The biological carbon pump (BCP) exports 5 - 12 Gt C yr−1 to the deep sea and is important for the distribution of carbon within the ocean. Previous studies proposed that the phytoplankton community structure and availability of dense biominerals are key in defining regional export. This thesis examines these factors and their influence on export in the Southern Ocean and the Arctic through the examination of upper ocean species composition, distribution and marine snow particles. In the Southern Ocean, the samples were collected from the high reflectance feature known as the Great Calcite Belt (GCB). The marine snow catcher was used to capture sinking particles and allowed the examination of both the large, fast sinking particles and the slow sinking fraction of particulate organic carbon (POC). The GCB was dominated by nanophytoplankton (<20μm), where the coccolithophore Emiliania huxleyi and diatoms Fragilariopsis nana, Fragilariopsis pseudonana and Pseudonitzschia sp. were the dominant species driving the variation in biogeography. The variation in biogeography was best described by a combination of temperature, nutrients and pCO2. E. huxleyi forms distinct features in the GCB on the Patagonian Shelf, near South Georgia and the Crozet Islands. A southwards progression of E. huxleyi occurs within High Nutrient Low Silica Low Chlorophyll waters in post-bloom conditions after silicic acid and iron drawdown by diatoms. When examined in terms of biomass, the diatoms dominate the GCB, although E. huxleyi was the single biggest contributor as a species. A statistical comparison of surface species and slow sinking material indicated that there was a degree of similarity between the surface and exported community but was regionally variable. Coccolithophores and diatoms contributed minimally (<10%) to upper ocean biomass and total carbon export. The results of this thesis indicate that even though the coccolithophores and diatoms are important phytoplankton for primary production, their direct contribution as cells to carbon export is low. POC flux correlated with opal flux but not calcite flux indicating that the opal was more important in driving POC flux in the GCB. Two types of sinking particles were examined, marine snow aggregates and faecal pellets and there was no significant difference between the sinking velocities. Marine snow sinking velocity was not dependent on size of the aggregate. The concentrations of biominerals and POC in the surface waters and the biominerals in the sinking particles did not influence the sinking velocity. This indicates that porosity and POC content could be more important in determining the sinking velocity and the carbon flux. The synthesis includes the species composition and biomass of the Arctic, which displayed similar trends to the GCB. The results from this thesis suggest that the slow sinking carbon export may not be significantly affected by potential changes in upper ocean biomineralising phytoplankton community structure and upper ocean chemistry. The effects of porosity and POC contents of the particles are here considered to be just as important for determining the export flux than upper ocean community structure and biomineral ballast availability. This implies that the impacts of ocean acidification will become more important deeper in the water column as biominerals become more important within sinking particles as POC is removed.

Phytoplankton growth is sustained by the supply of essential nutrients and balanced by mortality processes such as viral infection, both of which can give rise to stress. Remod- elling of cellular lipids in response to such stresses is common in unicellular organisms. Under phosphorus (P) stress, phytoplankton substitute glycerophospholipids with non- phosphorus analogues, reducing their demand for P. Reported herein, the model marine diatom Thalassiosira pseudonana degraded only a small proportion of its original glyc- erophospholipid. Most of the P remained incorporated in glycerophospholipids, but significant changes in the individual glycerolipid species were observed. Untargeted lipidomic screening highlighted diglycosylceramides, not previously ob- served in T. pseudonana, that increase with P stress and may be useful as biomarkers. The fatty acids comprising each individual diglyceride lipid were characterised filling a conspicuous gap in our knowledge. Preliminary results suggest partitioning of diacylglyc- erol lipids between subcellular compartments. Marine diatoms, rich in lipids such as triacylglycerols are potential feedstocks for bio- fuels, where nitrogen (N) starvation is common to increase lipid yield. Quantification of individual glycerolipid species under N stress revealed that polyunsaturated glycerophos- phatidylcholine species and the predominant chemotype of sulfoquinovosyldiacylglycerol displayed large increases. Total diacylglycerol increased 3 fold under N stress, comprised of increases in saturated/monounsaturated species. This appears to form part of the cell’s adaption to N limitation that ultimately leads to the accumulation of triacylglycerides. These findings provide insight on the diatom lipidic response to nutrient stress and their adaptations to life in low nutrient environments, with additional implications upon biofuel production. Marine viruses infect phytoplankton influencing host ecology and evolution. Emilia- nia huxleyi has a biphasic life cycle with a diploid and haploid phase. Diploid cells are susceptible to infection by specific coccolithoviruses, yet haploid cells are resistant. Anal- ysis of lipids from cultures of uninfected diploid, infected diploid and uninfected haploid E. huxleyi revealed that sialic-glycosphingolipid, previously linked with susceptibility to infection, was absent from the resistant haploid cultures. Additional untargeted analyses unveiled potential biomarkers furthering our understanding of E. huxleyi host/virus lipid dynamics and highlight potential novel biomarkers for infection, susceptibility and ploidy.

No description available.

Marine diazotrophs play an important role in marine biogeochemical cycles by fixing N2 into bioavailable forms, thus sustaining oceanic productivity over broad timescales through maintenance of bioavailable nitrogen stores. However, as assessments of diazotrophic organisms are traditionally constrained to the upper ocean, the fate of diazotroph-derived new nitrogen is not clear. Many previous assessments of the fate of diazotrophs has assumed that the majority of new nitrogen produced in these organisms is recycled in the upper ocean through the microbial loop and that diazotroph contribution to export is minimal except following blooms of diazotrophic diatom associations (DDAs). In this study, a combination of light microscopy, transmission electron microscopy, and qPCR of sinking particulate material from the subtropical and tropical Atlantic Ocean and Gulf of Mexico has revealed that filamentous, heterocystous and unicellular cyanobacterial diazotrophs are present below 100 m, and provides some of the first evidence that this appears to be a widespread occurrence. Herein we identify the mechanisms by which diazotrophs are exiting the mixed layer via passive sedimentation, aggregation, and incorporation in faecal material. Diazotrophs also appear to be contributing to the export of particulate organic nitrogen with Trichodesmium composing up to 3% of PON standing stock and 1 – 17.5% of PON flux at 10 m below the mixed layer in the (sub-)tropical Atlantic Ocean. The likelihood that the subsequent remineralisation of diazotroph-derived material at depth is contributing to the N* anomaly observed in the thermocline in the North Atlantic sub-tropical gyre is also discussed. This work provides some of the first descriptions of mechanisms by which diazotrophs contribute to these anomalous nutrient distributions, such as through remineralisation of diazotroph biomass following cellular lysis. These results aid in the elucidation of the extent to which Trichodesmium and other diazotrophs are contributing to the biogeochemistry of deeper waters and provides novel insight into the cycling of fixed nitrogen in the oligotrophic ocean.

This thesis uses a novel, combined mineralogical, geochemical (including stable S iso- topes), and microbiological approach to semi-quantitatively determine Scotia Sea sedi- ment formation processes. The factors that control the localisation of chemosynthetic, microbial consortia in metalliferous sediment beneath Southern Ocean vent fields is investigated along with the impact of hydrothermal venting on sediment composition. Circum-Antarctic ridges represent nearly 40 % of the Earth’s ∼58,000 km ridge crest, but remain severely understudied. In the austral summer of 2009–2010, the Royal Research Ship James Cook expedition JC42 explored the northernmost (E2) and southernmost (E9) bare-rock segments of the East Scotia Ridge, and the sedimented Kemp Caldera (a southern feature of the South Sandwich Arc), and collected >20 co-registered vent fluid, chimney sulfide and hydrothermally-influenced sediment samples using the ISIS remotely-operated vehicle. The hydrothermal materials from E9 and the Kemp Caldera are the focus of this thesis. E9 sediment composition is controlled by the simple mix- ing of >90 % local basalt that is affected by subduction-related and enriched mantle components, <10 % particulate plume fallout, which is dominated by an Fe-, Cu-, Zn-, Ba-, and Pb-rich, near-plume phase, and <1 % collapsed chimney material. The ma- jor, minor, trace, and rare earth element sediment content at E9 is largely determined by proximity to active venting. The thin sediment cover throughout E9, indicates an early stage of sediment formation and the recent onset of venting at this site. Kemp Caldera sediment components include 55–60 % phreatomagmatic shards of local basalt that were most likely deposited by a recent, volcanic event, 30–45 % crystalline elemental S derived from the magmatic disproportionation of SO2 (identified by a δ34S signature of +4.8 ‰ to +5.9 ‰), and 0–10 % buoyant plume particles (rich in P, K, Mn, Fe, and the rare earth elements). Biogeochemical Fe, Mn, and S cycling is investigated in two very different sediment systems of the Kemp Caldera: Toxic Castle and Tubeworm Field. Toxic Castle sediments are compiled from the episodic deposition of magmatic and hydrothermal components, while pore fluid composition is strongly influenced by diffuse, upwelling hydrothermal fluid. The original magmatic-hydrothermal signature is diagenetically altered in the solid phase Tubeworm Field sediments, likely initiated by dissimilatory sulfate reduction. Pore fluid Fe and Mn redox zonation in the surface sediments at Tubeworm Field is typical of biogeochemical cycling in stratified marine sediments. Microbial cell counts (identified by 4’,6-diamidino-2-phenylindole staining and fluorescent in situ hybridisation microscopy) are relatively consistent across the ma- jor Tubeworm Field redox boundaries, although there is a significant downcore shift in the microbial community structure. A dominant presence of δ-, E-, and γ-proteobacteria (which host known S metabolisers), confirms active, microbial S cycling in the deeper Tubeworm Field sediments. Sediment descriptions from modern hydrothermal (partic- ularly back-arc basin-associated) systems are relatively scarce, in comparison to those of vent fluid and chimney material, which is surprising given the potential economic im- portance of hydrothermally-derived, metalliferous, rare earth-enriched sediments. This thesis increases our knowledge of sediment formation processes and subsequent biogeo- chemical cycling, in a range of back-arc-associated bare-rock and sedimented systems, along poorly-surveyed circum-Antarctic ridges, and accentuates the requirement for continued, interdisciplinary hydrothermal surveys of the global, submarine ridge system. We must fully understand the complex interaction of geological, chemical, and biologi- cal components that constitute the complete hydrothermal system, before we allow the commercial exploitation of unique ecosystems that have forever changed our perception of life in the deep sea.

The late Palaeocene to late Eocene period of Earth's history is characterised by remarkable change. Temperate ice free poles at the beginning of this period gradually cooled until permanent ice formed on Antarctica around 33.5 million years before present (Ma) and sea ice formed in the Arctic. The intervening time was not stable and data, despite relatively low resolution, appear to show that the Eocene climate was dynamic. This period was the most recent time when atmospheric pCO2 concentrations were as high as predicted by models simulating the effects of anthropogenic fossil fuel burning on Earths' climate. The ability to understand the mechanisms of climate change in the Eocene will help to understand potential climate impacts in the future. This thesis examines 3 contrasting periods of climate change. Geochemical data indicate that a 3.5 million year period of high biogenic silica deposition during the Eocene was climatically relatively stable in the Arctic basin with only infrequent communication to the world's oceans outside. This period is correlated with high organic burial in the basin and global siliceous rich deposits which acted to gradually draw down pCO2. This period of `quiet' climate compares to two periods of warming where significant carbon isotope perturbations may indicate the forcing of the Earth's climate into an alternative quasi-stable state. The Palaeocene { Eocene Thermal Maximum (PETM) represents a significant input of exogenic carbon into the atmosphere over the course of several thousand years and significant warming of the Earth. Records of bulk carbonate isotopes from a section in NE Italy show several other Delta13C perturbations both before and after the PETM event, albeit a quarter to a half of the magnitude of the PETM, and having durations of only 40 { 60 thousand years (kyr). These events are thought to be the result of a re-arrangement of the internal carbon cycle of the Earth - atmosphere and may represent orbitally forced changes in deep water ocean ventilation similar to controls seen on modern day glacial { interglacial cycles. These rapid changes in the carbon cycle are shown to be inverse at the middle Eocene Climatic Optimum (MECO), where gradual warming over 400 kyr is ended abruptly by significant cooling. From the first marginal marine section of this event rapid organic carbon burial occurs over 50 { 100 kyr and is associated with previously unrecorded low oxygen bottom water conditions and high organic burial. We hypothesize that if this burial was extended over significant shelf areas then this could rapidly have returned the middle Eocene to the general cooling trend of the Eocene.