Dissertations / Theses on the topic 'Deep coal seam'

Lophelia pertusa is a cosmopolitan cold-water coral, often found in aphotic waters (>200m). Aggregations of L. pertusa (reefs) provide important habitat to many invertebrate and fish species and act as biodiversity hotspots in the deep sea. The health and diversity of these reefs is of vital importance to deep-sea ecosystems, and the microbial consortia associated with L. pertusa form the most basic ecological level. Deciphering the diversity and function of these microbes provides insight into the roles they play in maintaining reef health. This dissertation takes microbiological techniques that are used in shallow-water coral microbial research and applies them to L. pertusa. A flaw in a primer set, which is commonly used in the molecular genetics method Polymerase Chain Reaction (PCR) to obtain data on coral-associated microbes, is discussed and an alternative approach is presented. In addition, two culture-based studies are employed to catalogue diversity and explore functional differences in strains of both bacteria and fungi. The cultured bacteria were tested for resistance against six antibiotics that affect a variety of cellular targets to elucidate strain level differences. The first cultured fungi ever described from L. pertusa were identified by molecular techniques and assayed using Biolog plates to test their metabolic capabilities. Preliminary data analysis on metagenomic libraries of the microbial-size fraction of L. pertusa is presented and discussed in the context of microbial diversity and function, bridging the gap between culture-based work on function and culture-independent work on diversity.

Biology
Ph.D.
Deep-water or cold-water corals are abundant and highly diverse, greatly increase habitat heterogeneity and species richness, thereby forming one of the most significant ecosystems in the deep sea. Despite this remote location, they are not removed from the different anthropogenic disturbances that commonly impact their shallow-water counterparts. The global decrease in seawater pH due to increases in atmospheric CO2 are changing the chemical properties of the seawater, decreasing the concentration of carbonate ions that are important elements for different physiological and ecological processes. Predictive models forecast a shoaling of the carbonate saturation in the water column due to OA, and suggest that cold-water corals are at high risk, since large areas of suitable habitat will experience suboptimal conditions by the end of the century. The main objective of this study was to explore the fate of the deep-water coral community in time of environmental change. To better understand the impact of climate change this study focused in two of the most important elements of deep-sea coral habitat, the reef forming coral Lophelia pertusa and the octocoral community, particularly the gorgonian Callogorgia delta. By means of controlled experiments, I examined the effects of long- and short-term exposures to seawater simulating future scenarios of ocean acidification on calcification and feeding efficiency. Finally In order to understand how the environment influences the community assembly, and ultimately how species cope with particular ecological filters, I integrated different aspects of biology such functional diversity and ecology into a more evolutionary context in the face of changing environment. My results suggest that I) deep-water corals responds negatively to future OA by lowering the calcification rates, II) not all individuals respond in the same way to OA with high intra-specific variability providing a potential for adaptation in the long-term III) there is a disruption in the balance between accretion and dissolution that in the long term can shift from net accretion to net dissolution, and IV) there is an evolutionary implication for certain morphological features in the coral community that can give an advantage under stresfull conditions. Nevertheless, the suboptimal conditions that deep-water corals will experience by the end of the century could potentially threaten their persistence, with potentially negative consequences for the future stability of this already fragile ecosystem.
Temple University--Theses

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2012.
Cataloged from PDF version of thesis.
Includes bibliographical references.
Radioactive isotopes can be used in paleoceanography both for dating samples and as tracers of ocean processes. Here I use radiocarbon and uranium series isotopes to investigate the ocean's role in climate change over the last deglaciation. I present a new method for rapid radiocarbon analyses as a means of age-screening deep-sea corals for further study. Based on age survey results, I selected forty corals from the Drake Passage and thirteen from the Reykjanes Ridge off Iceland and dated them with uranium series isotopes. The uranium series dates give independent ages that allow radiocarbon to be used as a tracer of circulation and carbon cycle changes. The radiocarbon records generated from the Drake Passage corals show increased stratification in the Southern Ocean during the last glacial maximum (LGM) that disappeared during the start of the deglaciation as atmospheric CO2 began to rise during Heinrich Stadial 1 (HI). Considering these data and using a simple mass budget calculation, I show that the drop in atmospheric radiocarbon activity during H1 can be explained given direct carbon exchange between the radiocarbon-depleted deep ocean and atmosphere, e.g. through the Southern Ocean. The Drake Passage radiocarbon records also show evidence for decreased air-sea gas exchange in the Southern Ocean during the Antarctic Cold Reversal/Belling-Allered coincident with the hiatus in the deglacial CO2 rise. During this time period in the North Atlantic, radiocarbon reconstructions from deep-sea corals collected from off Iceland show a similar ventilation rate to that observed today and during the Holocene. To further investigate changes in North Atlantic ventilation over the last deglaciation, I used an inverse model to assess the consistency of sedimentary 2m1 Pa/ 230Th ratios from the Holocene, Hl, and the LGM with the modern circulation. Although sedimentary 231Pa/230Th has been used to infer changes in the strength of the meridional overturning circulation in the past, I find that published data are consistent with the modern circulation during the LGM and Hi. These findings highlight the importance of giving due regard to the uncertainties in the behavior and spatial distribution of paleoceanographic tracers.
by Andrea Burke.
Ph.D.

Coalbed methane (CBM) is basically naturally fractured, and the cleat network plays the main role in providing the fluid flow path, hence the permeability measure in CBM relies principally on the characteristics of this network. However, the permeability of the cleat network in coals is typically low. Moreover, fractures in coal seams might be partially to fully filled with minerals, a process called mineralization, as the result of which the permeability measure would decrease, sometimes leading to the total blockage of fractures. Therefore, to provide a promising cleat network permeability, reservoir stimulation is an important part in development of low permeability CBM to induce new fractures and demineralize the original cleat network. The current study, in general, focuses on two stimulation techniques aiming at enhancing the permeability and connectivity of coal cleat network, namely liquid nitrogen (LN2) fracturing, and acid stimulation. Several techniques and equipment were used to conduct this research, such as Micro Computed Tomography (μ-CT) scanning, medical CT scanning, Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), flooding set-ups, etc. Although LN2 fracturing has been studied previously, there are some gaps in the research in this field. The first matter to consider in LN2 fracturing is to investigate the mechanism of this technique in fracturing coals. Therefore, the research presented in the third chapter of the current study, examines and quantifies the pore structure and connectivity evolution of a bituminous coal frozen in LN2, based on the in-situ morphological analysis through μ-CT scanning. This helps us to investigate the associated in-situ fracturing mechanisms, and measure the extent of induced fractures and damage to the rock in 3D at micrometre-scale. The results of this study shows the considerable potential of LN2 freezing in coal cleat network permeability enhancement. The μ-CT results clearly demonstrate that the cleat network is boosted following the treatment, where thoroughgoing fractures with a maximum opening of 13 μm appear, some of which are rooted in the original cleat network. While this application increases the porosity measure of the bituminous coal by 11%, core flooding tests and Lattice Boltzmann simulations show over double increase in the coal’s permeability value after liquid nitrogen exposure. This noticeable permeability enhancement is not only due to generation of new fractures, but also is attributed to the connection establishment of the cleat network with originally isolated pores and micro-cleats following the freezing, thereby increasing pore network connectivity. Following conducting the above study, which revealed encouraging results in permeability and connectivity enhancement of the coal and illustrated the discovering mechanisms of LN2 fracturing approach, another research in this work focuses on examining the performance of this stimulation technique in different coal ranks. This research is presented in chapter 4 of the current study. This research thus is aimed at exploring the potential of this thermal shock in fracturing three main coal ranks, namely sub-bituminous, bituminous and anthracite. The 3D X-ray computed tomography results in μ-CT and macroscale (medical-CT) reveal a poor performance of LN2 fracturing in anthracite. On the contrary, the in-situ 3D visualization of the other two coal ranks suggests a promising fracturing performance. The porosity evolutions of bituminous and sub-bituminous coals through the treatment are 14% and 119% in microscale, respectively. Thus, this work suggests that LN2 fracturing approach may not be a reliable stimulation technique for high rank coals, although performs encouragingly in medium to low rank coals. In addition to the above studies on LN2 fracturing potential and mechanism as well as its performance in different coal ranks, another research completed in this study focuses on the potential of several cycles of LN2 freezing/unfreezing, a process called freeze-thaw, which is presented in chapter 5 of the current study. This research is aimed at comparing the performance of this fracturing technique in one freezing cycle with up to three freeze-thaw cycles, and quantifies the efficiency of each cycle in cleat network evolution. μ-CT images revealed a promising efficiency in cleat network evolution after three freezing cycles, where the number of pores increased by 50% (92715 142650), and the number of interconnected pores almost doubled (42060 78905). SEM along with μ-CT images highlight more encouraging efficiency of second and third freezing cycles, particularly in terms of enhancing fractures interconnection. Mechanical properties analysis reveals more significant damage in the coal in the latter freezing cycles, where the indentation modulus was initially 3.49 GPa and decreased to 2.81, 2.11 and 1.52 GPa through three freezing cycles. Finally, the permeability of the coal under 1000 kPa confining pressure increased from 0.035 mD to 0.18 mD, with larger increments in later cycles. Therefore, this research highlights the superiority of LN2 freeze-thaw cycling over single freezing of coals with LN2 through conducting a quantitative comparison on the efficiency of each freezing cycle. In addition to LN2 fracturing technique, this study works on acid stimulation of coals, and evaluates the potential of a combination of these two recovery enhancement approaches in coal’s permeability evolution, the results of which is presented in the form of a research article in chapter 6. This work suggests that a combination of these two techniques have a considerable potential for recovery enhancement in coals. In case where acidizing is performed first, in addition to the permeability enhancement because of cleat demineralization, a more promising LN2 fracturing application is expected, because the coal’s strength decreases following acidizing, and the coal is more prone to freezing. In the other sequence of applications, where LN2 freezing is accomplished first, not only the cleat network is extended and boosted due to the fracturing application, but also the following acidizing process benefits because of a better accessibility of the acid to remote mineralised fractures. The findings in the above research articles show how a coalbed methane could be treated to provide an enhanced cleat network, where fluid flow is facilitated, and the coalbed methane is extracted. Such coalbed methane reserve would be depleted from gas at this stage. Generally, underground reservoirs might have a potential for gas storage following depletion from gas/oil. This could be beneficial from environmental aspect, for example unwanted gases such as carbon dioxide could be injected into these reservoirs. Additionally, in the recent years, depleted underground reservoirs have attracted the attention of energy sector as a possible storage site for generated hydrogen, as it is not a safe practice to store massive amount of this gas in surface reservoirs. Indeed, hydrogen has become a significant topic recently due to its dramatic potential as an energy carrier as well as environmental friendliness, while its storage is a challenge, thus the viability of storing this gas into a depleted coal seam was investigated in this study. In this application, coal permeability is a key parameter which determines how fast H2 can be injected and withdrawn again. However, it is expected to observe coal swelling when subjected to several gases, as a result of which coal permeability reduces significantly. Therefore, chapter 7 presents a research article, in which H2 gas is injected into a coal core and dynamic permeability is measured, while imaging the core via x-ray micro-tomography at reservoir conditions. Importantly, no changes in coal cleat morphology or permeability were observed in this study. This research thus suggests that H2 geo-storage in deep coal seams is feasible from a fundamental petro-physical perspective.

Coral habitats span the range from tropical to polar, extremely shallow to thousands of meters deep. The differences in light and temperature experienced in these varied habitats likely affect the metabolic rates of the corals residing there. The metabolism of three coral species from different habitats have been examined to elucidate the effects of these environmental parameters on metabolism, an under-studied aspect of coral biology. For all three species, measurements of oxygen uptake, ammonium excretion, and activity of the enzymes lactate dehydrogenase (LDH), malate dehydrogenase (MDH), and citrate synthase (CS) were used to characterize their metabolism. Off Florida's Gulf coast, Cladocora arbuscula is known to be one of the species least damaged by bleaching events and is one of the quickest to recover, making it an ideal candidate for studying the effects of symbionts. The first set of experiments was designed to reveal the effect of disrupting the coral-algal symbiosis between this subtropical shallow-water coral and its dinoflagellate symbiont, Symbiodinium. The metabolic effects were described for "normal" C. arbuscula and those "bleached" by being held in total darkness for 4 months. Normal C. arbuscula had a relatively low rate of oxygen consumption at 21°C, averaging 2.43±0.65 µmol O2 gwm-1 h-1 (±S.E.), using tissue wet mass, while the bleached colonies had an average rate of 2.46±0.49 µmol O2 gwm-1 h-1. Ammonium excretion averaged 0.07±0.02 and 0.10±0.03 µmol NH4+ gwm-1 h-1 (±S.E.) for normal and bleached C. arbuscula, respectively. The activity values of the metabolic enzymes citrate synthase (CS) fell within the normal range expected for a cnidarian, averaging around 0.09±0.02 activity units (U) gwm-1 for both treatments, indicating normal aerobic ability. MDH was extremely high for the normal corals, compared to other cnidarians, averaging 2.5±0.4 U gwm-1, and a bit lower for the bleached corals, averaging 1.2±0.3 U gwm-1, indicating high MDH activity during both normoxia and hypoxia. LDH activity, also high, averaged 1.3±0.2 U gwm-1 for both treatments, indicating anaerobic competence. These experiments show that C. arbuscula is adept at maintaining almost completely normal metabolic function when bleached, although the corals quickly become re-inoculated with symbionts upon return to normal light conditions in a tank with normal corals. The second set of experiments served to characterize the metabolism of Lophelia pertusa, an azooxanthellate cold-water coral that thrives in water depths between 36 and 3383 m. L. pertusa is rather stenothermal, commonly found between 6-8°C, but in the Gulf of Mexico can be subjected to warm water incursions. This makes it an ideal candidate for the examination of the effects of temperature. L. pertusa exhibited a respiration rate of 1.14 µmol O2 gwm-1 h-1 at the control temperature of 8°C. Calculating the Q10 for bringing L. pertusa up to the environmental temperature of C. arbuscula results in a value of 1.8. The 11°C treatment group exhibited an 11% increase in respiration, while at 13°C, the corals showed a 23% rise from normal. The 5°C group showed a 32% decrease in respiration. The activity values of the metabolic enzyme citrate synthase (CS) fell into the normal range expected for a cnidarian, averaging 0.15, 0.20, 0.10, and 0.18 activity units (U) gwm-1 for the 8°C, 11°C, 13°C, and 5°C treatments, respectively. Malate dehydrogenase (MDH) values were unexpectedly high, averaging 2.05, 1.48, 1.48, and 1.82U gwm-1 for the 8°C, 11°C, 13°C, and 5°C treatments, respectively. Lactate dehydrogenase (LDH) was undetectable in this species, suggesting it has a different terminal glycolytic enzyme. Nonetheless, the other two enzymes indicate metabolic competence in both normoxic and hypoxic conditions. L. pertusa is adaptable to temperatures within its range, although its respiration rate is lower than that of tropical corals. The third set of experiments characterized the metabolism of the endemic Antarctic coral Flabellum impensum, one of the world's largest solitary corals. It resides at roughly the same depths as L. pertusa, but the water temperature in its habitat never strays far from 0°C. F. impensum had a low rate of oxygen consumption at 0°C, averaging 0.31 µmol O2 g-1 h-1, calculated using tissue wet mass. Calculating a Q10 for this species at C. arbuscula's habitat temperature results in a value of 2.7. Ammonium excretion averaged 4.21 nmol NH4+ gwm-1 h-1. The activity values of the metabolic enzymes citrate synthase (CS), malate dehydrogenase (MDH), and lactate dehydrogenase (LDH) fell within the normal range expected for a cnidarian, averaging 0.13, 1.01, and 0.42 activity units (U) gwm-1, respectively. A count of the skeletal growth bands on the calyx suggests that this species has a linear extension rate of approximately 1 mm per year. F. impensum is a long-lived, slow-growing coral, with a low metabolic rate.

Biology
Ph.D.
Cold-water corals act as critical foundation species in the deep sea by creating extensive three-dimensional habitat structures that support biodiversity hotspots. There is currently a paucity of data concerning the environmental requirements and physiology of cold-water corals, severely limiting our ability to predict how resilient they will be to future environmental change. Cold-water corals are expected to be particularly vulnerable to the effects of ocean acidification, the reduction in seawater pH and associated changes to the carbonate system caused by anthropogenic CO2 emissions. Here, the ecological niche and physiology of the cold-water coral Lophelia pertusa is explored to predict its sensitivity to ocean acidification. Species distribution models were generated in order to quantify L. pertusa’s niche in the Gulf of Mexico with regard to parameters including seafloor topography, the carbonate system, and the availability of hard substrate. A robust oceanographic assessment of the Gulf of Mexico was conducted in order to characterize the current environmental conditions at benthic sites, with a focus on establishing the baseline carbonate system in L. pertusa habitats. Finally, an experimental approach was used to test the physiological response of biogeographically separated L. pertusa populations from the Gulf of Mexico and the Norwegian coast to ocean acidification. Based on my findings, it appears that L. pertusa already persists near the edge of its viable niche space in some locations, and therefore may be highly vulnerable to environmental change. However, experimental results suggest that some populations may be surprisingly resilient to ocean acidification, yielding broad implications for the continued persistence of cold-water corals in future oceans.
Temple University--Theses

This thesis reveals atypical dynamic reservoir behaviour within Cooper Basin ultra-deep coal seams during gas production that calls for a paradigm shift in gas extraction technology, diametrically opposed to the evolutionary path of current drilling, wellbore completion, and reservoir stimulation practices. An anomalous geomechanical reservoir boundary condition is detected that is, by definition, mostly restricted to ultra-deep coal seams. The discovery has resulted in the formulation of a new coal seam reservoir concept - “Expanding Reservoir Boundary Theory”. Ultra-deep Permian coal seams of the Cooper Basin in central Australia represent a nascent thermogenic source rock reservoir play. Proof-of-concept gas flow occurred in 2007. The vast (100+ Tscf) potential resource is comparable in commercial significance, and technical challenge, to the shale gas plays of North America. As with shale, full-cycle, standalone commercial gas production from Cooper Basin ultra-deep coal seams requires a large, complex, permeable “stimulated reservoir volume” (SRV) domain having high fracture / fabric face surface area for gas desorption. This goal has not yet been achieved after 13 years of trials because, owing to the bipolar combination of coal-like geomechanical properties and shale-like reservoir properties, these poorly cleated, inertinitic coal seams exhibit “hybrid” characteristics. This is problematic for achieving effective reservoir stimulation, and poses the greatest immediate challenge. Stimulation techniques adopted from other play types are incompatible with the highly unfavourable combination of nanoDarcy-scale permeability, “ductility”, and high stress. The Cooper Basin Deep Coal Gas (CBDCG) Play commences 6,000 feet (1,830 metres) below the “commercial permeability depth limit” for most shallow coal seam gas (CSG) reservoirs but this does not reduce gas flow potential. Shale gas industry technologies have, in principle, eliminated the requirement for naturally occurring coal fabric permeability. Optimum reservoir conditions occur at depths beyond 9,000 feet (2,740 metres), driven by very low water saturation, high gas content, gas oversaturation, overpressure, rigid host rock strata, and high deviatoric stress. The limited literature does not yet adequately characterise the physical response of ultra-deep coal seams, and the surrounding host rock strata, to production pressure drawdown. It remains to be established how artificial fracture and coal fabric aperture width change as a consequence of the dynamic, diametric competition between gas desorption-induced coal matrix shrinkage and the omnipresent tendency for reservoir compaction caused by increasing production pressure drawdown-induced effective stress. This technical impasse, inhibiting commercialisation, is addressed by analysing the atypical flowback behaviour of hydraulically fracture stimulated coal seams within a dedicated vertical wellbore at 9,500 feet (2,900 metres). High-resolution, non-classical flowback analysis is performed on the pure dataset of Australia’s first ultra-deep coal gas well. Wellhead and fracture network pressures are recorded continuously for 8 1/2 years, at a 10-minute sample interval, while flowing to atmosphere. Natural flowback behaviour is analogous to that of a mechanical gas plunger artificial lift system. A low but gradually increasing quasi-steady state base gas flow, free of produced formation water, is overprinted by a non-steady state, cyclical pressure signature that is diagnostic of dynamic reservoir behaviour during gas production. A total of 114 high-rate, “geyser-like” gas surge events, gradually increasing in duration from 2 hours to 2 weeks, and in reservoir equivalent volume from 360 to 20,000 rcf (10 to 570 rcm), suggest the gas headspace compartment of a “down-hole void space domain” is steadily increasing in size. The gas surge events result from intermittent release of fracture network gas, hydrostatically compressed by flowback fluid slowly accumulating within the wellbore. A production “history match” for the gas surge event pressure profile is obtained by designing, fabricating, operating, and data logging a computer-controlled hydraulic apparatus within The University of Adelaide’s experimental wellbore, at a depth of 230 feet (70 metres). This physically simulates open-ended flowing manometer-like hydrodynamic behaviour of the wellbore-reservoir system. A postulated geological trigger mechanism for surge initiation is tested and validated; “wellbore hydrostatic back-pressure and reservoir stress-dependent leak-off”. Time-lapse pressure transient analysis (PTA) is performed on three extended wellbore pressure build-up tests, lasting 157, 259, and 295 days respectively. Increasing permeability is recognised within coal fabric surrounding the initial fracture network SRV domain. Time-lapse rate transient analysis (RTA) performed on the first two subsequent wellbore pressure “blow-down to atmosphere” (BDTA) gas flow rate decline profiles indicates that hydraulic fracture flow conductivity increased during the intervening 327-day flowback period. Interpreted dilation of hydraulic fracture apertures is supported by a 60% increase in the initial BDTA gas flow rates, from 7.5 to 12.0 MMscfd (212.4 to 340.0 Mscmd). Cooper Basin ultra-deep coal gas reservoirs behave differently to other deep, thermogenic source rock reservoirs, and require a paradigm shift in reservoir stimulation technology that does not rely exclusively upon hydraulic fracture stimulation and the “brittleness factor”. Pressure arching may fill this role by neutralising the omnipresent tendency for reservoir compaction caused by increasing production pressure drawdown-induced effective stress. The combined, mutually sustaining actions of desorption-induced coal matrix shrinkage and sympathetic pressure arch “stress shield” evolution generate an “expanding reservoir boundary and decreasing confining stress” condition that allows producing ultra-deep coal seams, and adjacent strata indirectly (which may include other reservoir types), to progressively de-stress and “self-fracture” in an overall state of endogenous tensile failure. As with underground coal mine excavations, pressure arching will deflect maximum stress vectors around the dilating “dispersed coal fabric void space” domain of a growing fracture network SRV domain that has developed reduced bulk structural integrity, and reduced bulk compressive strength, compared to the surrounding native coal seam and host rock strata. Size and effectiveness of pressure arching increases with depth. Cooper Basin ultra-deep coal seams, and adjacent “non-coal” reservoirs indirectly, may be effectively stimulated to flow gas on a large scale by harnessing this self-perpetuating, depth-resistant mechanism for creating coal fracture / fabric permeability and surface area for gas desorption. They may be induced to pervasively “shatter”, or “self-fracture”, naturally during gas production, independent of the lack of “brittleness”, analogous to the manner in which shrinkage crack networks slowly form, in a state of intrinsic, endogenous tension, within desiccating clay-rich surface sediment. Full-cycle, standalone commercial gas production is considered likely to occur when “Expanding Reservoir Boundary Theory” is applied, so as to replicate the very large, complex fracture network SRV domain of commercial shale gas reservoirs.
Thesis (Ph.D.) -- University of Adelaide, Australian School of Petroleum, 2020

Deep water corals are an understudied yet biologically important and fragile ecosystem under threat from recent increasing temperatures and high carbon dioxide emissions. Using 454 sequencing, we develop 14 new microsatellite markers for the deep water coral Eguchipsammia fistula, collected from the Red Sea but found in deep water coral ecosystems globally. We tested these microsatellite primers on 26 samples of this coral collected from a single population. Results show that these corals are highly clonal within this population stemming from a high level of asexual reproduction. Mitochondrial studies back up microsatellite findings of high levels of genetic similarity. CO1, ND1 and ATP6 mitochondrial sequences of E. fistula and 11 other coral species were used to build phylogenetic trees which grouped E. fistula with shallow water coral Porites rather than deep sea L. Petusa.

We generated records of radiocarbon and trace metals in deep-sea corals to investigate the role of the deep ocean during episodes of rapid environmental change. Our record of radiocarbon ages measured in a modern deep-sea coral from the northeastern Atlantic shows the transfer of bomb radiocarbon from the atmosphere to the deep ocean. We detect bomb radiocarbon at the coral growth site starting in 1975–1979. Our record documents a Delta14C increase from –80 ± 1‰ (average 1930–1979) to a plateau at –39 ± 2‰ (average 1994–2001). From a suite of fossil deep-sea corals, variability in North Atlantic intermediate water Delta14C during the Younger Dryas (13.0–11.5 ka) supports a link between abrupt climate change and intermediate ocean circulation. We observe rapid shifts in deep-sea Delta14C that require the repositioning of large Delta14C gradients within the North Atlantic. The shifts are consistent with changes in the rate of North Atlantic Deep Water formation. We also observe a decadal scale event at 12.0 ka that is marked by the transient return of radiocarbon to the eastern and western basins of the North Atlantic. To develop a nutrient proxy for use in deep-sea corals, we measured Cd/Ca in 14 modern corals. Several of these corals had anomalously high Cd/Ca that we explain with a systematic bias in Cd/Ca obscuring the signal of seawater Cd/Ca. When these high Cd/Ca corals are removed from the calibration, the best-fit coral-water partition coefficient is 1.3 ± 0.1. Examining Cd/Ca in fossil deep-sea corals, we find that our coral from the Younger Dryas (12.0 ka) resembles the high Cd/Ca corals of the modern calibration and probably does not reflect seawater Cd/Ca. The Cd/Ca record from a 15.4 ka coral resembles our low Cd/Ca calibration samples and probably reflects average seawater Cd/Ca.

Deep-sea corals have long been regarded as cold-water coral; however a reevaluation of their habitat limitations has been suggested after the discovery of deep-sea coral in the Red Sea where temperatures exceed 20˚C. To gain further insight into the biology of deep-sea corals at these temperatures, the work in this PhD employed a holotranscriptomic approach, looking at coral animal host and bacterial symbiont gene expression in Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus sp. sampled from the deep Red Sea. Bacterial community composition was analyzed via amplicon-based 16S surveys and cultured bacterial strains were subjected to bioprospecting in order to gauge the pharmaceutical potential of coralassociated microbes. Coral host transcriptome data suggest that coral can employ mitochondrial hypometabolism, anaerobic glycolysis, and surface cilia to enhance mass transport rates to manage the low oxygen and highly oligotrophic Red Sea waters. In the microbial community associated with these corals, ribokinases and retron-type reverse transcriptases are abundantly expressed. In its first application to deep-sea coral associated microbial communities, 16S-based next-generation sequencing found that a single operational taxonomic unit can comprise the majority of sequence reads and that a large number of low abundance populations are present, which cannot be visualized with first generation sequencing. Bioactivity testing of selected bacterial isolates was surveyed over 100 cytological parameters with high content screening, covering several major organelles and key proteins involved in a variety of signaling cascades. Some of these cytological profiles were similar to those of several reference pharmacologically active compounds, which suggest that the bacteria isolates produce compounds with similar mechanisms of action as the reference compounds. The sum of this work offers several mechanisms by which Red Sea deep-sea corals cope with environmental conditions in which no other deep-sea corals have yet to be reported. These deep-sea coral are associated with rich microbial communities, which produce molecules that induce bioactivity. The aggregate of this work provides direction for future research of Red Sea deep-sea coral and highlights the potential pharmacological benefit of conserving these species and their unique ecosystem.

Glacial-interglacial cycles, occurring at a period of approximately 100,000 years, have dominated Earth's climate over the past 800,000 years. These cycles involve major changes in land ice, global sea level, ocean circulation, and the carbon cycle. While it is generally agreed that the ultimate driver of global climate is changes in insolation, glacial cycles do not look like insolation forcing. Notably, there is a highly non-linear warming response at 100,000 years to a relatively small forcing, implicating a more complicated system of biogeochemical and physical drivers. The ocean plays a pivotal role in glacial-interglacial climate through direct equator-to-pole transport of heat and its role in the carbon cycle. The deep ocean contains 60 times more carbon than the atmosphere, and therefore even small changes in ocean circulation can have a large impact on atmospheric CO₂, a crucial amplifier in the climate system. In order to better understand the role that ocean circulation plays in glacial-interglacial climate we focus on the last glacial-interglacial transition. In this thesis, we present reconstructions of changes in intermediate water circulation and explore a new time-dependent dynamical box model. We reconstruct circulation using radiocarbon and clumped isotope measurements on U/Th dated deep-sea corals from the New England and Corner Rise Seamounts in the western basin of the North Atlantic and from south of Tasmania in the Indo-Pacific sector of the Southern Ocean. Our new time-dependent model contains key aspects of ocean physics, including Southern Ocean Residual Mean theory, and allows us to explore dynamical mechanisms which drive abrupt climate transitions during the last glacial period.

In Chapter 2 we present a compilation of reconnaissance dated deep-sea corals from the Caltech collection. Reconnaissance dating facilitates sample selection for our high-precision radiocarbon and temperature time series and patterns in the depth distribution of deep-sea corals over time contain additional relevant climate information. In Chapter 3, we present a high-resolution radiocarbon record from south of Tasmania which highlights variability in Southern Ocean Intermediate Water radiocarbon during the deglaciation, particularly during the Antarctic Cold Reversal. We use our radiocarbon data, in combination with other deglacial climate records, to infer changes in overturning circulation configuration across this time interval. In Chapter 4 we present our time-dependent dynamical box model. Our model displays hysteresis in basin stratification and Southern Ocean isopycnal outcrop position as a function of North Atlantic Deep Water formation rate. In a dynamical system, hysteresis implies that there are multiple stable states, and switches between these states can lead to abrupt transitions, such as those observed during the middle of the last glacial period. In Chapter 5 we present paired radiocarbon and temperature time series from the North Atlantic and Southern Ocean spanning the late part of the last glacial. We explore the mechanisms driving trends in radiocarbon and temperature by looking at cross-plots of the data, and we make inferences about changes in circulation configuration using insight gained from our dynamical box model.

The research presented here uses deep-sea bamboo corals (Family Isididae) to reconstruct ecosystem dynamics in southeast Australian waters over the past 50-100 years. The work is divided into two complimentary research themes: methodological considerations and case studies that apply amino acid compound specific isotope analysis (AA-CSIA) to specimens from three regions: the subtropical Lord Howe Rise, and temperate to subantarctic Tasmanian waters. These case studies test the central thesis that Australian marine ecosystems are sensitive to documented oceanographic change. First, improvements to the graphite preparation for radiocarbon analysis are presented. These improvements minimized sampling requirements and enabled routine analysis of less than 100 micrograms of carbon. Optimized protocols reduced sample requirements from 2.5 milligrams to 100 micrograms of coral protein, significantly improving the resolving power of the reconstructions. To improve the spatial resolution of the study, it was necessary to test for artefacts of preservation method from different coral collections. Preservation method had no effect on the composition of radiocarbon, AA stable carbon and nitrogen isotopes or elemental ratios in either the organic or carbonate fractions. However, minimal alteration to organic bulk carbon isotopes, and a significant offset in carbonate lattice Ba:Ca after storage in ethanol were observed. The differing distribution of AA between coral families has significant implications for how deep-sea coral isotope proxies are applied to decipher paleoclimate. Multivariate analyses demonstrated first, the need to consider tissue-specific fractionation before applying pre-existing trophodynamic parameters to coral protein, and second, that the carbon and nitrogen isotopic composition of several amino acids show promise as diagnostic biomarkers of dominant algal clades in surface waters. Second, the isotopic composition of deep-sea corals was used to track or trace the provenance and fate of organic matter produced in surface waters. On the Lord Howe Rise, reconstructions indicate that the input of nitrogen fixation to the 'new' nitrogen budget varies significantly (approximately 60 per cent) on timescales comparable to variability in the East Australian Current's (EAC) flow regime. It is hypothesized that a surface community shift toward unicellular diazatrophs occurs when flow is favoured along the Tasman Front. South of the Tasman Front, three distinct surface community structures emerge. Specimens collected in the northeast are influenced by the EAC, while an east-west dichotomy in particulate provenance is apparent on opposing sides of the South Tasman Saddle. In the east there is evidence of eukaryotic production with particulate delivery originating from the Subantarctic Zone. By contrast in the west there is a distinct prokaryotic isotope profile that shares properties with the Great Australian Bight. Non-essential amino acids distributions provide evidence that the delivery of high protein organic matter supports the region's recently discovered deep biomass maximum. This body of work demonstrates that there is distinct variability in ecosystem structure and function in southeast Australian waters. But moreover, it demonstrates that only AA-CSIA can provide the level of detail that can describe how these ecosystems respond to their changing environment.

Resolving diversity patterns and their underlying drivers has application for both ecological theory and ocean management. Because seafloor characteristics are often used to assess bottom habitat, I examined the relationship between deep-sea benthic (bottom-living) diversity and multi-scale topographic heterogeneity. Most work occurred on the Canadian Pacific continental shelf at Learmonth Bank with additional sites in Strait of Georgia (BC) and Gulf of Maine (Atlantic shelf). High-resolution species distribution and seafloor data were annotated from remotely operated vehicle benthic imagery surveys while large-scale seafloor data were derived from multibeam sonar. New method development to address problems of current methods and to facilitate comparison among ecosystems is a major outcome. My new MiLS method (microtopographic laser scanning) can profile the deep seafloor at a resolution of ~1-2 cm with high accuracy and precision. I also developed a new ACR (arc-chord ratio) rugosity index as a measure of 3-D topographic heterogeneity that is simple, accurate and highly versatile. Model systems and scales vary among my studies but results consistently yield a positive relationship between diversity and topographic heterogeneity and identify bottom hydrodynamics as an important underlying driver. Rockfish Sebastes spp. associate with higher seafloor rugosity non-randomly and select for deep-sea corals and sponges over inert substrata alone. Data indicate that degradation of biogenic structures is a long-term detriment to rockfish species. Gorgonian coral- and sponge-dominant biotopes strongly associate with a single substratum type. These relationships were used to map coral and sponge distributions. This work, which collectively adds new information on the ecological relevance and distribution of corals and sponges, is pertinent to the conservation and management of fish stocks and vulnerable marine ecosystems. Epibenthic community variables abundance, richness, and Shannon diversity positively correlated with both the local microtopographic heterogeneity on a scale of 10 m2 and with the surrounding regional large-scale topographic heterogeneity on scales of 25 to 250,000 m2. Relationships were strongest between epibenthic community variables and the largest scale rugosity and were used to generate and test predictive diversity models. Where management strategies rely on surrogate measures in data-poor areas, mapping benthic diversity using ACR rugosity will provide good indicators. Although bottom hydrodynamics is consistently identified as an underlying driver of epibenthic patterns related to topographic heterogeneity, data suggest the nature of the relationship varies across spatial scales. At small scales, high topographic heterogeneity likely increases diversity by increasing the number of available niches (including hydrodynamic gradients; e.g., the abrupt vertical rugosity created by tall corals and sponges provides rockfish refuge from currents) while at large scales, high topographic heterogeneity increases local diversity less directly through distant hydraulic events that alter bottom flow hydrodynamics.
Graduate
0329
0416
0799
cdupreez@uvic.ca

Deep-sea bamboo coral (Isidella sp.) SE000901A from the southern Oregon coast (water depth 1048m) provides a high-resolution record of variability of North Pacific Intermediate Water (NPIW) and carbon rain to the sea floor, related to coastal upwelling, from 1808 to 2000AD. Counting of annual layers in magnesium to calcium (Mg/Ca) variations, measured by electron microprobe analysis, yields a detailed age model that is transferred directly to records of carbon and oxygen isotope ratios (δ¹³C and δ¹⁸O) measured by isotope ratio mass spectrometry and trace element ratios measured by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). A significant linear relationship between δ¹³C and δ¹⁸O measured on the carbonate internode of the coral specimen revealed disequilibrium kinetic isotopic variations that depend on calcification rate. The stable isotopic time series are significantly correlated to cadmium to calcium ratios (Cd/Ca) in the carbonate internode, suggesting that cadmium uptake also reflects the rate of calcification. Comparison of phosphorus to calcium ratios (P/Ca) in the carbonate internode to historical records of oxygen concentrations of NPIW suggests that coralline P/Ca is related to the phosphate content of the ambient bottom water, which covaries inversely with oxygen concentration. Stable carbon and nitrogen isotopic ratios (δ¹³C and δ¹⁵N) were measured on two organic gorgonin nodes of our bamboo coral, but incomplete understanding of the gorgonin growth patterns and the difficulty in translating ages between the proteinaceous node and calcareous internode preclude detailed comparison between organic stable isotopes and the trace element and isotopic composition of the well-dated carbonate proxies. Based on correlation of the measured properties to historical variations in coastal upwelling, and high-latitude climate variability, we demonstrate the potential and challenges in using deep-sea bamboo corals to extend records of climate variability into the pre-historical past.
Graduation date: 2012