The applications of calcium-isotope measurements in marine carbonates are explored in several different contexts within this thesis. As a record of global ion fluxes, seawater calcium-isotope ratios can be used as tracers for large weathering imbalances, which develop as a feedback system in response to intervals of climate change. This approach provides valuable constraints on the complex climatic and oceanographic phenomena known as the Oceanic Anoxic Events. Over much longer timescales, the calcium-isotope ratio of seawater is influenced by steady-state processes that reflect the evolution of seawater chemistry. To understand these influences, the modern calcium-isotope budget is assessed quantitatively using a compilation of marine carbonate samples, revealing several distinctive components of the carbonate burial sink that can affect the steady-state balance of the calcium cycle. Changes in the major ion composition of seawater and in the organisms that contribute to sedimentary carbonate burial are shown to contribute significantly to the geological record of seawater calcium-isotope ratios. The importance of skeletal carbonate in the calcium cycle leads to another application of calcium isotopes towards understanding biomineralization. This large and complex topic is approached with calcium-isotope data from two unique growth experiments that constrain some of the mechanisms by which biogenic aragonite acquires its geochemical signatures. This range of topics presents a diverse, but by no means exclusive, sample of the topics that are accessible for investigation through calcium-isotope analysis. The potential of this isotopic tool is demonstrated by the breadth of environments and timescales represented in this work.

A remoção de nitrogênio via processos biológicos de nitrificação e desnitrificação foi estudada utilizando-se um reator operado em bateladas seqüenciais submetido a períodos aeróbios e anóxicos. Metano foi adicionado como doador de elétrons na etapa desnitrificante nos períodos anóxicos. Foram testadas diferentes condições operacionais e nutricionais com o objetivo de se alcançar a melhor eficiência de remoção de nitrogênio. Quando o reator operou com elevadas concentrações de biomassa em suspensão (6 g/L), a oxidação completa do nitrogênio amoniacal foi alcançada sob períodos aeróbios de 6 e 3 horas e anóxicos de 16,5 e 4 horas adotados nas etapas 1 e 2, respectivamente. Porém, a desnitrificação foi principalmente associada com o uso de subprodutos metabólicos no lugar do metano. De forma a diminuir o consumo de material endógeno, a biomassa foi imobilizada em material suporte (espuma de poliuretano) e os períodos aeróbios e anóxicos foram diminuídos para 3 horas cada (etapa 3) e posteriormente, 0,5 h e 1,5 h (etapa 4). Nesta última etapa, as maiores eficiências de remoção de nitrogênio, (~35%) foram verificadas somente nos primeiros dias de operação. O processo de desnitrificação utilizando metano como doador de elétrons também foi estudado sob condições anóxicas tendo nitrato e, posteriormente, nitrito como fontes de nitrogênio oxidadas. Nesses experimentos, as eficiências de remoção de nitrogênio foram de 75% e 90%, porém foram obtidos baixos valores de constantes cinéticas aparentes de primeira ordem, \'K IND.NO3\' = 0,007/h e \'K IND.NO2\' = 0,0278/h, respectivamente, para ambos os aceptores de elétrons. Os resultados obtidos a partir de ensaios de número mais provável (NMP) para a quantificação dos organismos metanotróficos resultaram em 5,1 x \'10 POT.3\' (etapa 3, biomassa em suspensão) e 3,5 x \'10 POT.7\' NMP/g sólidos totais voláteis (etapa 4, biomassa aderida). Portanto, a presença de meio suporte para a adesão de biomassa aliado aos ciclos de aeração mais freqüentes favoreceram o crescimento dessas bactérias. Sulfato e cloreto, nas concentrações de, aproximadamente, 100 mg/L, afetaram a eficiência de remoção de nitrogênio quando associado ao processo metanotrófico. Os resultados das análises de biologia molecular revelaram a presença de organismos metanotróficos semelhantes a Methylomonas sp. tanto em amostras de biomassa retiradas do reator quando este operou sob condições desnitrificantes na presença de oxigênio, como também, naquelas retiradas quando o reator operou em condições anóxicas. / Nitrogen removal via biological nitrification and denitrification was studied in a sequencing batch reactor submitted to aerate and anoxic periods. Methane was added as electron donor for denitrification in the anoxic periods. Different operational and nutritional conditions referred to as stages in this text were tested aiming to achieve the best nitrogen removal efficiency. When the reactor operated with high suspended biomass concentration (6 g/L), complete ammonia nitrogen oxidation was obtained in 6 to 3 hours aerobic periods and 16.5 to 4 hours anoxic periods defined for stage 1 and stage 2, respectively. However, denitrification was mainly associated with the use of endogenous metabolic byproducts instead of methane. In order to diminish endogenous material uptake, the biomass was immobilized in support material (polyurethane foam) and aerobic and anaerobic periods were reduced to 3 hours each (stage 3), followed by another reduction to 0.5 and 1.5 hours, respectively (stage 4). The highest nitrogen removal efficiencies (~35 %) were identified in this last stage, but only during the initial days of operation. The denitrification process using methane as electron donor was also studied under anoxic conditions, separately from nitrification by adding nitrate and nitrite as the oxidized nitrogen sources. In these experiments, nitrogen removal efficiencies were of 75% and 90%, but very low first order kinetic constants \'K IND.NO3\' = 0,007/h e \'K IND.NO2\' = 0,0278/h, respectively, were obtained with both the electron acceptors. The most provable number (MPN) tests carried out for methanotrophic bacteria quantification resulted in 5,1 x \'10 POT.3\' MPN/gVSS (stage 3 - suspended biomass) and 3,5 x \'10 POT.7\' MPN/gVSS (stage 4 - attached biomass). Therefore, the presence of a support media for biomass adhesion as well as more frequent aeration cycles enhanced the growth of such bacteria. Sulfate and chloride at concentrations of 100 mg/L, approximately, affected the nitrogen removal efficiency associated to methanotrofic process. The presence of methanotrops identified by molecular biology tests as Methylomonas sp was observed in samples taken from reactor in presence of oxygen and under anoxic operational conditions.

Fire is a natural process that has existed on our planet for more than ~350 million years, and is a process that continues to influence our everyday lives. On Earth, a relationship exists between the process of combustion and the natural functioning of the Earth system. Here, the process of combustion has been implicated in playing an essential role for life on Earth, where natural Earth system processes have been shown to influence ignition probability, fire spread and fire behaviour, and where fire can provide a variety of feedbacks, to the Earth system over different timescales. Over medium timescales of decades to hundreds of thousands of years, the likelihood and behaviour of fires are controlled by regional climate changes and vegetation type, whilst the occurrence of fire can play a crucial role in influencing biome persistence and development. Over long timescales (hundreds of thousands to multi-million year), the components influencing the probability of fire and fire behaviour not only involve processes occurring over local and regional spatial scales, and over short and medium timescales, but also long term processes occurring globally, such as changes in atmospheric oxygen concentration and the evolution of vegetation. Across these timescales in Earth’s past, combustion has been shown to impact global ecosystems, climate and the carbon cycle by generating feedbacks that influence Earth’s biogeochemical cycles. However, it is clear that our understanding of the role that fire plays in the Earth system, although improving is still developing. This thesis provides an analysis of these Earth system - fire relationships and feedbacks across medium and long timescales in deep time, in order to understand the role that fire may have played and what the record of fire can tell us about the functioning and re-equilibrating of the Earth system during and after significant carbon-cycle perturbation events occurring in Earth’s deep past. The results presented in this thesis contribute what is believed to be the first fossil evidence that rising atmospheric oxygen and fire feedbacks may have aided in the termination of a significant carbon-cycle perturbation event, termed the ‘Toarcian oceanic anoxic event’ that occurred ~183 million years ago during the Jurassic period, and the return of the Earth system towards ‘background functioning’. This thesis also provides an analysis of the record of wildfire in the form of fossil charcoal across the initiation of an anoxic event that occurred ~93 million years ago, during the Cretaceous period. The results illustrate that CO2 - climate driven changes in wildfire activity can be observed across medium timescales even during times of significant carbon-cycle perturbations, and modelled high atmospheric oxygen concentrations. These results illustrate how hypothesized changes in the hydrological cycle, and likely moisture content of fuel, appear to be the dominant control on wildfire activity during this period. Finally, this thesis provides an analysis of charcoal abundance variations occurring across natural, orbitally forced cycles, termed the Milankovitch cycles. The results presented illustrate that natural variations in charcoal abundance are possible over intermediate timescales within the geological record. This thesis therefore illustrates a need to take into consideration and incorporate ‘natural background’ fluctuations in fire activity occurring over medium timescales, when analysing and predicting past and future climate change patterns.

The biodiversity of two distinct marine environments was observed to describe the biogeocomplexity of these extreme ecological systems. A shallow-water hydrothermal vent in Papua New Guinea served as a study of a thermophilic ecosystem influenced by arsenic rich vent fluids while a 60 m deep offshore primarily anoxic karst sink served as a study of an anaerobic sulfur-influenced habitat. Both environments support unique biological communities that are influenced by the physical and chemical pressures imposed on them by the harsh conditions of these systems. In Tutum Bay, Ambitle Isle, Papua New Guinea, a transect was created from a shallow hydrothermal vent that extended 120 m away from the vent. Previous studies have shown that the geochemistry of the system is heavily influenced by arsenic which is toxic to most organisms. In this study, macro- and meiofauna were collected and scored and combined with bacterial sequence data collected along the length of the transect. It was found that near vent sites harbored biological communities more similar than sites further from the vent. Many species were found only at sites near the hydrothermal vent. Near-vent communities were less diverse than those away from the vent, and biodiversity generally increased as distance from the vent increased. Distinct correlations between thermophilic organisms and temperature were observed. The metabolic repertoire of the microbial communities suggests that many strategies are used to obtain energy and carbon. The relative abundance of bacteria containing genes to reduce arsenic was comparable to those able to reduce sulfur compounds. Primary production appeared to be a mix of chemo- and phototrophy. Food webs and association analysis suggest a complex interplay between macrofaunal, meiofaunal and bacterial communities. While the system is heavily influenced by arsenic, no specific correlation between the relative abundance of arsenic metabolizing organisms and the amount of arsenic in the system could be drawn. This is likely due to the fact that most of the arsenic produced by the system is readily adsorbed onto iron oxyhydroxides, reducing the arsenic's bioavailability. The anoxic conditions at Jewfish sink provide a different hurdle than the hot arsenic conditions found in Papua New Guinea. The anoxic conditions are shared by other pit features found in karst geography, but the metabolic processes between Jewfish sink and these other karst habitats are different. The blue holes and black holes of the Bahamas are some of the most well-studied of these karstic pits. In these features, which are large circular pits with diameters of over 300 m, light and sulfur are used as a means of energy acquisition. Jewfish sink, having an opening only 6 m in diameter, is light restricted compared to these systems. As a result, the strategy of organisms dwelling in the anoxic conditions of the sink is different than those found at the well-studied holes in the Bahamas. Geochemical measurements were recorded over two time periods spanning a combined total of 6 years. The anoxic bottom waters of Jewfish sink remain stable and contained high levels of sulfide throughout most of the seasons studies. Sequence analysis of prokaryotes within the sink showed that sulfur reducers had the highest relative abundance compared to other functional guilds. To monitor the changes of the microbial communities within the sink, bacterial communities were examined at 4 depths within the sink at 9 different intervals over a period of 685 days. Denaturing Gradient Gel Electrophoresis (DGGE) was used to fingerprint 16s rRNA bacterial communities and dissimilatory sulfite reducing communities by targeting the 16s rRNA bacterial gene and the dsr gene associated with dissimilatory sulfite reducing bacteria and archaea. The lowest depth studied within the sink (40 m) remained stable chemically and biologically until a turnover event occurred within the second winter of the study. This turnover event disrupted the biological communities at 40 m and led to a reestablished community comprised of different species that those found prior to the event. Upper waters within the sink show that clines establish themselves seasonally and partition zones that confine bacterial communities that are more similar to each other within these zones while excluding bacterial communities that are outside of these zones. Oxygenated water was shown to not contain prokaryotes containing the dsr gene. As the oxycline changed seasonally, dissimilatory sulfite reducing prokaryotes containing the dsr gene remained in the anoxic zone and required time to reestablish themselves whenever oxygenated water displaced them.

<p>Inorganic chlorine (Clinorg) is generally considered to be inert and has been used as a tracer for groundwater movements. This assumption is thereby fundamental for current knowledge about soil biogeochemistry. However, recent work showed that Clinorg can be retained, i.e. immobilised, in soil, which contradicts the previous assumptions. The aim of this laboratory study was to investigate if the processes that immobilise Clinorg in soil are affected by molecular oxygen (O2), and if the immobilisation occurs in the top soil layer only or also further down were the soil structure is different from the upper soil layer. Two experimental set-ups have been established. In the first experiment regarding the O2 regime (OXANIS), the immobilisation of Clinorg was studied in soil under oxic and anoxic conditions, respectively. In a second incubation study (SOLIS) the immobilisation was studied under oxic conditions in different layers of a coniferous forest soil. To investigate the immobilisation of Clinorg, a method using radiolabelled chloride 36 (36Clinorg) was applied. The use of radiolabelled chloride is an excellent and reliable method for studying transformation processes in soil systems. The results of the laboratory study showed that Clinorg retention rates under oxic conditions were much higher than retention rates under anoxic conditions, indicating an important role of O2. Furthermore, the immobilisation of Clinorg occurred in all soil layers were oxygen is provided, but rates were highest in the top soil layer (organic layer, O-horizon). Clearly, O2 influenced the net Clinorg retention, but additional studies are required to identify the processes behind this result. The calculated immobilisation rates for Clinorg in the three soil horizons correspond to the amount of organic material detected in the different soil horizons indicating a strong connection between the occurrence of organic matter in soil and the immobilisation of Clinorg.</p>

Inorganic chlorine (Clinorg) is generally considered to be inert and has been used as a tracer for groundwater movements. This assumption is thereby fundamental for current knowledge about soil biogeochemistry. However, recent work showed that Clinorg can be retained, i.e. immobilised, in soil, which contradicts the previous assumptions. The aim of this laboratory study was to investigate if the processes that immobilise Clinorg in soil are affected by molecular oxygen (O2), and if the immobilisation occurs in the top soil layer only or also further down were the soil structure is different from the upper soil layer. Two experimental set-ups have been established. In the first experiment regarding the O2 regime (OXANIS), the immobilisation of Clinorg was studied in soil under oxic and anoxic conditions, respectively. In a second incubation study (SOLIS) the immobilisation was studied under oxic conditions in different layers of a coniferous forest soil. To investigate the immobilisation of Clinorg, a method using radiolabelled chloride 36 (36Clinorg) was applied. The use of radiolabelled chloride is an excellent and reliable method for studying transformation processes in soil systems. The results of the laboratory study showed that Clinorg retention rates under oxic conditions were much higher than retention rates under anoxic conditions, indicating an important role of O2. Furthermore, the immobilisation of Clinorg occurred in all soil layers were oxygen is provided, but rates were highest in the top soil layer (organic layer, O-horizon). Clearly, O2 influenced the net Clinorg retention, but additional studies are required to identify the processes behind this result. The calculated immobilisation rates for Clinorg in the three soil horizons correspond to the amount of organic material detected in the different soil horizons indicating a strong connection between the occurrence of organic matter in soil and the immobilisation of Clinorg.

This study explored the effects of seasonal variability on the geochemistry of sinking pthesiss and on the nitrogen cycle of the Cariaco Basin. Pthesis fluxes were measured at the base of the euphotic zone (the depth of 1% of photosynthetically active radiation - PAR) with drifting sediment traps during months of upwelling and non-upwelling regimes from March 2007 to November 2009. Flux estimates were analyzed in the context of seasonal variations in sea surface temperature, primary productivity, and chlorophyll a concentrations using data generated by the CARIACO Time-series Program as well as satellite data. Additionally, nine years (1996-2000 and 2004-2007) of nutrients, phytoplankton taxonomy and δ15N of sinking pthesis data within the twilight zone (225 m) from the CARIACO Time-series Program were examined. Results showed that the flux of organic matter responded to changes in surface chlorophyll a but not to primary production. Sinking organic matter decreased by an order of magnitude from the base of the euphotic zone to the oxic-anoxic interface; most of the organic matter produced in surface waters was remineralized before leaving the upper 50-100 m. Lithogenic material often represented a large fraction of the flux. Isotopic analyses showed that 13C/12C ratios of sinking organic carbon were enriched (~-19‰) during the upwelling period and depleted during relaxation (~-23‰). This reflects seasonal changes in inorganic carbon utilization by phytoplankton and suggests that the δ13C of organic carbon in Cariaco sediments can be used as a proxy for carbon fixation by primary producers. The δ15N of the settling flux was influenced by the strength of the upwelling and the presence of the nitrogen fixer Trichodesmium thiebautii in the basin in different seasons; the 15N/14N ratio of sinking nitrogen reflects both imported and local nitrogen fixation signals. This result argues against previous interpretations of the δ15N from the basin's sedimentary record, which suggested that the nitrogen isotopic composition of flux is influenced by denitrification at the oxic-anoxic interface. Dissolved gas samples from the Cariaco eastern and western sub-basins from September 2008 (non-upwelling) and March 2009 (upwelling) were studied to assess the production of biogenic nitrogen gas through mass spectrometric N2/Ar ratiometry. Excess nitrogen gas indicated that upwelling affects the intensity of denitrification at the oxic-anoxic interface. In four of the six stations the concentration of biogenic nitrogen gas at the oxic-anoxic interface was 2.7-6.1 µM N higher during the upwelling period than during the relaxation season (p< 0.001), implying that denitrification in the basin was stimulated by the vertical flux of organic matter and/or the ventilation of the oxic-anoxic interface by oxygenated and nutrient-rich intermediate Caribbean waters.

In natural waters, high concentrations of ammonia are toxic to fish, and the oxidation of ammonia to nitrate (NO₃-) consumes large quantities of dissolved oxygen. The influent to municipal wastewater treatment plants in the United States typically contains approximately 40 mg/L of ammonia nitrogen (NH₃₋ N). Almost all of this ammonia must be removed in a wastewater treatment process before the effluent is discharged to the natural environment. This dramatic decrease is accomplished by the aerobic biological process of nitrification, in which ammonia is oxidized to nitrate Biological denitrification is an anoxic biological process in which nitrate (NO₃-) is reduced to nitrogen gas (N₂). Denitrification can increase the alkalinity in activated sludge aeration basins and decrease the concentration of filamentous organisms. The staff at the City of Austin Water Utility decided to implement a denitrification system at Walnut Creek Wastewater Treatment Plant to control filamentous organisms and increase the alkalinity within the aeration basins. The denitrification configuration that the staff implemented was unconventional because no structural changes were made to the aeration basins to encourage denitrification. However, the system functioned well and allowed operators to turn off one of the two air blowers, which saves the plant a significant amount of energy. The current operation has occasional problems, where the alkalinity in the aeration basin decreases or the effluent ammonia increases. When the alkalinity decreases to the point where the pH drops to near 6.0, operators are forced to add chemicals to increase the alkalinity. When the effluent ammonia increases to near the permitted concentration (2.0 mg NH₃-N/L),operators are forced to turn back on the second blower which eliminates the anoxic zone. These problems occur most often during the winter, when the wastewater is the coldest. The wastewater temperature at Walnut Creek varies from a high of 30°C during the summer to a low of 18°C during the winter. The goal of this research was the identification of ways to make the operation more robust which would prevent the need for chemical addition and minimize the use of the second blower. Laboratory-scale reactors were operated to assess possible improvements that could be made to the operation and configuration of the denitrification system at Walnut Creek. The data observed in the laboratory scale experiments showed that the population of denitrifying bacteria limits denitrification and is especially important during the winter. Increasing the solids retention time to 20 days appeared to be the best way to increase the population of denitrifying bacteria and improve denitrification. Improvements can also be made by increasing the volume of the anoxic zone. Increasing the volume of wastewater and biomass recycled will most likely not benefit denitrification until other improvements have been made. Recommendations to the City of Austin Water Utility include the following: 1) increase the solids retention time at Walnut Creek, 2) Increase the volume of the anoxic zone, 3) Separate the anoxic zone from the aerobic section of each aeration basin, 4) During the winter, operate the flow equalization basins to reduce the dissolved oxygen entering the anoxic zone, 5) Continually mix some of the effluent from the aeration basins with the primary effluent in the flow equalization basins. / text

Carbon/phosphorus ratios for late Devonian-early Mississippian marine black shales along a transect from the Illinois Basin, across the Cumberland Saddle, and into the Appalachian Basin were evaluated to assess the role of productivity in organic carbon accumulation. Phosphorus is a key limiting nutrient for biological productivity in marine environments and may be regenerated preferentially relative to organic carbon, the amount of regeneration possibly being related to bottom-water anoxia. A positive feed-back mechanism (more specifically, productivity-anoxia feedback or PAF) has been proposed between water-column anoxia, high benthic regeneration of phosphorus, and marine productivity. This regeneration of phosphorus under anoxic conditions and overturn of surface waters has been proposed as an explanation for enhanced organic matter accumulation in the Appalachian Devonian Basin. The Cumberland Saddle is a structurally low segment of the Cincinnati Arch that lies at the crest of the arch between the Jessamine and Nashville domes that connects the Illinois and Appalachian basins. C/P data for two cores in the Illinois Basin, four cores across the Cumberland Saddle, and two cores in the Appalachian Basin are discussed in light of the productivity-anoxia feedback model.

A biological front at the mouth of Saanich Inlet results in higher rates of primary productivity at the inlet mouth relative to the head creating a gradient that could influence zooplankton distribution. A shallow sill (75m) at the inlet mouth restricts circulation below sill depth, isolating the deep basin for much of the year. Anoxia develops in the isolated basin and the depth of the anoxic layer changes during the year. During the day, pelagic zooplankton form a deep scattering layer. Between April 2005 and March 2006. I conducted monthly 200kHz acoustic surveys between the mouth and head of Saanich Inlet to test the hypothesis that zooplankton density was greater near the mouth relative to the head. I was also interested in how changing anoxic layer depth affected the distribution of the deep scattering layer. I found that zooplankton density followed a headward gradient in the spring and summer. with the highest densities near the mouth. Zooplankton density was higher near the mouth or the mid-inlet relative to the head in 75% of transects. I did not observe a zooplankton density gradient during the winter. Zooplankton distribution was affected by dissolved oxygen concentration. Deep scattering layer depth was significantly correlated with the depth of the anoxic layer and vertical compression of the deep scattering layer increased as the anoxic layer moved upwards. When the depth of the anoxic layer was less than 90 meters. zooplankton were nearly absent. Vertical migration of the deep scattering layer to surface waters at night has been well documented. but zooplankton migration patterns in the shallow waters of Saanich Inlet have not been described. I used 200kHz acoustic data collected by the VENUS observatory (96m) and an autonomous acoustic system deployed at a shallow site (62m) in Patricia Bay to study zooplankton migration patterns. Horizontal movement of the deep scattering layer over shallow depths following vertical migration was infrequent. Over 41 days of observation at the shallow site. I only observed deep scattering layer zooplankton on 12 days. At the shallow site. night-time volume backscatter was dominated by the emergence of benthic zooplankton. The movement of these scatterers into the water column at night resulted in a 14-fold increase in volume backscatter over daytime values. I observed this emergence pattern at both sites. which represents an important component of benthic-pelagic coupling in Saanich Inlet. In contrast to the deer scattering layer. which migrated to the surface each night, emergent zooplankton remained within 30-40 meters of the seafloor and did not ascend into surface waters.