Most global calcification is carried out by organisms which are also photosynthetic. In this study, the coccolithophore Emiliania huxleyi (Lohmann) Hay and Mohler and two species of hermatypic coral were used to: examine the effect of dissolved inorganic carbon (DIC) and light on photosynthesis and calcification; and determine the extent to which these two processes interact. A novel method of producing coccolith-less (non-calcifying) cells from calcifying cells of the same strain of E huxley! was developed thus allowing photosynthesis and calcification to be studied separately. The kinetics of photosynthesis in both types of cell, and of calcification in coccolith-bearing cells, were shown to be biphasic with respect to DIC concentration. The hiatus in all three cases was located at 1 mM DIC. This unusual pattern was shown to be the product of two carbon uptake mechanisms: an anion exchanger working at all DIC concentrations and an external carbonic anhydrase active only at low DIC concentrations. In contrast to the commonly-held view, this study demonstrated that calcification did not promote photosynthesis in E. huxleyi. Nevertheless, there was clearly strong biological control of calcification in this alga since DIC uptake was mediated by an anion transporter and a dehydroxylating enzyme. This work also showed that in E huxleyi, DIC addition enhanced photosynthesis at both limiting and saturating photon flux densities and that bicarbonate affected photochemical processes directly. Photosystem II activity was stimulated and non-photochemical quenching was reduced, possibly protecting the photosynthetic apparatus from damage by light. In the two corals; Porites porites and Acropora sp., strong biological control of calcium carbonate precipitation was also evident. Again, calcification did not stimulate photosynthesis. Calcification rates of Acropora sp. were monitored in the dark and although these were lower than in the light, they still increased dramatically with bicarbonate addition. This showed that high concentrations of the bicarbonate ion can compensate for the lack of light. Hence, it seems that in hermatypic corals, light-dependence of calcification may be facultative and not obligate. It is therefore clear from the results of this study that calcification and photosynthesis are not as closely coupled as has been previously thought. In neither E. huxleyi, nor in the hermatypic corals, were photosynthetic and calcification rates saturated at the present ambient DIC concentration of seawater.

Photosynthesis is the unique biological process that converts carbon dioxide into organic compounds, for example sugars, using the energy of sunlight. Thereby solar energy is converted into chemical energy. Nearly all life depends on this reaction, either directly, or indirectly as the ultimate source of their food. Oxygenic photosynthesis occurs in plants, algae and cyanobacteria. This process created the present level of oxygen in the atmosphere, which allowed the formation of higher life, since respiration allows extracting up to 15-times more energy from organic matter than anaerobic fermentation. Oxygenic photosynthesis uses as substrate for the ubiquitous water. The light-induced oxidation of water to molecular oxygen (O2), catalyzed by the Mn4CaO5 cluster associated with the photosystem II (PS II) complex, is thus one of the most important and wide spread chemical processes occurring in the biosphere. Understanding the mechanism of water-oxidation by the Mn4CaO5 cluster is one of today’s great challenges in science. It is believed that one can extract basic principles of catalyst design from the natural system that than can be applied to artificial systems. Such systems can be used in the future for the generation of fuel from sunlight. In this thesis the light-induced production of molecular oxygen and carbon dioxide (CO2) by PSII was observed by membrane-inlet mass spectrometry. By analyzing this observation is shown that CO2 not only is the substrate in photosynthesis for the production of sugars, but that it also regulates the efficiency of the initial steps of the electron transport chain of oxygenic photosynthesis by acting, in form of HCO3-, as acceptor for protons produced during water-splitting. This finding concludes the 50-years old search for the function of CO2/HCO3− in photosynthetic water oxidation. For understanding the mechanism of water oxidation it is crucial to resolve the structures of all oxidation states, including transient once, of the Mn4CaO5 cluster. With this application in mind a new illumination setup was developed and characterized that allowed to bring the Mn4CaO5 cluster of PSII microcrystals into known oxidation states while they flow through a narrow capillary. The optimized illumination conditions were employed at the X-ray free electron laser at the Linac Coherent Light Source (LCLS) to obtain simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) at room temperature. This two methods probe the overall protein structure and the electronic structure of the Mn4CaO5 cluster, respectively. Data are presented from both the dark state (S1) and the first illuminated state (S2) of PS II. This approach opens new directions for studying structural changes during the catalytic cycle of the Mn4CaO5 cluster, and for resolving the mechanism of O-O bond formation. In two other projects the mechanism of molecular oxygen formation by artificial water oxidation catalysts containing inexpensive and abundant elements were studied. Oxygen evolution catalyzed by calcium manganese and manganese only oxides was studied in 18O-enriched water. It was concluded that molecular oxygen is formed by entirely different pathways depending on what chemical oxidant was used.  Only strong non-oxygen donating oxidants were found to support ‘true’ water-oxidation. For cobalt oxides a study was designed to understand the mechanistic details of how the O-O bond forms. The data demonstrate that O-O bond formation occurs by direct coupling between two terminal water-derived ligands. Moreover, by detailed theoretical modelling of the data the number of cobalt atoms per catalytic site was derived.

The Ross Sea, the southernmost sea on Earth, presents several iconic features of polar seas: sites of deep water formation, high summer primary production, floating ice shelves, the annual cycle of advance and retreat of sea ice, polynyas and katabatic winds. Furthermore, sea ice in McMurdo sound (western Ross Sea) is one of the most productive marine environments. However, sea ice inorganic carbon dynamics and related air-ice CO2 fluxes have never been documented in the Ross Sea.Two surveys were carried out in the western Ross Sea to bridge over a critical gap in the current understanding of sea ice: autumn and winter processes. The land-based YROSIAE project was a temporal survey from late winter to summer within landfast sea ice. The ship-based PIPERS project was an unique opportunity to study the early stages of sea ice formation (in polynyas) and more common consolidated pack ice in autumn. Based on these two consistent surveys, this work aims to (i) examine the bulk ice pCO2 dynamics in landfast sea ice from late winter to summer (ii) investigate the seasonal pattern (net source vs net sink) and diurnal pattern of air-ice CO2 fluxes (iii) analyse the depth-dependent physical and biogeochemical processes involved in inorganic carbon dynamics (iv) assess the precipitation of calcium carbonate in autumn and during a full bloom season.CO2 fluxes were measured using the chamber technique in autumn, late winter and spring, over open surface water, frazil ice patch, grey unconsolidated ice and consolidated first-year ice. These new autumn and winter data provide a first step to set up the budget of air-ice CO2 fluxes over the year and evaluate the large-scale influence of these fluxes on the annual uptake of CO2 by ice-covered oceans. Our results confirm that sea ice acts as a CO2 source for the atmosphere during ice growth, with enhanced fluxes reported at the early stages of sea ice formation, and shifts to a sink in spring. In late spring, diel pattern superimposed upon this seasonal pattern and was potentially assigned to either ice skin freeze-thaw cycles or diel changes in net community production. The snowpack plays a complex role in CO2 exchanges and can no longer be considered as an inert reservoir lying at the sea ice surface.The main features of the normalized DIC distribution (DIC35) through the ice column were: (i) a marked depletion at the surface from autumn to spring induced by the CO2 releases to the atmosphere (ii) bubble-driven gas enrichment below or within impermeable layers and (iii) an initial DIC35 enrichment in the bottom layer disappearing in spring when the seasonal peak in biomass occurs. At the bottom of landfast ice, in spring, a particular assemblage of microorganisms, the biofilm, led to a massive biomass build-up counterintuitively associated with nutrients accumulation. This biofilm formation may also promote calcium carbonate precipitation. However, in young pack ice or in cold landfast ice in early spring, limited calcium carbonate precipitation was reported. This suggests that calcium carbonate precipitation is not an ubiquitous process, especially in winter and autumn Antarctic sea ice. Comparison of calcium carbonate precipitation and pCO2 measurements advocates that the calcium carbonate precipitation is rather controlled by pCO2 than temperature. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

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Diffuse reflectance spectroscopy (DRS) is a rapid proximal-sensing method that is being used more and more in laboratory settings to measure soil properties. Diffuse reflectance spectroscopy research that has been completed in laboratories shows promising results, but very little has been reported on how DRS will work in a field setting on soils scanned in situ. Seventy-two soil cores were obtained from six fields in Erath and Comanche County, Texas. Each soil core was scanned with a visible near-infrared (VNIR) spectrometer with a spectral range of 350-2500 nm in four different combinations of moisture content and pre-treatment: field-moist in situ, air-dried in situ, field-moist smeared in situ, and air-dried ground. Water potential was measured for the field-moist in situ scans. The VNIR spectra were used to predict total and fine clay content, water potential, organic C, and inorganic C of the soil using partial least squares (PLS) regression. The PLS model was validated with data 30% of the original soil cores that were randomly selected and not used in the calibration model. The root mean squared deviation (RMSD) of the air-dry ground samples were within the in situ RMSD and comparable to literature values for each soil property. The validation data set had a total clay content root mean squared deviation (RMSD) of 61 g kg-1 and 41 g kg-1 for the field-moist and air-dried in situ cores, respectively. The organic C validation data set had a RMSD of 5.8 g kg-1 and 4.6 g kg-1 for the field-moist and air-dried in situ cores, respectively. The RMSD values for inorganic C were 10.1 g kg-1 and 8.3 g kg-1 for the field moist and air-dried in situ scans, respectively. Smearing the samples increased the uncertainty of the predictions for clay content, organic C, and inorganic C. Water potential did not improve model predictions, nor did it correlate with the VNIR spectra; r2-values were below 0.31. These results show that DRS is an acceptable technique to measure selected soil properties in-situ at varying water contents and from different parent materials.

Diffuse reflectance spectroscopy (DRS) is a rapid proximal-sensing method that is being used more and more in laboratory settings to measure soil properties. Diffuse reflectance spectroscopy research that has been completed in laboratories shows promising results, but very little has been reported on how DRS will work in a field setting on soils scanned in situ. Seventy-two soil cores were obtained from six fields in Erath and Comanche County, Texas. Each soil core was scanned with a visible near-infrared (VNIR) spectrometer with a spectral range of 350-2500 nm in four different combinations of moisture content and pre-treatment: field-moist in situ, air-dried in situ, field-moist smeared in situ, and air-dried ground. Water potential was measured for the field-moist in situ scans. The VNIR spectra were used to predict total and fine clay content, water potential, organic C, and inorganic C of the soil using partial least squares (PLS) regression. The PLS model was validated with data 30% of the original soil cores that were randomly selected and not used in the calibration model. The root mean squared deviation (RMSD) of the air-dry ground samples were within the in situ RMSD and comparable to literature values for each soil property. The validation data set had a total clay content root mean squared deviation (RMSD) of 61 g kg-1 and 41 g kg-1 for the field-moist and air-dried in situ cores, respectively. The organic C validation data set had a RMSD of 5.8 g kg-1 and 4.6 g kg-1 for the field-moist and air-dried in situ cores, respectively. The RMSD values for inorganic C were 10.1 g kg-1 and 8.3 g kg-1 for the field moist and air-dried in situ scans, respectively. Smearing the samples increased the uncertainty of the predictions for clay content, organic C, and inorganic C. Water potential did not improve model predictions, nor did it correlate with the VNIR spectra; r2-values were below 0.31. These results show that DRS is an acceptable technique to measure selected soil properties in-situ at varying water contents and from different parent materials.

In this MSc thesis I determine if wind-generated bubbles elevated measurements of above-water normalized water-leaving radiance (nLw) and subsequent remote sensing estimates of particulate inorganic carbon (PIC) in a coccolithophore bloom on the Patagonian Shelf. Although no measurements were made of bubbles, shipboard wind speed was used as a proxy for bubble backscattering. An empirical orthogonal function (EOF) analysis was performed on nLw. The first EOF accounted for 95% of the variance, and was attributed to changes in spectral amplitude. Scores of the first EOF were positively correlated with flow-through PIC backscattering (bb′) > 5x10-4 m-1, indicating that above this threshold PIC was an optically active seawater constituent. There was only evidence for a bubble elevation of nLw at values of bb′ < 5x10-4 m-1 and wind speeds > 12.5 m s-1. There was no evidence for a bubble elevation of PIC estimated using the two-band PIC algorithm.

The northern margin of South China Sea contains several favorable areas for occurrence of gas hydrate. In this study, we collected pore water samples in two piston cores (X-01 and D-01) from Xisha Trough and Dongsha area, respectively, and the concentrations of sulfate and carbon isotopic compositions of dissolved inorganic carbon (DIC) were measured. The results showed different geochemical characteristics in these two sites. The X-01 core shows relatively constant δ13C-DIC values and sulfate concentrations, which suggest that anaerobic methane oxidation (AMO) processes did not occur in this site. In contrast, very large variation in δ13C-DIC values and sulfate concentrations are revealed in D-01 core, and good linear correlations for sulfate gradients and δ13C-DIC values are observed. The calculated sulfate-methane interface (SMI) depth is 9.6 mbsf. These data indicate that an AMO process occurred in sediments with large methane flux from depth in the Dongsha area, which are comparable to other gas hydrate locations in the world oceans such as the Blake Ridge. We suggest that the Dongsha area is one of the most favorable targets for future gas hydrate exploration.

Much research has been devoted to understanding the ocean carbon cycle because of its prominent role in controlling global climate. Coastal oceans remain a source of uncertainty in global ocean carbon budgets due to their individual characteristics and their high spatial and temporal variability. Recent attempts to establish general patterns suggest that temperate and high-latitude coastal oceans act as sinks for atmospheric carbon dioxide (CO2). In this thesis, carbon cycling in two Canadian coastal ocean regions is investigated, and the uptake of atmospheric CO2 is quantified. A combination of ship-board measurements and highly temporally resolved data from an autonomous mooring was used to quantify the seasonal to multi-annual variability in the inorganic carbon system in the Scotian Shelf region of the northwestern Atlantic for the first time. The Scotian Shelf, unlike other shelf seas at similar latitude, acts as a source of CO2 to the atmosphere, with fluxes varying over two orders of magnitude in space and time between 1999 and 2008. The first observations of the inorganic carbon system in the Amundsen Gulf region of the southern Beaufort Sea, covering the full annual cycle, are also presented. Air-sea CO2 fluxes are computed and a carbon budget is balanced. The Amundsen Gulf system acts as a moderate sink for atmospheric CO2; seasonal ice-cover limits winter CO2 uptake despite the continued undersaturation of the surface waters. Biological production precedes the ice break-up, and the growth of under-ice algae constitutes nearly 40% of the annual net community production. The Scotian Shelf may be described as an estuarine system with an outflow of surface water, and intrusion of carbon-rich subsurface water by a combination of wind-driven mixing, upwelling and convection, which fuels the CO2 release to the atmosphere. In contrast, Amundsen Gulf may be described as an anti-estuarine, or downwelling, system, with an inflow of surface waters and an outflow of subsurface waters. Wind-driven and convective mixing are inhibited by ice-cover and restrict the intrusion of carbon- and nutrient-rich waters from below, maintaining the CO2 uptake by the surface waters. / PhD Thesis