although there is a growing awareness for conservation in the deep-sea, scientific knowledge to underpin these strategies is still inadequate. Often what is known to the scientific community is not properly conveyed to policy makers. Hence, implementation of marine spatial management is not always successful. This thesis provides a scientific framework to underpin ecosystem-based management. It examines the seabed spatial structure in submarine canyons by 1) developing a mapping procedure to represent the spatial structure using commonly available data types for seabed studies, 2) proposing an approach to quantify the structural variability as an indicator for biodiversity to aid decision-making in prioritising conservation areas and 3) evaluating the spatial structure information transfer across different spatial scales and data types. As a result, a novel technique that is objective, automated and statistically robust is developed to map marine landscapes, which are geomorphologically and ecologically meaningful. The marine landscape map is found to be the best representation of environmental characteristics in submarine canyons. Based on this finding, marine landscape configuration and composition is quantified as a proxy for habitat heterogeneity and potentially an indicator of biodiversity. Additionally, the method is transferred to a high-resolution dataset for marine landscape mapping at a local scale, in order to evaluate the evolution of spatial characteristics across data scales. This study reveals that a link between regional and local scale spatial structure can be identified and mapped, and that information from one scale can be transferred to the other. Additionally, regional scale marine landscape maps provide first-level structural information that is suitable and sufficient to facilitate marine spatial management for large heterogeneous areas such as submarine canyons.

The Labrador Sea plays an important role in the Meridional Overturning Circulation (MOC), due to the seasonal occurrence of deep convection in this region. Heat loss during mixing is balanced by heat import from the boundaries, while the seasonal freshening plays an important role in the restrati?cation of the water column. Recent increases in freshwater input to high latitudes through accelerated rates of pack ice and glacial melt, has the potential to a?ect the convection in the Labrador Sea and therefore the global ocean circulation. It is more important than ever to understand the in?uence these changes have on the dynamics in the Labrador Sea. Understanding pathways of freshwater ?uxes into the region of deep convection and the impact of storms on the mixing in the Labrador Sea will help to predict potential changes in the MOC. To analyse recent changes in freshwater water in the Labrador Sea, an ARGO-based heat and freshwater budget of the Labrador Sea is calculated for 2002 – 2011. Over this time period a freshening of the surface waters (0 – 100 m) is observed. Between the ?rst and second 5-year period, observations indicate a gain of 40 cm of freshwater to the surface. The surface freshening is comparable to past freshening periods associated with a reduction of deep convection (e.g. the Great Salinity Anomaly). However, the observed surface freshening is o?set by subsurface warm-ing and enhanced salinities (100 – 2000 m), distinguishing it from the past freshening periods. To investigate pathways of freshwater ?uxes a particle tracking tool is used in a NEMO 1/12o ocean model. Seasonally, two peaks of freshening are observed (in spring and fall), consistent with observations. The freshening is due to the freshwater content of the coastal water along the coast of Greenland and the rate of advection of West Greenland Water. The large year-to-year variability in advection can mainly be attributed to changes in Ekman transport. To analyse recent changes in freshwater water in the Labrador Sea, an ARGO-based heat and freshwater budget of the Labrador Sea is calculated for 2002 – 2011. Over this time period a freshening of the surface waters (0 – 100 m) is observed. Between the ?rst and second 5-year period, observations indicate a gain of 40 cm of freshwater to the surface. The surface freshening is comparable to past freshening periods associated with a reduction of deep convection (e.g. the Great Salinity Anomaly). However, the observed surface freshening is o?set by subsurface warm-ing and enhanced salinities (100 – 2000 m), distinguishing it from the past freshening periods. To investigate pathways of freshwater ?uxes a particle tracking tool is used in a NEMO 1/12o ocean model. Seasonally, two peaks of freshening are observed (in spring and fall), consistent with observations. The freshening is due to the freshwater content of the coastal water along the coast of Greenland and the rate of advection of West Greenland Water. The large year-to-year variability in advection can mainly be attributed to changes in Ekman transport. The relationship of convection to air-sea ?uxes and the character of observed mixed layers in the Labrador Sea are explored by using wintertime hydrographic data from February – March 1997. The greatest number of storms occurred in December 1996 but the strongest winds and highest heat ?uxes were observed in February 1997. Analysing storm tracks showed that storms in February 1997 followed more organized tracks extending from the Gulf Stream region to the Irminger Sea where they slowed and deepened. Investigation of the small scale variability within the mixed layers reveals that temperature and salinity intrusions are more common at the base of the mixes layers. During storms there were more non-density compensating intrusions present compared to the periods between storms, and the small scale variability was enhanced near the top of the mixed layers. This study underlines the importance of understanding the mechanisms through which water can reach the basin and potential implications of changes in the storm frequency and tracks under a changing climate.

The west Svalbard continental margin has been in the spotlight since 2008, when more than 200 active methane seeps were reported near the landward edge of the gas hydrate stability zone (GHSZ). Several additional seeps have since been reported in the continental shelf area, some of which are likely to be associated with shallow hydrate dissociation and ocean warming. In addition, active seeps and seafloor pockmarks were also reported along the crest of the deep water Vestnesa Ridge area, which is also a known area of gas hydrate presence. However, the seeps at the ridge are unlikely to be related to ocean warming. Nevertheless, improved estimates of the amount of methane trapped within hydrate and gas in the west Svalbard continental margin are necessary to evaluate seafloor methane fluxes and its impact on future climate. Hydrate presence in the two study areas, the Vestnesa Ridge and the continental slope of the margin were traditionally inferred from the presence of bottom simulating reflectors (BSR) in seismic reflection data and high seismic velocity anomalies observed within the GHSZ. Bulk resistivity estimates obtained from marine controlled source electromagnetic (CSEM) data are highly sensitive to the presence of both hydrate and free gas within the sediment pore spaces. The presence of hydrate leads to an increase in the bulk resistivity and seismic velocity, whereas the presence of free gas leads to an increase in bulk resistivity but decrease in seismic velocity. These complementary attributes, combined with seismic reflection data provide a unique opportunity to obtain improved constraints on hydrate and free gas saturations in the margin. Therefore, CSEM data were acquired in 2012 at the two locations, to complement coincident seismic reflection and seismic refraction data. The CSEM data were acquired using a 100 m long horizontal electric dipole antenna that transmitted a 81 A, 1 Hz pseudo-square wave current. It was recorded using two sets of CSEM receivers: ocean bottom electric-field (OBE) sensors recorded the long offsets (850-3000 m), whereas a towed receiver, Vulcan recorded the data at a constant offset of 300 m. Synthetic model studies presented here suggest a maximum depth sensitivity of 200 m for Vulcan and about 1.5 km for the OBEs. Resistivity models obtained from the inversion of CSEM data show high resistivities (2-30 ?m) within the GHSZs of the Vestnesa Ridge and continental slope sediments. The high resistivities and presence of BSRs provide further evidence for the presence of hydrates within the west Svalbard margin. Significant heterogeneity in hydrate distribution can also be inferred across the margin, based on lateral resistivity variation in these models. The Vestnesa Ridge contains several pockmarks along the ridge crest. Periodic gas re-lease are reported through these pockmarks, based on observations of high intensity flares near the seabed on hydro-acoustic data. Fluid escape through the GHSZ to the seafloor pockmarks were also suggested by previous studies, which is supported by the observations of coincident high resistivity (from CSEM), high velocity (from seismic refraction) and acoustic chimneys (from seismic reflection). In addition, the observations of coincident high resistivity features and high amplitude reflectors at the continental shelf edge of the margin and beneath the crest of the Vestnesa Ridge suggests the presence of free gas outside the GHSZ of the west Svalbard margin. A joint resistivity and velocity analysis shows the presence of high hydrate (up to 73%) and gas saturations (up to 28%) within a fluid flow feature beneath a pockmark at the Vestnesa Ridge. Variation in resistivity and seismic reflection characteristics beneath different pockmarks indicate differences in fluid composition within each chimney feature. At the continental slope area, saturation estimates based on resistivity models, using modified Archie’s Law suggest highest hydrate saturations (around 40%) within the lower slope sediments. A BSR is also observed within these sediments, whereas the BSR is absent within sediments beneath water depths shallower than 700 m. Based on high resistivities observed within the upper slope sediments, around 20% hydrate is estimated within the GHSZ and around 30% free gas is estimated at the edge of the continental shelf.

Human activities have caused the atmospheric concentration of carbon dioxide (CO2) to increase by 120 ppmv from pre-industrial times to 2014. The ocean takes up approximately a quarter of the anthropogenic CO2, causing ocean acidification (OA). Therefore it is necessary to study the ocean carbonate system, including alkalinity, to quantify the flux of CO2 into the ocean and understand OA. Since the 1970s, carbonate system measurements have been undertaken which can be analyzed to quantify the causes of alkalinity variation in the surface ocean. A tracer of the oceanic calcium carbonate cycle (Alk*) was created by removing alkalinity variation caused by other processes: evaporation and precipitation, river input, and the biological production and dissolution of organic matter. The remaining variation is similar to the distribution of the major nutrients with low values in the tropical surface ocean and values 110 μmol kg-1 and 85 μmol kg-1 higher in the Southern Ocean and the North Pacific respectively. The causes of longitudinal Alk* gradients in the Pacific Ocean were then analyzed. The results indicate that outcropping of isopycnals and upwelling of water enriches Alk* in the subpolar North Pacific and along the North American margin. On the other hand, the eastern equatorial upwelling appears to be from depths too shallow to contain enhanced Alk*. Two algorithms to predict alkalinity were then created for the surface Pacific with r values between predictions and measurements of 0.970 for the entire Pacific Ocean algorithm and 0.991 for the North Pacific eastern margin. A method using in-situ Alk* and velocity measurements to estimate calcium carbonate export was developed. This method estimates a summer and autumn export in the Southern Ocean of 0.31 Pg C yr-1 with the majority occurring around the Polar and Subantarctic Fronts. The Alk* tracer is shown to be a useful tool which could be improved by further research into riverine alkalinity inputs and the influence of sea ice formation on alkalinity.

The biological carbon pump plays a key role in regulating the ocean-atmosphere balance of CO2, without it atmospheric CO2 would likely be 200ppm higher than it is today. The most rapid attenuation of downward particulate organic carbon (POC) flux typically occurs in the upper few hundred meters of the water column, yet the practical difficulties of making measurements in this dynamic region of the ocean mean that the processes controlling POC flux attenuation are still poorly understood. In this thesis, Marine Snow Catchers were deployed in the Scotia Sea, Antarctica and the northeast Atlantic to obtain intact sinking particles and investigate the relationship between particle type and attenuation rate. Faecal pellets (FP) were a major component of the flux at all stations, yet total POC attenuation varied between sites in relation to zooplankton composition and bloom timing. A novel method was employed to characterise particle-associated microbial respiration on FP, which is currently a poorly understood term. Oxygen microsensors were used to measure small scale oxygen gradients through the boundary layer at the interface of FP. Rates of particle-associated microbial respiration were too low to account for the observed large decreases in FP flux over the upper 200 m, and evidence suggests that losses via zooplankton grazing and fragmentation are more important. The importance of Antarctic krill for setting the export efficiency of POC in the marginal ice zone (MIZ) of the Scotia Sea is highlighted through unique comparisons between observed mesopelagic krill FP fluxes and predicted surface FP production. Krill FP are transferred through the upper mesopelagic much more efficiently than values of POC attenuation typically used in global biogeochemical models. I conclude that improved, regionally specific knowledge of the zooplankton community composition is vital to understand global variations in POC flux attenuation, and hence allow better predictions of ocean carbon sequestration. Ultimately carbon is lost from the organic carbon pool as CO2 via respiration, and hence in theory, at steady state, the attenuation of POC should be balanced by community respiration. In reality this balance is difficult to achieve, suggesting that our understanding is incomplete. Very low rates of both absolute and carbon specific particle-associated microbial respiration (a term missing from previous budget studies) were measured on marine snow particles collected in the northeast Atlantic and hence cannot resolve imbalances in the upper mesopelagic POC budget. Microbial disaggregation and solubilisation of POC as well as fragmentation of large particles into slowly sinking and non-sinking POC by zooplankton, may help to explain imbalances in the carbon budget, highlighting the need to measure respiration losses on both fast, slow and non-sinking pools of POC.