School of Earth Sciences - Theses

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The role of soil microorganisms in the solubilisation of secondary lanthanide phosphate minerals in weathered granite

Voutsinos, Marcos Yianis ( 2022)

During the weathering of granite, a major component of Earth’s continental crust, many elements are redistributed from metastable minerals into new, more stable ones, a critical process in soil formation. Microorganisms are key drivers of mineral weathering, but the mechanisms by which they promote mineral dissolution and the connections between microbial metabolisms and element redistribution are poorly understood. Understanding the biogeochemical controls involved in the remobilisation of rare earth elements (REEs, ‘lanthanides’) from relatively insoluble minerals to uptake for cofactors of lanthanide-dependent microbial metabolism is an important and topical area of study. This thesis was developed around investigating highly insoluble secondary lanthanide phosphate mineral formation and dissolution in weathered granite profiles. Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals is critical for releasing phosphate into the biosphere. For decades, a question has prevailed regarding how highly insoluble secondary lanthanide phosphate minerals dissolve during rock weathering. It was hypothesised that microorganisms play a role in this process; however, REEs were considered biologically inert at the time. Recently, following the discovery of a lanthanide-dependent methanotroph, studies have shown that lanthanide-dependent methanol oxidation is common in many environments, including soils, but the mechanisms responsible for lanthanide acquisition and uptake from the environment remain poorly understood. The thesis reviews and discusses the major outstanding questions and mechanisms involved in the biogeochemical mobilisation of lanthanides in weathered granite (Chapter One). Field emission-SEM/EDX (scanning electron microscopy with energy dispersive X-ray) and mass spectrometry were used to study primary and secondary mineral formation and dissolution in granite material while genome-resolved metagenomics, enrichment, isolation and bioleaching were utilised to study the capability of the microbial community to break down REE minerals and utilise lanthanides (Chapter Two). The process of secondary lanthanide phosphate formation and dissolution was investigated in different granite types of variable mineralogy. The phenomenon of REE mobilisation, precipitation of nanocrystalline REE/P minerals, and ultimately REE/P mineral dissolution, during granite weathering was documented in three major granitic types (I-, A-, and S-type). It was documented that the dissolution of highly insoluble secondary REE/P minerals, as well as monazite, can precede soil formation and occurs in soils (Chapter Three). Using genome-resolved metagenomics alongside enrichment and isolation methods, the work aimed to characterise the microbial community of a weathered granite profile, to detect the presence of lanthanide-dependent genes, and to assess their potential REE/P- bioleaching capabilities. One well-developed granite weathering profile in which lanthanum phosphate formation and dissolution were documented was selected for further biological analysis. Genome-resolved metagenomic analyses revealed microbes including Verrucomicrobia, Acidobacteria, Gemmatimonadetes, and Alphaproteobacteria with the capacity to utilise lanthanide-dependent methanol oxidation (XoxF) are prevalent in the region where insoluble lanthanide-phosphate minerals dissolve. Conserved hypothetical proteins and transporters not previously associated with xoxF systems were also identified across diverse phyla suggesting lanthanide usage is prevalent and highlights targets for further investigation. Biosynthetic gene clusters of predicted siderophores containing xoxF systems were identified and may be involved in dissolving REE/P minerals (Chapter Four). Enriched microbial co-cultures capable of producing siderophores were capable of dissolving lanthanum from highly insoluble rhabdophane in the laboratory at essentially circumneutral pH suggesting dissolution mechanisms independent of organic acids (Chapter Five). This study's genome-resolved metagenomic analysis identifies mechanisms in moderately weathered granite that may promote REE/P mineral dissolution and general rock weathering. The study also successfully demonstrates a new in situ sampling approach for enriching and isolating microorganisms capable of solubilising lanthanum from highly insoluble lanthanide phosphate minerals. The findings and methodology of this study have relevance and application suitable for experimental studies looking to describe new lanthanide-based systems, express and characterise novel siderophore gene clusters, improve lanthanide recovery technology, and further describe the microbial controls on mineral weathering prior to soil formation.
Nonlinear, statistical and stochastic dynamics of geophysical fluids with application to state estimation and prediction

O'Kane, Terence John ( 2021)

Many important results underpinning our understanding of variations in the climate have been achieved by linearizing the deterministic equations of motions or through Markovian and Gaussian assumptions on the statistical representation of the systems probability distribution. With the accrual of several decades of ocean and weather observations of sufficient spatial density and homogeneity to resolve the climate modes of variability, it has become evident that the climate system is highly nonlinear, non-stationary and non-Gaussian with transitions between persistent or metastable regimes ubiquitous across all scales. As a result, our ability to make skilful predictions of the state of the various weather systems and climate teleconnections and their causal relationships requires a foundational understanding of the dynamics and life cycles of instability processes that determine predictability. While state of the art operational numerical weather prediction systems now routinely apply aspects of mathematical methods from dynamical systems to characterise the impact of small-scale growing disturbances (error modes) on the predictability of the large scale quasi-stationary structures of the synoptic weather, these approaches are largely empirical. Ideally, a modern mathematical representation of the dynamics of the Earth’s weather and climate must necessarily be cast in terms of a nonlinear, stochastic and multiscale system. However, the sheer complexity and dimensionality of the problem makes development of a foundational theoretical basis for climate variability and predictability a distinct challenge. With the development of novel data driven stochastic optimization methods, high dimensional weather and climate data can now be reduced to low dimensional systems of stochastic differential equations that retain the essential dynamics but make tractable the extraction of regime behaviours of persistent states in systems where the signal to noise ratio is low. The body of work contained in this thesis represents a sustained effort to advance a deeper understanding of the role of nonlinear processes in geophysical fluids with specific application to the development and analysis of weather, ocean and climate prediction systems. Chapter 1 develops the statistical mechanics and dynamics of inhomogeneous turbulent flows with application to modelling unresolved (subgrid) processes associated with the interactions between eddies and topography, and methods of ensemble numerical weather prediction and data assimilation. Mathematically, this is the foundational problem of strong interactions across scales in systems with a quadratic nonlinearity. In essence, one is required to find tractable and accurate representation of an infinite hierarchy of moment equations. The work presented in this chapter develops theoretical approaches borrowed from modern physics and novel computational methods that achieve this goal. This is one of the most technically and intellectually challenging problems in mathematical physics manifesting in areas as diverse as quantum electro- and chromo-dynamics and plasma physics. The theory is validated against ensemble direct numerical simulations of the primitive equations and is shown to enable deep insights into a range of problems of direct societal relevance and in particular weather prediction and state estimation. Chapter 2 describes the development of weather (p228), mesoscale ocean (p242), cyclone (p258) and climate (p296-399) prediction systems. The ensemble weather prediction system described on pages 228-241 forms the basis of the current operational system at the Australian Bureau of Meteorology. The Climate Analysis Forecast Ensemble (CAFE) system described on pages 296-399 is currently operational at CSIRO and is the first system developed in the Southern Hemisphere to contribute to the official World Meteorological Organization near term climate predictions. These systems implement state of the art data assimilation methods to constrain models to observations to generate initial forecast conditions. For the climate, this requires observations of the atmosphere, ocean, land and sea ice to be assimilated and a large ensemble (order of 100) of model forecast simulations employed to generate covariances between the respective domains. The insights gained from statistical dynamics provides additional insights to tackling these challenges. A severe challenge to the analysis of the aforementioned ensemble prediction systems is the dimensionality of the state estimation and forecast data. To underpin the development of such systems, a deeper understanding of the processes and timescales whereby long-term predictive skill resides in the climate system is required. This is a massive challenge given the short observational record in the ocean and large ensembles of initialized forecasts necessary to identify predictive skill. Despite the huge data sets generated, the number of data instances is far exceeded by the dimensionality of the problem, hence the challenge is a classically “small data” issue. The work in Chapter 3 describes the development and application of novel advanced methods from across applied mathematics (dynamical systems, optimization, numerical methods) applied to better interrogate both model and observational data by extracting, not simply correlations between the respective climate modes of variability, but their (conditionally) causal relationships, including the anthropogenic factors that drive their changing relationships and regime transitions over time. This work reveals a detailed understanding of the abrupt climate regime shift that occurred in the Southern Hemisphere climate during the late 1970s. This change in the large-scale circulation precipitated the prolonged periods of reduced rainfall and heat extremes experienced in recent decades over the Australian continent and changes in the statistics of persistent synoptic scale weather patterns. Low frequency variability in the climate system occurs principally via the coupling of the ocean to the atmosphere. The work in Chapter 4 is primarily concerned with understanding the ocean’s response to the constituent components of the atmospheric forcing. Specifically, this work shows how information is communicated via coherent waves in internal oceanic pathways that are analogous to the storm tracks of the atmosphere. The specific role of baroclinically unstable Rossby waves and density compensated salinity anomalies and the mechanisms by which they are excited are examined revealing the importance of coherence resonance processes whereby the synoptic scale atmosphere excites coherent oceanic disturbances on inter-annual timescales. In the final Chapter 5, a range of approaches to deriving reduced order models of the climate modes of variability are presented. Dynamic Bayesian Networks and directed graph methods are employed to quantify causal relationships between the major climate teleconnections in reanalysis data. A minimal skeleton model specific to the Madden Julian Oscillation is identified based on coherences between Kelvin and Rossby waves from a normal mode decomposition of observations. Finally, stochastic linear inverse models are applied to construct reduced order models of the tropical-extra tropical South Pacific Ocean with the synoptic scale Pacific South American (PSA) mode of tropospheric variability identified as the key stochastic forcing.
Cultivation-based and metagenomic studies of engineered thiocyanate-degrading microbial communities: applications to mine waste bioremediation

Shafiei, Farhad ( 2022)

Bioremediation systems have been applied to mitigate potential environmental impacts of thiocyanate (SCN-) that is generated by specific industries. In gold mining, this compound is typically formed by chemical reaction of cyanide (CN-) with reduced sulphur forms that are present in mining effluents. Accumulation of this chemically stable substance in mining wastes, which are often stored at mine sites, can eventually contaminate the underlying groundwater, necessitating adopting suitable approaches to destruct this environmental pollutant in mining effluents and contaminated waters. In this regard, biodegradation is favoured over physicochemical methods considering its sustainability, lower operational costs and substrate specificity. Bioremediation systems harness the metabolic activities of microorganisms capable of degrading SCN-. In engineered bioremediation systems, mixed microbial cultures or microbial consortia are often preferred over clonal populations. Although some aspects of SCN--degrading microbial communities were already investigated, many questions remained unanswered. Most prior studies on SCN--degrading microbial consortia were limited to laboratory-scale experiments with synthetic wastewater as the influent. This thesis examined some of the microbial aspects of this process in a larger scale. We also exploited cultivation techniques to experiment potential effects of heavy metals on an autotrophic microbial consortium. Also, similarities and differences between microbial communities that degraded SCN- in various bioreactors were investigated using a comparative metagenomic approach. All the studied systems were autotrophic bioreactors, i.e. SCN- served as the sole source of carbon. After an introductory chapter, in Chapter 2, a cultivation-based approach was adopted to investigate the effects of heavy metals on SCN- biodegradation by an autotrophic mixed microbial culture. Heavy metals that coexist with gold in minerals are released during ore processing. While the presence and the quantity of metals in mining environments greatly depend on geochemical processes, it is likely that their toxic effects on microbial communities hamper the performance of SCN--degrading bioreactors. A set of shake flask experiments were designed to evaluate this inhibitory effect on an autotrophic microbial consortium. Five metals of Zn, Cu, Ni, Cr and As were selected, each at four concentrations, based on the literature and the real chemical data from a Victorian mine site. The experiments were conducted at 30 oC and pH 7.8 over 5 days of incubation. Biodegradation of SCN- was completely inhibited by Zn, Cu, Ni and Cr and Ni at concentrations of 20, 5, 10, and 6 mg/L, respectively. Concentrations lower than these values reduced the rate of SCN- biodegradation. The microbial consortium tolerated As at a high concentration of 500 mg/L. This high tolerance of As may be attributed to the selective effect of environmental conditions. The reason for this speculation is that the mine area where this consortium was originally enriched from, Stawell in Victoria, is known for high As content in minerals such as arsenopyrite. Overall, in terms of the SCN- biodegradation ability of the microbial culture at similar metal concentrations, the ordering of metal tolerance of this consortium from the highest to the lowest was as As, Zn, Ni, Cu and Cr. Geochemical modelling analyses also showed the importance of geochemical phenomena in metal speciation that in turn affects their availability to microbial communities in these systems. The results indicated the potential influence of these co-contaminants on bioreactors that remediate SCN--contaminated environments at mine sites. Chapter 3 is dedicated to a detailed metagenomic analysis of microbial communities from a 1000-L SCN--degrading bioreactor in a pilot plant bioremediation system that has been operating at the Stawell Gold Mine (SGM) site in Victoria. This flow-through moving bed biofilm reactor (MBBR) system has been remediating SCN--contaminated groundwater at the mine site. High-throughput metagenome sequencing data were generated for both planktonic and biofilm samples from this bioreactor. The analyses for these two growth modes were performed independently. The results showed that microbial communities in this system were dominated by Thiobacillus and Gammaproteobacteria, some of which capable of SCN- biodegradation using thiocyanate hydrolase (SCNase). Some non-SCN- degraders such as Flavobacteriales and Caulobacterales were also abundant in planktonic microbial communities. Genome-based metabolic predictions indicated metabolic potential for sulphur oxidation in the abundant bacteria. Changes in microbial community structure between sampling points were attributed to operational perturbations in aeration and pH in the system, while the likely effect of the change in seasonal temperature was acknowledged. In Chapter 4, a comparative metagenomic study of three autotrophic SCN--degrading systems is demonstrated. These systems included a flow-through lab-scale bioreactor, a set of mesocosm experiments conducted in batch mode and pilot-scale bioreactor studied in Chapter 3. Results revealed that microbial communities from pilot bioreactor were more diverse than those from the other two systems. Shifts in microbial community compositions indicated the effects of environmental parameters on these consortia. Generally, biofilm microbial communities showed more resilience to operational perturbations compared to planktonic consortia of the same system. Genome-based predictions revealed that SCN--degrading bacteria in all these bioreactors belonged to the genus of Thiobacillus and metagenome bins assigned as Gammaproteobacteria. While sequences related to nitrite-oxidising bacteria (NOB) were found in several metagenome bins, those that encode for ammonium oxidation were not binned with one exception of Nitrosomonas. Eukaryotic content of microbial consortia in these systems was also evaluated using different metagenomic pipelines. Overall, a relatively higher algal content in some batch bioreactors, which has also been observed during the experimentation, proposed potential environmental outcomes of in situ bioremediation or natural attenuation approaches. Chapter 5 summarises the results from studies presented in Chapters 2, 3 and 4 of this thesis along with a general discussion of the findings and final conclusions. Environmental constraints on microbial communities in a SCN--degrading bioreactor were dealt with in this thesis using both cultivation-based and metagenomic studies. Heavy metals affected SCN- biodegradation in lab-scale batch experiments. In pilot bioreactor, the system performance and microbial community composition were influenced by perturbations in aeration and pH. This thesis serves as the first study using metagenomic analyses to characterise microbial communities in a scaled-up bioreactor that receives real SCN--contaminated water. Also, the thesis contributed to improving our understanding of possible outcome of long-term operations of SCN- bioremediation systems implemented at mine sites. In this regard, it is of great importance to consider environmental phenomena such as eutrophication that may occur as a result of the accumulation of SCN- biodegradation products in the effluent of engineered systems and in natural attenuation or in situ bioremediation systems.
An Investigation of Fission Tracks in Monazite: Development of a New Ultra-Low Temperature Fission Track Thermochronometer

Jones, Sean Curtis ( 2022)

Monazite, a rare-earth element (REE) phosphate mineral, is found as an accessory in a variety of rock types. Suitable uranium and thorium content make it a useful mineral for isotopic and chemical dating using the (U-Th)/He and U-Th-Pb methods. However, unlike other uranium-bearing minerals, apart from a few reconnaissance studies, its potential for fission-track dating has not been systematically investigated. Earlier studies produced very young ages suggesting that fission tracks may be annealed at very low temperatures. This study explores the fission track properties of monazite and presents the findings of a new track etching protocol and thermal annealing experiments. These are accompanied by a case study in SW Japan, demonstrating how a new fission track thermochronometer can be applied in a young and small orogenic belt. The previously reported concentrated (12M) HCl etchant at 90 degrees C for 45 min was found to cause grain loss from epoxy mounts and high degrees of grain erosion. Therefore, in efforts to reduce these hindrances, an alternative etching protocol of 6M HCl at 90 degrees C for 60 – 90 min has been established for monazite after testing several alternative etchants. However, it was found in an isothermal annealing experiment that ~4 percent annealing occurs after one hour exposure to this etching temperature. Thus, a key concern is that some track annealing could occur during track etching before the etchant reaches the track ends. To investigate this, possibility the application of focused ion beam scanning electron microscopy was used to mill progressively into implanted 252Cf fission tracks after slight etching, followed by an etch-anneal-etch experiment. Results showed that the etchant penetrated to the track ends in <15 min, suggesting less than ~1 percent of fission track length reduction is likely to occur during etching. Other etching experiments performed show that crystal settling during standard epoxy mounting means that (100) faces are preferentially displayed so that subsequent experiments were weighted towards this orientation. The size and shape of well-etched spontaneous fission track openings in monazite were also constrained to be rhombic in shape. Average rhombic etch pit diameters Dpc and Dpb, parallel to the crystallographic c- and b-axes on (100) faces are 0.81 +/- 0.20 micrometer and 0.73 +/- 0.26 micrometer, respectively. An angular distribution experiment on (100) faces found that spontaneous fission tracks initially etch anisotropically, being preferentially revealed at an azimuth of 90 degrees to the crystallographic c-axis up to ~60 min of etching. As etching continues, however, the distribution becomes progressively more uniform and is essentially isotropic by 90 min. Electron microprobe analyses also showed a correlation between etching rate and elemental composition, with over-etched grains tending to have higher U and Th concentrations, also suggesting a radiation damage effect. A series of isochronal laboratory annealing experiments were then performed on collimated 252Cf fission tracks implanted into monazite crystals on both (100) and ~(001) faces over 1, 10, 100 and 1000 hour schedules at temperatures between 30 degrees C and 400 degrees C. In all cases, the mean equivalent confined track length was always less than that in unannealed control samples. Monazite fission track annealing also appears to be anisotropic, with tracks on surfaces perpendicular to crystallographic c-axis consistently annealing faster than those parallel to the (100) face. To investigate how mean track lengths decreased as a function of time and temperature, one parallel and two fanning Arrhenius models were fitted to the empirical dataset. The temperature limits of the monazite partial annealing zone (MPAZ) were defined as length reductions to 0.95 (lowest) and 0.5 (highest) for these experiments. Extrapolation of the laboratory experiments to geological timescales indicates that for a heating duration of 107 years, estimated temperature ranges of the MPAZ are -71 to 143 degrees C (both +/- 6-21 degrees C, 2 standard errors) for the best fitting linear fanning model (T0 = infinity). If a monazite fission-track closure temperature is approximated as the mid-point of the MPAZ, it is estimated that the closure temperature (Tc) for fission tracks in monazite ranges between ~45 and 25 degrees C over geological timescales of 106 – 107 yrs, making this system potentially useful as an ultra-low temperature thermochronometer. Even ambient surface temperatures remain well within the MPAZ over these time scales. The final chapter of this study presents a low-temperature thermochronology study of Cretaceous granitoid samples from the Ryoke belt, located in eastern Yamaguchi and Nara Prefectures, SW Japan. Historically, low-temperature thermochronology techniques such as apatite fission track (AFT) and apatite (U-Th-Sm)/He (AHe) have been limited in their applicability to uncover the neotectonic evolution of Japan. This is predominantly due to the young age and small amount of total denudation the Japanese island arc has experienced since initiation of uplift. However, the monazite fission track (MFT) system provides an opportunity for the first time to directly analyse the neotectonic and denudation history of this area. Zircon (U-Th)/He (ZHe), AFT and AHe data and modelled thermal histories reveal Late Cretaceous - Pliocene cooling related to paleo-Izanagi and Pacific plate subduction along the eastern Eurasian continental margin. MFT dating reveals Plio – Pleistocene central ages interpreted to reflect elastic loading caused by Philippine Sea plate subduction since the Middle - Late Miocene, along with Quaternary collision of NE and SW Japan at the Itoigawa-Shizuoka Tectonic Line (ISTL). Estimated denudation rates based on MFT dating are in the order of 0.10 – 0.47 mm/yr and 0.15 – 0.56 mm/yr in the eastern Yamaguchi and Nara Prefectures, respectively, which are in accord with estimated rates calculated using geomorphological and altitude dispersion methods. No relationship with topography or geomorphological factors has been established to explain the higher denudation rates in the Nara Prefecture. Instead, differences are likely to reflect variations in the tectonic regime, timing of uplift and uplift mechanisms of the two regions.
Arc segmentation and landscape evolution in the Bhutan Himalaya

Wood, Matthew Peter ( 2022)

The principal structural elements of the Himalayan arc can be traced nearly continuously for 2500 km. Historically, along-strike variations in structure and denudation have not received the same attention as equivalent arc-normal trends. Yet research has demonstrated that arc segmentation can be controlled by lateral variations in the geometry of the Main Himalayan Thrust (MHT). The Bhutan Himalaya has a distinctive physiography and hosts nominal instrumental seismicity despite experiencing long-term strain accommodation comparable to the wider arc. This enigmatic section of the orogen presents an opportunity to test the case for local arc segmentation through applied tectonic geomorphology. By integrating low-temperature thermochronology – including apatite fission track (AFT), and apatite and zircon (U-Th-(Sm))/He thermochronometry of in situ bedrock, synorogenic sediments and modern detrital samples – cosmogenic radionuclide methods (10Be concentrations from detrital quartz samples that add to a nation-wide compilation of published data) and quantitative geomorphometry, this study documents the spatial and temporal variability of denudation to infer partitioning of deformation across crustal structures. Results show prominent along- and across-strike variation in denudation within Bhutan. Contiguous geomorphic zones are defined based on millennial-scale erosion rates and their morphometric proxies, including the physiographically distinct low-relief belt and southeast range front. Profile curvature statistics of central range front ridges are linked to earthquake-triggered landsliding and define the Naka Zone, which overlies a historically seismogenic MHT decollement flat. Synorogenic detrital thermochronometers provide information on source area bedrock cooling and the thermal evolution of the Indo-Gangetic paleo-basin. Linking the depositionally-adjusted age spectra of Siwaliks thermochronometers to an analogous modern detrital suite allows the estimation of sedimentary provenance. The dominant Lesser Himalaya source has been tectonically constructive since at least ~5 Ma, while the secondary Greater Himalaya source is ‘steady state’, as evidenced by a persistent ~4 Ma ZHe age peak. Range front and Siwaliks thermochronometers show that the structural succession is complicated near the eastern border. Southward decreasing detrital AFT exhumation rates in hinterland mountain catchments document progressive, semi-horizontal, post-cooling translation across the basal thrust flat. Decoupled intra-catchment millennial-scale erosion rates are a transient response to geologically recent rock uplift westward of the southeast range front. Exhumation rate modelling of individual in situ samples and elevation sampling transects show that geothermal gradients of at least 35 degrees C km-1 – and long-term erosion rates of ~1 km Myr-1 – have persisted across much of the study area. Multi-thermochronometric thermal history modelling results indicate that the locus of exhumation is offset by ~20 km towards the front southeast of Drangme Chu, predictive of a mid-crustal ramp beneath the Tawang River valley and Lumla window. An oblique ramp is invoked to reconcile differing orogenic sections. A synthesis of findings leads to the proposal of an obliquely oriented, second-order segment boundary within Eastern Bhutan, which may help constrain the seismic potential of adjacent arc segments.
Neotectonic Evolution of an Incipient Continental Plate Boundary Fault Intersection, Hope-Kelly Fault System, New Zealand

Vermeer, Jessica LeeAnne ( 2022)

The Hope-Kelly fault system forms the intersection between the plate boundary Hope and Alpine faults in the South Island of New Zealand. New fault mapping, paleoseismology, slip-rates, and low temperature thermochronology provide insights into the structure, kinematics and evolution of this fault intersection zone. Lidar, photogrammetry and field-based fault mapping reveals the transition from a dextral fault zone in the east to a splay-like zone of distributed oblique dextral-normal faults that abut the Alpine fault in the west. Structural interactions between the Hope-Kelly faults and the Alpine fault influence surface rupture geometries and kinematics, accommodate differential orogenic growth, and facilitate N-S extension that enables a slip rate change between the central and northern Alpine fault sections. Radiocarbon (14C), optically stimulated luminescence (OSL; quartz), and infrared stimulated luminescence (IRSL; feldspar) ages of fault-proximal sedimentary deposits are combined with geomorphic surface displacement measurements to derive fault slip-rates. Dextral slip-rates on the Hope Fault decrease westward from 5.6 (+2.0/-0.8) mm/yr to 1.7 (+1.0/-0.5) mm/yr. Dextral slip-rates on the Kelly Fault vary from 6.2 (+2.5/-1.2) mm/yr (east) to 2.0 (+2.5/-0.7) mm/yr (central) to 6.4 (+7.8/-1.4) mm/yr (west). Subsidiary faults have minimum slip-rates of 1.3 (+0.1/-0.4) mm/yr. Spatial variations in apparent slip rates are proposed to reflect complexities in slip localization and transfer across the complex deformation zone, slip on unrecognized, buried, and/or blind faults, and possible temporal transience in slip behaviours. Paleoseismic trenching and 14C dating of dead trees provides preliminary evidence for the most recent surface rupturing earthquake on the Taramakau section of the Hope Fault between ca. 1680 and 1840 AD, with a preferred age of ca. 1800-1840 AD. Coulomb fault stress transfer modelling of the 3D Hope-Kelly-Alpine fault intersection zone shows that slip on either the central Hope, Kelly, or central Alpine (source) faults increases Coulomb stress on the other (receiver) faults in the network, highlighting the potential for earthquake spatio-temporal clustering in this region. Zircon and apatite (U-Th)/He thermochronology is used to investigate the thermal-exhumational evolution of rocks in the Hope-Kelly-Alpine fault interaction zone. Late Miocene exhumation (3.4 - 0.8 km/Myr, assuming geothermal gradients of 33 - 40 degrees C/km) through crustal depths of approximately 5-6 km is interpreted to be controlled by proximity to the Alpine Fault, with rocks more proximal to the fault recording faster exhumation rates relative to more distal samples in the east. Establishment of the Hope-Kelly fault system in the Quaternary structurally juxtaposed rocks with discordant cooling histories. Rocks throughout the study region record increased cooling rates from circa 2 Ma. Possible causal mechanisms include increases in rock uplift and denudation rates associated with kinematic changes along the Australia-Pacific plate boundary, Quaternary glaciation, and/or increases in rock mass erodibility associated with Hope-Kelly fault system. This thesis provides new insights into a structurally complex plate boundary, with implications for analogous settings globally.
Neoproterozoic marine oxygenation and environmental evolution

O'Connell, Brennan ( 2022)

The Tonian and Cryogenian periods (1000–635 Ma) of the Neoproterozoic era (1000–541 Ma) witnessed changes in Earth’s oxidation state, the breakup of the supercontinent Rodina, massive swings in oceanic dissolved carbon, and two extreme global glaciations. The evolving environment set the stage for advances in ecosystem complexity and the evolution of multicellular animals in the late Neoproterozoic. Despite recent advances in understanding environmental broad-scale changes through time, an in-depth understanding of links between environment, ocean oxygenation, global glaciation, and early life is still lacking. This thesis examines Neoproterozoic sedimentary environments of the Adelaide Fold Belt, South Australia. Links are explored between nearshore to deep marine sedimentation, ocean oxygenation, environments of early microbial life, and paleoenvironmental change/environmental evolution. Sedimentology, stratigraphy, and petrology reveal insights into mixed carbonate-siliciclastic beach-barrier systems (Burra Group), backreef peritidal settings (Angepena Formation), and deep–shallow ramp settings (Trezona Formation). Coupled sedimentological and biological (stromatolite) data are explored to understand links between environmental change and biologic change. Geochemical data from major/trace element data, including rare earth element data are coupled with sedimentary facies to provide a window into the paleo-redox scape and ocean oxygenation. Cryogenian oceans were iron-rich and stratified suboxic/oxic-ferruginous. The earliest sites of marine oxygenation were Cryogenian tidal flats at the interface of the atmosphere and ocean ~650 Ma. In slightly younger settings ~650–640 Ma, giant iron-oxide-rich ooids with micrite hematite tidal rhythmite(?) couplets record rapid ooid precipitation and short-term redox variability facilitated by tidal mixing in a stratified suboxic/oxic ferruginous Cryogenian ocean.
The Impacts of Atmospheric Rivers in Australia and New Zealand

Reid, Kimberley Jane ( 2022)

Atmospheric Rivers (ARs) are narrow filaments of strong water vapour transport in the lower troposphere. They are responsible for about 90% of the meridional moisture transport over the globe and are comparable in magnitude to water transport in the largest terrestrial rivers on Earth. Globally, ARs can be associated with numerous hazards including heavy rainfall, floods, blizzards, landslides, strong winds and polar heatwaves. For these reasons, it is imperative for scientists to understand and ultimately be able to predict AR behaviour in the present and future climate. Atmospheric River research has been concentrated in the Northern Hemisphere particularly over North America and Europe. This is the first thesis to explore AR impacts over Australia. We developed a global AR identification algorithm and tested the sensitivity of the AR frequency results to the input dataset parameters including resolution, regridding method and moisture transport threshold. The results showed that the combination of low moisture thresholds and restrictive geometric requirements can lead identification algorithms to miss the strongest ARs especially in the Pacific Ocean. Additionally, the resolution and regridding method of the input data, and the order of regridding and calculating moisture flux, can all impact the final AR frequency results. We applied this identification algorithm to the European Centre for Medium-Range Weather Forecasts reanalysis (ERA5) and used this new dataset to analyse AR impacts over Australia and New Zealand (NZ). It was found that nine of the ten most expensive floods in NZ between 2007-2017 were associated with AR events and seven to ten of the ten wettest rainfall days at eleven different stations occurred at the same time as an AR over that station. In Australia, ARs contribute about 10-20% of annual rainfall except in the Murray-Darling Basin region, in the southeast, where ARs are associated with approximately one-third of the mean annual rainfall. Similarly, 30-40% of the heaviest rainfall days over southeast Australia occur during the passage of an AR. Using composites of the vertical structure of ARs in ERA5, we showed that the intensity of ARs that form at tropical and subtropical latitudes is driven by the wind component of the moisture flux, while ARs that form in the extratropics are strengthened by an increase in the specific humidity component of the moisture flux. Following widespread flooding over eastern Australia associated with persistent and high integrated water vapour transport (IVT), we evaluated and assessed future IVT changes in the latest generation of the Coupled Model Intercomparison Project (CMIP6) global climate models. We found that daily IVT would likely become more extreme over Sydney – Australia’s most populated city. This thesis fills a key regional gap in AR science and furthers understanding of extreme rainfall over Australia. It also contributes to our understanding of AR structure and potential response to climate change, which is valuable globally. This thesis provides the foundation for future AR work in the areas of climate change impacts and forecasting extreme rainfall over Australia and New Zealand.
Age and Petrogenesis of Kimberlites and Related Rocks from Finland

Dalton, Hayden Boyd ( 2022)

Kimberlites are rare, small volume ultramafic igneous rocks found on every continent on Earth, with eruption ages spanning almost 3 billion years. These rocks are derived from the deepest magmas that reach Earth’s surface (>150-200 km) and provide unique insights into the nature of the convecting mantle. In addition, their cargo of entrained mantle xenocrysts (including diamonds) and xenoliths permit examination of the subcontinental lithospheric mantle (SCLM), while ‘deep’ diamonds give insights into the composition of the underlying asthenospheric mantle. Despite their significant scientific and economic importance, and decades of research, particularly in regions of southern Africa, North America and Siberia, questions remain as to the petrogenesis of kimberlites. Contention persists around the depth of origin of kimberlites, melting trigger(s) including tectonic settings, and the composition and evolution of kimberlite melts during their ascent. To provide new insights on these issues, this study presents a comprehensive petrographic, geochemical and geochronological investigation on samples from three occurrences of kimberlite and related magmatism in Finland, comprising the Lentiira-Kuhmo cluster of olivine lamproites, Kuusamo cluster of kimberlites and ultramafic lamprophyres (UMLs) and the Kaavi-Kuopio kimberlites. Finland represents an optimal location for testing various petrogenetic models, particularly regarding the links to geodynamic processes as the tectonic evolution of the Baltic Shield and its role in supercontinent cycles are well constrained. This work presents the first petrological account of the Kuusamo kimberlites, revealing that they represent highly differentiated magmas with scarce olivine macrocrysts and other mantle-derived xenocrysts. These characteristics contrast with the neighbouring Kaavi-Kuopio kimberlites, which are inferred to have crystallised from less differentiated magmas that were modified by mantle assimilation, as evidenced by correlations between the Mg# of xenocrystic (mantle-derived) olivine cores and the composition of magmatic olivine rims, spinel, and groundmass modal mineralogy. New radiometric ages show that at least ~100 Myr separates the emplacement of the Kuusamo kimberlites (~735-750 Ma) from those at Kaavi-Kuopio (~625-585 Ma). These new age data also indicate temporal overlap between ultramafic lamprophyre magmatism at Kuusamo and the eruption of olivine lamproites at Lentiira-Kuhmo (~1180-1220 Ma), some 100 km to the northeast. As part of this geochronological investigation, the robustness of Rb-Sr phlogopite, U/Pb perovskite and 40Ar/39Ar phlogopite dating methods were evaluated by applying multiple geochronometers to individual intrusions. It is evident that each radiometric system can yield both precise and accurate emplacement ages, with important caveats regarding best practice and interpretation. Radiogenic isotope data (Sr-Nd-Hf) indicates that the olivine lamproites and UMLs were contemporaneous, but have distinct source compositions. The highly unradiogenic Nd-Hf isotope compositions of the former are consistent with derivation from the metasomatised SCLM whereas the UML compositions suggest they were sourced from predominantly asthenospheric melts that were modified by (up to 15%) incorporation of enriched SCLM components. The Mesoproterozoic timing of their emplacement suggests that eruption of the olivine lamproites and UMLs was facilitated by the extensional regime associated with the separation of Baltica from Laurentia. The Kuusamo and Kaavi-Kuopio kimberlites were also emplaced at a time of supercontinent disruption. The Kuusamo eruptions occurred as the break-up of Rodinia was initiated, while the Kaavi-Kuopio rocks were emplaced as Rodinia break-up was completed, contemporaneous with the formation of the Central Iapetus large igneous province. In keeping with their petrographic disparities, the Sr-Nd-Hf isotopic composition of these kimberlites indicates that they were sourced from distinct source regions in the convective mantle. The homogenous composition of the Kuusamo rocks overlaps the prominent PREMA-like signature of kimberlites globally, whereas the Kaavi-Kuopio samples exhibit an extreme range in Hf isotope compositions with a temporal trend from PREMA-like towards lower epsilon Hf(i) values in younger kimberlites. Isotopic modelling suggests that this temporal enrichment of the kimberlite source region was due to increasing entrainment (of up to 10%) of subducted material. These findings are consistent with mounting evidence for subducted material being an important source ‘pollutant’ for kimberlites globally and a petrogenetic link with supercontinent cycles and/or the large mantle plumes that initiate supercontinent disintegration.
Generating Improved Regional Inventories, Using Remote sensing and Inverse Modelling

Shahrokhishahraki, Nasimeh ( 2022)

Air pollution is among the most crucial environmental concerns in the world. Releasing toxic and dangerous gases and particulate matter into the air causes various types of human diseases. Moreover, air pollution negatively impacts plants, animals, and even buildings, especially monuments and historical places. This study investigates carbon monoxide (CO) and oxides of nitrogen (NO2), as typical air pollutants in urban areas. Improving air quality forecasts can be achieved by improving the modelling system and its inputs. Among such inputs, emission inventories (EIs), which provide emission rates for various pollutants in space and time, have a significant impact but are often associated with large uncertainties. Most cities do not have reliable atmospheric emission inventories. Different methodologies can be utilised to improve the existing EIs. One of these is to try to update the inventories to match measurements of concentration, usually termed an inverse method. This study generates urban scale emission data for Tehran, using globally accessible datasets and applies satellite measurements and an inverse approach to refine emission inventories. A downscaling approach is used to apply the Emissions Database for Global Atmospheric Research (EDGAR), Gridded Population of the World and Fossil Fuel Data Assimilation System to generate high-resolution EIs. The resultant urban scale inventory (also called as `prior EIs') is applied to run an offline WRF-CMAQ Modelling System (also called as `forward model') to simulate the concentrations of gaseous air pollutants. The modelled concentrations during August 2018, November 2018, February 2019 and May 2019 are compared with the TROPOspheric Monitoring Instrument (TROPOMI) satellite data, and surface observations (split into `road' or `city' type stations) to assess the performance of the system. The model overestimates the amplitude of NO2 tropospheric column satellite data by a factor of ~1.2-2.1, while it overestimates the amplitude of CO column data with a ratio of ~0.61-0.88. Comparison with surface measurements shows that the model with the prior EIs overestimates diurnal cycle of NO2 concentrations in both city and road types during all studies months with more than 0.70 correlation, between less than 1 ppb for road sites in August, up to around 70 ppb for city sites in November and February. For CO there is no similar pattern for the diurnal cycle of city sites and road sites. In city sites, except August, the model overestimates the CO with a bias of 0.05-0.8 ppm, while the negative bias values in road sites (-0.1 to -1.4 ppm) indicate that the model underestimates the observations. Analysis of concentration structures and meteorological fields suggests the modelling system is good enough to apply in an inverse system. A regional-scale inverse-modelling system has been established using remote sensing to regenerate emission data for Tehran. A Python-based four-dimensional variational (Py4DVar) data assimilation approach is applied to refine CO-EIs (`posterior EIs') for Tehran. This system applies the TROPOMI retrievals and two forms of allowed emissions variations: One with fixed temporal variation (FTV) and the other with emissions varying by diurnal categories (CTV). The posterior results show that the model captures the amplitude of CO column data with ratios of 0.94-1.02 through the CTV scheme and 0.75-0.98 through the FTV scheme. Comparisons with surface measurements also indicate that the posterior shows some improvements in simulating observations but not in all cases. Although we solve for aspects of the lateral boundary condition, our results are sensitive to their prior values. This suggests that future studies should use larger domains where boundary condition influence can be reduced. Similarly, the inability to match simultaneously the surface and column-integrated observations is most likely a manifestation of the longstanding problems in vertical tracer transport. Finally the temporal limitation of the satellite data we used limits improvement at unobserved times of the day. Notwithstanding these weaknesses, the system has already provided some useful information on the local EI and the approach shows considerable promise in regions lacking good local inventories.

School of Earth Sciences - Theses

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