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Coral reefs are important to sustain marine ecosystems and provide a reliable resource for studying past climate. Corals are increasingly challenged by changing environments. The marginal corals of Hong Kong provide a natural laboratory to study the combination of environmental conditions controlling coral distribution and growth. Salinity and pH were found to impact corals in studies of coral distribution, extension, and culture. Hong Kong corals have low extension rates (1.2-11.4 mm/yr) and do not colonize in areas of low in salinity and pH. Ten years of instrumental records showed extension related positively to summer salinity and dissolved oxygen. Winter seawater temperature was inversely related to extension, while chlorophyll a showed positive relationship in autumn and winter. Culture results show low salinity negatively impacted coral calcification, photosynthesis, and extension. Corals exhibited reduced growth, paling and bleached. In contrast, coral growth increased under high pCO2, but corals decalcified in dark indicating underlying mechanisms may be altering coral physiology. The boron isotope (δ11B) proxy in corals is able to reconstruct past seawater pH when the pH of the extracellular calcifying fluid (ECF) is considered. A pH offset (ΔpH) was recorded in reconstructed pHsw due to ion pumping to ensure the ECF is saturated with respect to aragonite. By incorporating carbon isotopes (δ13C) into the δ11B-ΔpH relationship, δ11B can be corrected to remove ECF processes and reconstruct seawater pH. Culture results indicated δ11Baxial from axial tip recorded pH similar to other studies while low salinity impacted δ11Bbasal at the base. The different relationship shown from the same colony within the same cultured conditions suggested vital effects with differing coral metabolisms. δ11Baxial and δ11Bbasal related to extension but insignificantly. The large isotopic offset between δ11Baxial and δ11Bbasal indicated different growth mechanisms could possibly affected boron incorporation. The δ11B variation within a coral colony suggested careful and precise sampling for pH reconstructions is important. / published_or_final_version / Earth Sciences / Doctoral / Doctor of Philosophy

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In the eutrophic waters of the Indian River Lagoon (IRL), decreases in overall shellfish size have been reported, which may be related to coastal acidification. To understand the relationship between acidification and eutrophication, water samples from 20 sites spanning the IRL were collected and analyzed for dissolved nutrients and omega values in spring (dry season) and fall (wet season), 2016-2017. Additionally, three sites were sampled weekly to observe temporal variability of nutrients and omega values. For the IRL-Wide sampling, sites with higher dissolved nutrient concentrations showed lower omega values with significant negative relationships. Both sampling programs showed an overall positive linear relationship between salinity and omega values. This work suggests that salinity and dissolved nutrients have implications for acidification in the IRL and must be considered for future water quality, shellfish and coral reef restoration. / Includes bibliography. / Thesis (M.F.A.)--Florida Atlantic University, 2018. / FAU Electronic Theses and Dissertations Collection

Le groupe des agrumes d’acidité intermédiaire (orange, clémentine et mandarine) perd l’acidité au cours de la maturation (stade III), mais cette chute semble plus forte depuis quelques années dans la zone méditerranéenne. Il a été suggéré que cette perte d’acidité serait liée au climat (automnes plus doux) ce qui entraînerait une augmentation de la respiration des fruits avec une photopériode plus courte à cette période et se traduirait par un déséquilibre carboné. Pour tester cette hypothèse, nous avons choisi d’étudier l’effet d’un déséquilibre carboné, induit par une défoliation partielle, soit en début soit en fin de stade II, qui est la phase de grossissement cellulaire où les sucres et les acides organiques s’accumulent dans la vacuole des cellules des sacs à jus. Nous avons établi un bilan sucres-acides des fruits soumis aux différentes réductions d’apport carboné et identifié la ou les périodes où la réduction de l’apport carboné a le plus d’impact sur les teneurs en sucres et en acides organique. Puis, nous avons regardé l’impact de ce déséquilibre sur le métabolisme du fruit en étudiant l’activité spécifique d’enzyme spécifiques (phosphofructokinase, invertase acide, phosphoénolpyruvate carboxylase, isocitrate déshydrogénase cytoplasmique) et l’expression de gènes d’intérêts (CsCit1, succinate semialdéhyde déshydrogénase, Δ1-pyrroline-5-carboxylate synthétase) et identifié les mécanismes biochimiques impliqués dans la réponse à la limitation des apports carbonés.Les résultats obtenus montrent que les fruits ne sont pas capables de compenser la réduction des apports carbonés (poids et calibre) que la réduction foliaire soit précoce ou plus tardive au cours du stade II. Lorsque la réduction foliaire est précoce et à court terme (48h et une semaine), l’apport carboné n’est pas affecté puisque les teneurs en saccharose sont similaires à celles du témoin. Nous avons observé une augmentation de l’activité enzymatique de la PFK qui est envisageable grâce au déstockage de la vacuole par l’action de l’invertase acide. La PEPC permet la synthèse d’oxaloacétate et maintient la production d’acide citrique, qui sera dégradé dans le cytoplasme par la NADP-IDH en α-cétoglutarate qui va donner du glutamate et du GABA. La voie du GABA « shunt » semble favorisée puisque l’expression du gène codant pour la SSADH est augmentée. A long terme (7 semaines), l’apport carboné a été affecté puisque les teneurs en saccharose ont fortement diminué par rapport au témoin. Il y a un déstockage de l’acide citrique de la vacuole par CsCit1 mais pas d’activation de la voie du GABA shunt ce qui est compatible avec l’hypothèse que cette voie serait activée par un stress. Lorsque la cellule est en phase d’accumulation des acides organiques, elle privilégie la synthèse d’acide citrique. En revanche, lorsque la réduction foliaire est tardive, les teneurs en sucres sont fortement affectées 48h après la réduction, le flux glycolytique est ralenti et il ne semble pas y avoir un déstockage de la vacuole. Les teneurs en acide malique et en acide malique chutent également mais l’activité de la PEPC est augmentée pour favoriser la synthèse d’acide citrique. Nous avons observé une formation importante de proline qui provient du glutamate. Comme nous n’avons pas observé, 48h après la réduction foliaire, une augmentation des niveaux de transcrits de la P5CS, la voie de l’ornithine serait impliquée. Il serait intéressant de confirmer ou non l’hypothèse de la formation de ROS lors des deux réductions foliaires ce qui nous permettrait de savoir si la voie du GABA « shunt » lors de la réduction foliaire précoce ou bien la formation de proline lors de la réduction foliaire tardive sont fortement sollicitées afin de lutter contre le stress oxydatif provenant de la réduction des apports carbonés. / The intermediate acidity group of citrus (orange, clementine and mandarin) loses acidity during maturation (stage III). But this decrease seems to get stronger since several years in the mediterranean basin. It has been suggested that the wider loss of this acidity could be linked to climate (warmer autumns) which would increase fruit respiration at the time when photoperiod is short inducing a carbon imbalance. To check this hypothesis, we chose to study the effect of a carbon imbalance induced by partial defoliation, either at the beginning or at the end of stage II, which is the phase of cell enlargement where sugars and organic acids accumulate in the juice cells bags vacuole. We have established a sugar-acid balance of fruit submitted to different carbon reductions and identified the period or periods for which the reduction of the carbon input had the greatest impact on sugars and organic acids contents. Then, we watched the impact of this imbalance on fruit metabolism studying specific enzyme activity (phosphofructokinase, acid invertase, phosphoenolpyruvate carboxylase, cytoplasmic isocitrate dehydrogenase) and genes of interest expression (CsCit1, succinate semialdehyde dehydrogenase genes Δ1-pyrroline-5-carboxylate synthetase). We also identified the biochemical mechanisms involved in the response to the carbon inputs limitation.The obtained the results showed that fruits are not able to offset the limitation of carbon inputs (weight and size) whether the leaf reduction is early or late during stage II. When the leaf reduction is early, for a short-term (48 hours and one week), the carbon contribution is not affected since sucrose contents are similar to those of the control. We observed an increase in PFK enzymatic activity of which is suitable through the destocking of the vacuole due to the action of acid invertase. PEPC allows oxaloacetate synthesis and maintains citric acid production, which will be degraded in the cytoplasm by the NADP-HDI in α-ketoglutarate which will give glutamate and GABA. The GABA "shunt" response seems to be promoted since the expression of the gene encoding the SSADH is increasing. In long-term (7 weeks), the carbon contribution was affected since sucrose contents decreased significantly compared to control fruit. Citric acid is destocked from the vacuole by CsCit1 but no activation of the GABA shunt occurs which is consistent with the hypothesis that this pathway would be activated by stress. Thus, when the cell is in the process of organic acids accumulation, it seems the synthesis of citric acid. In return, when the leaf reduction is late, the sugar contents are strongly affected 48h after reduction, the glycolytic flux is slow and it does not seem to have remobilization of sugars from vacuole. The contents of malic acid and citric acid also fall but PEPC activity is increased to promote the synthesis of citric acid. A significant formation of proline from glutamate is observed. Since we did not observe, 48 hours after foliar reduction, an increase in P5CS transcript levels, ornithine pathway could be involved. It would be interesting to confirm or not the hypothesis of ROS inducing in both foliar reductions in order to see if the GABA "shunt" for early leaf reduction or the proline formation for late leaf reduction are heavily involved in oxidative stress response that might be induce by carbon inputs limitation.

The end-Permian extinction at 252 Ma is widely regarded as the most severe of the Phanerozoic mass-extinctions and enabled the evolution of the modern carbon cycle and ecosystem structure. The cause of the extinction is still debated but the synergistic pressures of global climate change, such as anoxia and ocean acidification, were clearly important. The extinction occurred in two phases and is marked by a uniquely protracted recovery period of ~ 5 Myrs where diversity fails to reach pre-extinction levels until the Middle Triassic. This period is characterized by an unstable global carbon cycle, secondary extinctions, reef, chert and coal gaps, and changes in the carbonate factory from reef to microbial and abiotic dominated deposition. This thesis focuses on using geochemical data from the Arabian Margin to investigate the carbon cycle record and the links between kill mechanisms and carbon cycle dynamics. A new record of carbon cycling is presented for the Tethys in the form of a carbon isotope record for the entire Early Triassic from the Musandam Peninsula, United Arab Emirates (UAE). The Musandam carbon isotope record can be broadly correlated with global isotopic events but also resolves additional secondary excursions. These new short-lived events are probably related to the occurrence of the more widely recognized Early Triassic excursions, and may represent fluctuations in the driving mechanisms superimposed on the continued instability of the global carbon cycle in the aftermath of the end-Permian extinction. To unravel palaeo-depositional redox conditions this work utilizes geochemical proxies based on Fe systematics (Fe-speciation). To date, however, these proxies have only been calibrated in relation to modern and ancient siliciclastic marine sediments. This clearly limits the use of the Fe-speciation proxy, particularly in relation to carbonate-rich sediments and rocks. This thesis explores the use of Fe-speciation in carbonates using compiled literature and new data from modern oxic and anoxic settings. This new assessment expands the utility of Fe-based redox proxies to also incorporate carbonate-rich rocks that contain significant total Fe (>0.5 wt%), providing care is taken to assess possible impacts of diagenetic processes such as dolomitization. Based on this calibration work Fe-speciation is used to reconstruct the redox structure for the Arabian Margin mixed carbonate and clastic sediments, from the late Permian to the Middle Triassic. Fe-S-C systematics are utilized to identify the spatial and temporal dynamics of anoxia for a Neo-Tethyan shelf-to-basin transect. The unique spatial resolution afforded by this transect allows a direct link to be drawn between biodiversity, carbon cycling and anoxic events. For the first time we can directly observe a switch from deep-ocean dominated anoxia to a dynamic anoxic wedge at the end-Permian extinction. Additionally the data suggest that ferruginous conditions (anoxic non-sulphidic) were dominant in the Tethyan Ocean throughout the Early Triassic, proposing that euxinia was restricted regionally with potential implications for nutrient recycling, carbon cycle models and driving mechanisms. Redox dynamics may have had important implications for the wider carbonate cycle. These two themes are particularly inter-related with regards to oceanic alkalinity and pH. This thesis presents the first shallow water boron isotope record for the Permian Triasssic Boundary, used as a proxy for pH. The record demonstrates some unexpected results; firstly a sudden increase in pH is observed, prior to the first phase of the extinction and interpreted to reflect alkalinity supply from the development of slope anoxia. Secondly there is no evidence for an acidification event at the first phase of the extinction where pH remains stable. A rapid acidification event is, however, seen in the earliest Triassic, contemporary to the second phase of the mass extinction, but delayed compared to the main negative carbon isotope excursion that indicates the main phase of Siberian Trap volcanism. These events may be explained by dramatic changes in ocean the ocean’s buffering capacity linked to changes in alkalinity supply and the carbonate factory.

Marine phytoplankton is responsible for ~50% of global primary productivity, it supports the oceanic food web and affects biogeochemical cycles. I participated in a large mesocosm experiment that observed altered community structure and carbon drawdown in response to increased CO2. There was a 27% reduction in community primary production at the peak of an Emiliania huxleyi-dominated bloom in mesocosms initially at 760 ppm CO2 compared to present day pCO2. There were changes in community structure but not dominance; Synechococcus and large pico-eukaryote abundances were reduced by ~60%, E. huxleyi was reduced by ~50%. A number of E. huxleyi strains persisted throughout the experiment in both treatments and no malformation or significant change in lith size occurred at increased CO2. In a second field experiment in the oligotrophic ocean off the Canary Islands, 760 ppm pCO2 did not change community structure or cell division rates of Synechococcus, Prochlorococcus or pico-eukaryotes.In laboratory experiments, I maintained the diatom, Thalassiosira pseudonana CCMP1335 at 760 ppm and present day pCO2 for ~100 generations in gas equilibrated continuous cultures – one of the longest experiments that has been attempted to investigate the effect of increased CO2 on marine phytoplankton. No clear evidence of adaptation or acclimation to increased CO2 was found, neither were there consistent changes in transcription of RuBisCO or carbonic anhydrase genes. Non-calcified E. huxleyi CCMP1516 and calcified CCMP371 grown in gas equilibrated semi-continuous cultures for several weeks showed no change in cell division rate at 760 ppm CO2. An understanding of the underlying changes in communities is required for modelling responses to increasing CO2, molecular tools may prove useful for this task. The strong community response in the mesocosms shows that rising atmospheric CO2 can greatly affect phytoplankton productivity and biogeochemical cycling.

Aluminium (Al) has been recognised as a main toxic factor alongside pH in acidified water ecosystems. The toxic effect of Al has been attributed to inorganic Al (Ali), though there are few in situ studies in ambient humic waters which are the focus of this thesis. The aim was to estimate Ali toxicity and thus also Ali concentrations in Swedish humic streams. Subsequently it is necessary to analyse Ali correctly, which was studied by modelling and method intercalibrations. The hypothesis was that the effect of Ali could be followed via physiological effects and Al accumulation, as well as by mortality. Toxicity was studied by in stream exposures of brown trout (Salmo trutta L.) and two salmonid prey organisms (Gammarus pulex and Baetis rhodani) during spring flood. The modelling of the Ali fraction was performed using monitoring data covering all of Sweden with satisfactory results. The essential variables for Ali modelling were determined; Al, DOC, pH and F, while Fe, Ca and Mg had less effect. The automated analytical procedure for Ali (with cation exchange followed by complexation with pyrocatechol violet) was modified and validated and showed to be the preferred method for laboratory analyses. To avoid detrimental effects for brown trout Ali should be <20 µg/L and pH >5.0; mortality was high when the Ali was above 50 µg/L. The invertebrates were more sensitive, as mortalities occurred at pH <6.0 and Ali >15 µg/L for G. pulex, and at pH <5.7 and Ali >20 µg/L for B. rhodani. It is prudent to use a wide view and let the most sensitive species set the tolerance limits; a pH above 5.7-6.0 and Ali below 15-20 µg/L allows the stream ecosystems to thrive. Today, as waters are recovering from acidification, the aim of mitigating liming is to carefully adjust dosage to avoid suboptimal water quality. The thresholds found in this thesis can be used to efficiently but carefully decrease liming, as both Ali and pH levels have to be balanced to sustain the recovering aquatic biota.

Phagocytosis is an innate immune response that is paramount in the clearance of pathogenic particles. Recognition of target particles by phagocytic receptors expressed on phagocytes induces modifications in the underlying actin cytoskeleton to form pseudopods that encircle and internalize the target particle into a membrane bound organelle called the phagosome. The nascent phagosome undergoes a maturation sequence that is characterized by substantial remodeling of the membrane and its luminal contents through interactions with components of the endocytic pathway, culminating in an acidic and hydrolytic organelle capable of digesting and elminating pathogens. Phagosome maturation is a complicated pathway that involves many protein and lipid signaling molecules. Several factors that influence phagosome maturation particularly the participation of pH, lysosome-associated membrane proteins-1 and –2, cholesterol, in addition to the survival and escape mechanisms used by, Burkholderica cenocepacia were explored. All three tenets are essential for phagosome maturation, although each factor has different mechanistic consequences. Acidification alters Rab5 activation, while ablation of LAMPs and accumulation of cholesterol interferes with various aspects of Rab 7 turnover in phagosomes and/or endosome membranes. Moreover, Burkholderia cenocepacia, an intracellular pathogen, inactivates Rab7 on phagosome membranes from within the vacuole lumen. Herein, mechanisms that govern phagosome maturation are explored and several molecules are added to the long list of essential players in this complicated pathway.

Phagocytosis is an innate immune response that is paramount in the clearance of pathogenic particles. Recognition of target particles by phagocytic receptors expressed on phagocytes induces modifications in the underlying actin cytoskeleton to form pseudopods that encircle and internalize the target particle into a membrane bound organelle called the phagosome. The nascent phagosome undergoes a maturation sequence that is characterized by substantial remodeling of the membrane and its luminal contents through interactions with components of the endocytic pathway, culminating in an acidic and hydrolytic organelle capable of digesting and elminating pathogens. Phagosome maturation is a complicated pathway that involves many protein and lipid signaling molecules. Several factors that influence phagosome maturation particularly the participation of pH, lysosome-associated membrane proteins-1 and –2, cholesterol, in addition to the survival and escape mechanisms used by, Burkholderica cenocepacia were explored. All three tenets are essential for phagosome maturation, although each factor has different mechanistic consequences. Acidification alters Rab5 activation, while ablation of LAMPs and accumulation of cholesterol interferes with various aspects of Rab 7 turnover in phagosomes and/or endosome membranes. Moreover, Burkholderia cenocepacia, an intracellular pathogen, inactivates Rab7 on phagosome membranes from within the vacuole lumen. Herein, mechanisms that govern phagosome maturation are explored and several molecules are added to the long list of essential players in this complicated pathway.