The diagenetic re-mineralisation of seafloor-sulphide deposits and the role of microbes in the metal-exchange processes were investigated in metalliferous sediments from the Alvin relict hydrothermal zone in the TAG area at 2608'N (Mid- Atlantic Ridge). The solid-phase and concomitant pore water concentrations of AI, Si, Ca, Clot, Corg, S, Fe, Mn, Cu, Zn, P, V, Co, U, Mo, Au, Ag and REE's were measured in a 230 cm long gravity core from the southern periphery of the relict vent field. These measurements were complemented by detailed analysis of bacterial abundance and specific activity. The altered sulphidic sediments are capped with a ~30cm thick layer of carbonate-rich (~60% CaCO3), Fe-stained sediments. Two distinct sulphide layers, interbedded with Fe-oxysilicates, and overlain by a thin layer of Fe/Mn oxyhydroxides, were found in this core. The dominant mineral-phase in both sulphide layers, which originate from mass-wasting of mound sediments, is pyrite with some goethite. Reaction of the exposed metal-sulphides in the upper sulphide layer with seawater has produced a thin layer of secondary atacamite, which is enriched in Au. Primary sphalerite is dissolved in the upper sulphide layer and re-precipitation as secondary sphalerite directly above and below. U continues to be scavenged from the porewater, producing marked enrichments on oxidised sulphide rims. The re-mineralisation processes identified in this core are in close analogy to the large-scale zone-refining that has been described for the active TAG mound and ancient ore-deposits. REE/Fe ratios clearly distinguish between plume derived sediments in the carbonate cap and slumped material from the hydrothermal mound. The REE signature of bulk sediments and clay phases imply multiple stages of alteration by diffuse fluids in the upper sulphide layer and intermediate layer, whereas the lower sulphide layer is not affected. Alteration by reactive low-temperature hydrothermal fluids is also inferred to be responsible for the observed diagenetic overprinting of trace-metal distributions in the upper sulphide layer. The intermediate layer is rich in nontronite, which has been precipitated in situ from diffuse fluids. The presence of Mn- and Fe-reducing bacteria coincide with elevated porewater concentrations of Mn and Fe, indicating direct involvement of bacteria in the cycling of these metals. Total counts of viable cells and general activity measurements show that although bacterial populations are relatively small, they are healthy and well adapted to this potentially toxic environment. The existence of active microbial communities in metalliferous sediments may therefore provide a continuum of bacterial populations between high and low temperature hydrothermal systems, thus representing an important transitional stage in the hydrothermal ecosystem. Microbial reduction and oxidation of S was observed throughout the core, indicating that microorganisms are particularly active in terms of S-cycling. For deep-sea sediments extremely high sulphate reduction rates (67 nmol/cm3/d) were measured in the ironstained carbonate cap. In the absence of significant organic carbon (~0.2 %) this strongly suggests the synthesis of alternative electron-donors by chemolithotrophic bacteria to support the observed high rates of heterothrophic activity in these sediments.

The marine biogeochemistry of dissolved organic carbon (DOC) has come under increased scrutiny because of its involvement in the global carbon cycle and consequently climate change. Dissolved organic nitrogen (DON) and phosphorus (DOP), which have historically been ignored because of their suggested “biological unavailability”, have now received greater attention due to their importance in nutrient cycling, particularly in oligotrophic ecosystems. DOM, a byproduct of photosynthetic production, has important ecological significance as a substrate that supports heterotrophic bacterial growth, thereby causing oxygen consumption and regenerating inorganic nutrients. In the open ocean the net production of DOC is ultimately due to the decoupling of biological production and consumption processes. Concentrations of DOM in the surface oceans, therefore, are controlled by both physical and biological processes. This research investigates the biological factors that control the distributions of DOC, DON and DOP in surface waters, the importance of DOC degradation to oxygen consumption, the importance of DON and DOP degradation to remineralised dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphorus (DIP), and the C:N:P stoichiometry of DOM pool in the Atlantic Ocean. Samples were collected on Atlantic Meridional Transects (AMT) cruise 16 and 17, which crossed the southern temperate region, the southern subtropical gyre, the equatorial region, the northern subtropical gyre, and the northern temperate region. This work described here was performed as a component of the AMT programme. Concentrations of DOC and TDN were determined using a high-temperature catalytic combustion technique, and TDP concentrations were determined using a UV oxidation method. Concentrations of DON and DOP were estimated as the difference between the independent measurements of TDN and TDP. The results showed that the highest DOM concentrations were found in surface (0-30 m) waters, ranging from 70-80 µM DOC, 4.8-6.5 µM DON and 0.2-0.3 µM DOP, and decreased with increasing water depth to 45-55 µM DOC, 2.6-4.0 µM DON and 0.04-0.05 µM DOP at 300 m. The lowest DOM concentrations were observed in the deep (>1000 m) ocean, averaging 44 µM DOC, 2.3 µM DON and 0.02 µM DOP. In the upper 300 m, the concentrations of semilabile (and labile) DOC decreased by 45-95% from the surface values. DON and DOP were the dominant components of the total dissolved nutrient pools in the upper 50 m, accounting for up to 99% and 80% of the TDN and TDP pools, respectively. In the upper 300 m, semilabile (and labile) DON and DOP decreased by 50-65% and 90-95% from the surface values, respectively. The decoupled correlations between DOC/DON/DOP and chlorophyll-a and rates of carbon fixation suggested that phytoplankton biomass and rates of primary production were not the important controls of the cumulative DOC, DON and DOP. Zooplankton grazing was hypothesised to be an important factor in regulating the distributions of DOC, DON and DOP in surface waters. Poor correlations between DOC/DON/DOP and DIN/DIP suggested that inorganic nutrients were not the significant controls in DOC, DON and DOP distributions. N and P were probably retained mainly in the organic pool in the surface waters due to a hypothesised insufficient functioning of the microbial degradation. If the vertical migration of zooplankton was significant in bringing new nutrients into the surface waters, strong correlations between dissolved organic and inorganic nutrients should not be anticipated. Prochlorococcus spp. abundance was statistically linked with the concentrations of DOC, DON and DOP. The significant correlations may reflect the ability of Prochlorococcus to assimilate the labile forms of dissolved organic nutrients (including DOC), which may be quantitatively significant in surface waters of the Atlantic Ocean. The C:N, N:P and C:P stoichiometry of the bulk DOM pool deviated from the Redfield ratio of 6:1, 16:1 and 106:1, ranging from 12-18, 20-100 and 300-1400, respectively, in the upper 300 m, suggesting that the cumulative DOM was rich in C relative to N and P, and N relative to P compared to the Redfield trajectories. The offsets of the C:N:P stoichiometry relatively to the Redfield ratio were due to nutrient limitations that imposed on prokaryotic and eukaryotic microbial populations. The C:N:P stoichiometry of the bulk DOM pool showed an increased trend, with C:N = 12-16, N:P = 20-25, and C:P = 300-350 in the upper 30 m, C:N = 12-18, N:P = 50-100, and C:P = 700-1400 at 300 m, and C:N = 17-24, N:P = 79-132; C:P = 1791-2442 at 1000 m. The differences in the C:N:P stoichiometry of the bulk DOM pool between the upper and deep waters suggested preferential remineralisation of P relative to C and N, and N relative to C. A greater remineralisation length scale for DOC relative to DON and DOP produced a long-term, steady flux of C from the surface to the deep ocean. Therefore, CO2 fixed in the upper ocean during planktonic photosynthesis was continuously “pumped” into the ocean interior, and stored in the deep ocean up to thousands of years. The C:N, N:P and C:P stoichiometry of the semilabile (and labile) DOM pool generally agreed with the Redfield ratio (C:N = 6; N:P = 16; C:P = 106) in the upper 30 m. At 100 m C:N ratio was 5-12, C:P ratio was 20-30, and C:P ratio was 100-150. At 300 m, C:N ratio was 5-12, N:P ratio was 25-100, and C:P ratio was 150-500. The findings suggested that in the upper 300 m, there was no preferential remineralisation between the semilabile (and labile) DOC and DON, however, the semilabile (and labile) DOP seemed to be preferentially remineralised relative to the semilabile (and labile) DOC and DON. In the upper thermocline (i.e. above 300 m), DOC degradation was important with respect to oxygen consumption, contributing to as much as 25% of the apparent oxygen utilization (AOU). The remaining of 75% was attributable to POC decomposition. However, the AOU contributable to DOC showed a function of latitude, with 15-55% found in the central subtropical Atlantic gyres and 15-25% in the equatorial region. The most likely explanation for the variation of DOC relative to POC degradation with respect to AOU was the regional variability in the export of POC, which was suggested to be highest in the high nutrient regions of the equator and at the poleward margins of the subtropical gyres. As a result, DOC formed an important contribution to AOU in oligotrophic regions, while POC was the dominant control of AOU in upwelling regions. Some freshly-produced fractions of DON and DOP with turnover times of months to years were capable of escaping rapid microbial degradation in surface waters and became entrained into deep waters via diffusive mixing. Subsequent microbial degradation of these DON and DOP took place in the thermocline, regenerating inorganic nutrients. Statistically significant correlations were observed between the DON-to-DIN and DOP-to-DIP relationships. Calculations of the fluxes of dissolved organic nutrients relative to inorganic nutrients suggested that in the upper thermocline (i.e. above 300 m), the downward fluxes of DON and DOP contributed to a total of 4% and 5% of the upward fluxes of DIN and DIP, respectively, into the euphotic zone. The remaining of 95% of the upward dissolved inorganic nutrients fell out of the euphotic zone as particles in order to prevent nutrient accumulation and to maintain nutrient integrity of the pelagic ecosystem.

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.

The aim of this thesis is to contribute to the observational database in order to address fundamental questions as to how dissolved organic nutrients influence N and P budgets, how they affect nutrient cycling and the sustainment of biological production within two major ocean oligotrophic gyres: the Southern Indian Ocean gyre and the subtropical North Atlantic gyre. A transect across the Indian ocean at 32°S conducted in March/April 2002 was sampled for dissolved oxygen, inorganic and organic nutrients and phytoplankton pigments concentrations. A second cruise was undertaken in April/May 2004 across the oligotrophic North Atlantic Ocean at 24oN. A similar set of samples were collected on the second cruise and in addition the stable nitrogen isotopic signature of particulate organic matter was determined plus surface enzymatic activity and primary production incubation measurements. The Indian ocean basin is characterized by low N:P ratios both in the inorganic and organic fractions with respect to phytoplankton nutrient requirements driven by an excess of denitrification over N2 fixation. The strongly non-Redfieldian TON:TOP ratio suggests a decoupling of TON and TOP remineralization processes and indicates a severe TON deficiency brought by the strong nitrate limitation that leads to a community demand for TON. TON and TOP Ekman meridional advection played a small but not trivial role in providing N and P into the gyre to support export production. It is estimated that the contribution of TON advection is of the same order as the new N supplied by N2 fixation into the gyre. In the Indian Ocean 40% of the net N transported by the overturning circulation across the boundary at 32°S, is attributable to organic nutrients. To close the N budget assuming the upper range estimates of denitrification to be correct, the inclusion of organic nutrient transport by the ITF is required. Hence, the Indian Ocean N budget conforms to a steady state where excess of denitrification over N2 fixation is compensated for by atmospheric, riverine and a hypothesized flux of DON in through the ITF. In the permanently stratified North Atlantic subtropical gyre, nutrient supply pathways for the growth of phytoplankton are unclear and appear inadequate for the maintenance of the observed export production. Here the significance of two mechanisms, N2 fixation and the bioavailability of organic nutrients, has been investigated. The computation of a new geochemical proxy, TNex, for the determination of N to P anomalies suggests that N2 fixation is more important than previously thought. The spatial distribution of the isotopic composition of particulate organic matter shows a N2 fixation signal across most of the basin with the exception of the coastal margins and a central region. Thus no latitudinal gradient in diazotrophy, as suggested by other workers, is apparent. TON and TOP represented not only the major component of the upper ocean N and P pools but were also bioavailable to the community through the release of extracellular enzymes. The cycling of TON and TOP was decoupled, with higher turnover rates of the TOP pool as compared to the TON pool. Both TON and TOP could potentially sustain a significant fraction of primary production and TOP could potentially provide nearly all the P needed by N2 fixers. In conclusion, in the permanently stratified North Atlantic subtropical gyre, N2 fixation and the bioavailability of organic N and P appear to be major mechanisms for supplying nutrients and sustaining phytoplankton growth.

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.

No description available.

Nanoparticles of many varieties are increasingly studied for use in the physical, chemical, and biological sciences. Metallic nanoparticles exhibit morphology-dependent localised surface plasmon resonances (LSPR), which couple to propagating light, and manifest as a resonant particle polarisability at the LSPR frequency. These resonances can be harnessed for a variety of applications. Many of these applications require characterisation of NP properties, such as their optical response, summarised by the ab- sorption and scattering cross sections. Quantitative measurement of individual NPs is technically difficult, and ensemble measurement techniques, such as absorption spectroscopy, are frequently employed. However, individual NP properties can vary significantly, within the ensemble. In this work, we present a novel, and easy to implement, wide-field extinction microscopy technique, capable of analysing hundreds of nanoparticles simultaneously. Using this technique, we are able to characterise individual gold nanoparticles down to 5 nm diameter, and collate the data to produce ensemble statistics. Furthermore, we developed a program for the rapid analysis of the acquired image, enabling implementation by others in a cost-effective and efficient manner. Using the wide-field extinction technique, we have studied several sizes of gold, platinum, silver, and diamond nanoparticles. We used gold nanoparticles to pro- vide a proof of concept, and found good agreement with the literature. We also present an experimental investigation towards an in-vitro plasmon ruler. Coupled metallic NPs exhibit a LSPR, which is dependent on interparticle distance. The four-wave mixing technique we employ is phase-sensitive, allowing measurement of the shift of the res- onance frequency of gold NPs. To provide proof-of-principle of the plasmon ruler, we correlatively studied gold nanoparticle dimers, with transmission electron microscopy, and four-wave mixing microscopy. In this way, we obtained a direct measure of the interparticle distance, and could relate it to the measured phase shift in four-wave mixing.

This thesis is concerned with the study of biophysicochemical processes using electrochemistry and related techniques. The first part of the thesis discusses the electrochemical detection of biological species, and characterisation of the electrode materials employed. A comparison of two novel forms of carbon electrode, namely carbon nanotubes and polycrystalline boron doped diamond (pBDD), with more conventional carbon electrode materials reveals their enhanced characteristics for bioelectrochemistry, with improved sensitivity and resistance to fouling. These materials are further characterised using novel high-resolution electrochemical imaging methods, to determine heterogeneous electron transfer rates for a number of different redox species. The kinetic rate constants are determined from measured electrochemical currents using finite element method (FEM) modelling, which proves to be a powerful technique for the quantitative analysis of intrinsic system parameters that cannot be studied directly. The electrochemical response of isolated regions of pristine SWNTs is investigated using scanning electrochemical cell microscopy, demonstrating high electrochemical activity at the nanotube sidewalls. A similar analysis of the different facets of pBDD is performed using intermittent contact scanning electrochemical microscopy coupled with FEM simulations, revealing that the electroactivity is strongly in uenced by the local density of states of the material. New techniques are also presented for the investigation of transport processes at membrane interfaces. A new method of bilayer formation is developed, which overcomes many of the limitations of current techniques, and is used to investigate the permeation rates of a series of aliphatic carboxylic acids. Using confocal laser scanning microscopy (CLSM) with a pH-sensitive uorophore, the pH change as a weak acid permeates across the bilayer can be visualised, and the permeation coefficient determined by comparison with FEM simulations. This reveals a trend of increasing permeability with lipophilicity. Finally, CLSM is used to study the lateral diffusion of protons at lipid bilayers and other surfaces. Protons are generated galvanostatically by a UME positioned close to the substrate, altering the local pH which can be visualised by means of a pH-sensitive uorophore. The uorescence profile is again compared to FEM simulations, allowing the lateral diffusion coefficient to be determined.

This thesis examines the development of a novel in vitro biological caries model and its suitability in testing the efficacy of anti-caries approaches. Dental caries remains a public health concern worldwide; with extensive treatment costs and impacts on quality of life. Ineffective removal of all dental plaque from tooth surfaces after brushing, the insufficient delivery of anti-caries therapies; along with continuing shifts towards high frequency, sucrose-rich food consumption, expedites the caries disease process. It is, therefore, important to explore caries risk and development at these sites, particularly when representatively assessing the efficacy of a test agent in preventing caries. This caries model enabled the study of the anti-caries effects of fluoride to assess its efficacy in conditions simulating the modern diet. The current methodology employed the Constant Depth Film Fermenter (CDFF) to investigate the caries disease process in response to fluoride delivered continuously; twice and thrice daily; and at different concentrations. The approach is the first in CDFF research modelling caries inclusive of a biologically relevant microcosm biofilm in addition to enamel demineralisation. Specific members of multispecies biofilm were selectively enumerated using traditional microbiological culture techniques whilst caries was simultaneously quantified with Transverse Microradiography (TMR), Quantitative Light-Induced Fluorescence (QLF), and Non-Contact Surface Profilometry (NCSP). The fluorescence of biofilm illuminated by QLF was also investigated. Results indicated that quantities of total or specific members of the microbial community are not direct indicators of caries risk and turning focus towards the metabolism of oral biofilm bacteria, and how it may be affected, is vital in caries research. TMR and QLF agree when quantifying caries whilst NCSP shows promise in studying surface changes. At 0.05 ppm, fluoride was unable to exert a significant anti-caries effect despite being continuously present during and between sucrose exposures. Laminated lesions confirmed the importance of maintaining elevated levels of fluoride in the oral environment throughout the day. At higher concentrations (1,450 and 228 ppm fluoride) the anti-caries efficacy of fluoride when supplied in frequent applications throughout the day was confirmed. A third application of fluoride did not appear to additively benefit enamel, since all strategies were effective after 10 days regardless of frequency. Nonetheless the increased plaque fluoride reservoir and subtle antimicrobial effects than in twice daily pulsed biofilm, mean the benefit of a third application is likely more discernible in the long term. Scanning Electron Microscopy (SEM) and Energy-Dispersive X-ray Spectroscopy (EDX) elucidated significant calcium fluoride deposits of enamel surfaces beneath biofilm exposed to 1,450 ppm fluoride continuously. In conclusion, the CDFF can produce multispecies biofilm under conditions similar to those of the oral milieu and investigate its cariogenicity in response to diet and experimental anti-caries agents. The model could be examined using an array of techniques to obtain information about aspects of the biofilm, the substratum, and to validate upcoming methods in an orally representative environment. In this regard, the current study contributes not only to enamel caries research but to biofilm research in general by minimising variation.