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(2014)Journal ArticleClimate extremes, such as heat waves and heavy precipitation events, have large impacts on ecosystems and societies. Climate models provide useful tools for studying underlying processes and amplifying effects associated with extremes. The Australian Community Climate and Earth System Simulator (ACCESS) has recently been coupled to the Community Atmosphere Biosphere Land Exchange (CABLE) model. We examine how this model represents climate extremes derived by the Expert Team on Climate Change Detection and Indices (ETCCDI) and compare them to observational data sets using the AMIP framework. We find that the patterns of extreme indices are generally well represented. Indices based on percentiles are particularly well represented and capture the trends over the last 60 years shown by the observations remarkably well. The diurnal temperature range is underestimated, minimum temperatures (T-MIN) during nights are generally too warm and daily maximum temperatures (T-MAX) too low in the model. The number of consecutive wet days is overestimated, while consecutive dry days are underestimated. The maximum consecutive 1-day precipitation amount is underestimated on the global scale. Biases in T-MIN correlate well with biases in incoming longwave radiation, suggesting a relationship with biases in cloud cover. Biases in T-MAX depend on biases in net shortwave radiation as well as evapotranspiration. The regions and season where the bias in evapotranspiration plays a role for the T-MAX bias correspond to regions and seasons where soil moisture availability is limited. Our analysis provides the foundation for future experiments that will examine how land-surface processes contribute to these systematic biases in the ACCESS modelling system.
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(2013)Journal ArticleThe last interglaciation (similar to 130 to 116 ka) is a time period with a strong astronomically induced seasonal forcing of insolation compared to the present. Proxy records indicate a significantly different climate to that of the modern, in particular Arctic summer warming and higher eustatic sea level. Because the forcings are relatively well constrained, it provides an opportunity to test numerical models which are used for future climate prediction. In this paper we compile a set of climate model simulations of the early last interglaciation (130 to 125 ka), encompassing a range of model complexities. We compare the simulations to each other and to a recently published compilation of last interglacial temperature estimates. We show that the annual mean response of the models is rather small, with no clear signal in many regions. However, the seasonal response is more robust, and there is significant agreement amongst models as to the regions of warming vs cooling. However, the quantitative agreement of the model simulations with data is poor, with the models in general underestimating the magnitude of response seen in the proxies. Taking possible seasonal biases in the proxies into account improves the agreement, but only marginally. However, a lack of uncertainty estimates in the data does not allow us to draw firm conclusions. Instead, this paper points to several ways in which both modelling and data could be improved, to allow a more robust model-data comparison.
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(2022)ThesisSponges can harbour diverse communities of microbial symbionts, collectively referred to as a holobiont. Sponge symbionts play important ecological and mutualistic roles, including cycling of carbon, nitrogen, and sulfur; provisioning the host with essential compounds; and producing bioactive metabolites that confer fitness advantages to the holobiont. Recent metagenomics and bioinformatics advances facilitate genomic reconstruction and metabolic characterisation of uncultured prokaryotic species. Leveraging these tools, I reconstructed 75 metagenome-assembled genomes (MAGs) that represent 21 novel sponge-associated species: ten Gammaproteobacteria, six Acidimicrobiia, and five Acidobacteriota. The gammaproteobacterial species were metabolically diverse, likely representing adaptations to diverse habitats associated with different sponge species. Two species from the Candidatus genus Azotimanducus comprised almost identical patterns of organoheterotrophy that likely enabled them to colonize the same sponge host, but differed in other features that likely allowed for niche partitioning and cohabitation. Unlike the sponge-associated Gammaproteobacteria, the Acidimicrobiia shared very similar genomic features. Of particular interest, sponge-associated Acidimicrobiia were predicted to produce bioactive compounds that may modulate host signalling pathways, suggesting a potential role in host health. The sponge-associated Acidobacteriota likely predominantly formed symbiosis with their hosts prior to the phylogenetic split between sponges and corals. All five acidobacteriotal species shared similar patterns of organoheterotrophy, likely allowing for scavenging organic substrates from the host environment. Another feature that was specifically enriched in the novel sponge-associated Acidobacteriota was their capacity to produce diverse B-vitamins, with Candidatus Versatilivorator vitaminiformans comprising the genetic capacity to produce all of them. All 21 novel species also comprised unique respiratory, degradation, biosynthetic, and defensive features that likely mediate their interactions with the corresponding hosts. Features shared by the majority of the species were also identified. Altogether, the comprehensive genomic characterisation of sponge symbionts in this thesis has uncovered unique and shared features, highlighting the importance of extensive surveys into uncultured sponge symbiont diversity and function.
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(2020)ThesisPseudomonas aeruginosa causes both contact lens and non-contact lens-related keratitis (corneal infection). This opportunistic bacterium naturally has the ability to resist the mechanism of action of many antibiotics which are used for treatment. P. aeruginosa resistance patterns and the mechanism of resistance in isolates from keratitis are not well understood. This thesis described the phenotypic and genotypic patterns of antimicrobial resistance and compared these between ocular isolates of P. aeruginosa from Australia (contact lens) and India (non-contact lens). Changes in the antimicrobial susceptibility between isolates over time were also analysed. Susceptibility to antibiotics, multipurpose disinfecting solutions and disinfectants was analysed for twenty-seven Australian isolates from contact lens-related keratitis and forty non-contact lens-related isolated from India. The whole genomes of fourteen Australian (historical and recent) and twelve Indian isolates were sequenced using Illumina® MiSeq®. Computational analysis of the genomes was performed to analyse their core and pan genomes and these were examined for the presence of acquired resistance genes, virulence genes, gene mutations, and these compared to their phenotypic resistance to antibiotics. Indian isolates possessed large pan genomes with more acquired resistance (30) genes and larger numbers of genetic variations. The Indian isolates contained clones of three sequence types ST308, ST316 and ST491, whereas Australian isolates contained only one sequence type ST233. Isolates with larger gene variations had mutations in the DNA mismatch repair system. Most multi-drug resistant Indian (non-contact lens) isolates were exoU +. Indian isolates had large accessory genes compared to Australian isolates and this increased the pan genome size of the Indian isolates. The number of core genome mutations were larger in the Indian isolates a median of 50006 (IQR=26967-50600) compared to Australian isolates a median of 26317 (IQR=25681-33780). There were differences between isolates from Australia and India with respect to their antibiotic resistance and associated genes. Indian strains had more genetic diversity and were multi-drug resistant. However, there was no evidence of substantial genetic or phenotypic changes within isolates from their respective countries.
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(2023)ThesisAustralia’s arid zone small mammals are primarily governed by rainfall. With extreme rainfall events often being separate by prolonged periods of drought, long term data sets (> 10 years) are generally required to study small mammal ecology. In this thesis, I leverage two long term data sets collected in arid New South Wales and South Australia to investigate drivers of small mammal population dynamics at both the local and regional scale. At the local scale, I investigate the relationship between Landsat Fractional Cover (FC) measurements to assess their potential to identify small mammal habitat. By associating FC measurements with 12 years of small mammal surveying, I find evidence Landsat FC measurements are closely related to the population dynamics of rodent species Leggadina forresti and Mus musculus but not marsupial species Sminthopsis macroura and Sminthopsis crassicaudata. This suggests that Landsat FC measurements could capture suitable habitat for small mammal species with boom-and-bust population dynamics in arid rangelands. On a regional scale, I investigate Mus musculus population synchrony throughout a roughly 25 000km2 region of the Strzelecki desert and Barrier Range. By assessing the correlation between sub-population dynamics and regional rainfall, I identify groups of synchronous sub-populations that are not spatially autocorrelated or driven by regional rainfall variability. Analysis of the synchronous groups subsequently reveals that variable predator assemblages drive regional asynchrony, suggesting that while M. musculus may be more persistent where dingoes occur, they reach greater abundances where they do not. The results from these chapters highlight how various management actions impact several arid zone small mammal populations, while also identifying key areas for future research that will assist conservation land managers in identifying and mitigating threats to vulnerable species.
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(2024)ThesisPortunid crabs such as the Blue Swimmer Crab (BSC, Portunus armatus) are a high-value species in NSW, but catches are highly variable. Such variation in catch of portunid crabs is not unique, and other jurisdictions across Australia have sought to understand this variation by identifying links between environmental variability, recruitment, and catch for BSC. This thesis has four main chapters which investigated a novel research trap design for use in fisheries independent surveys of BSC populations; the spatial and temporal variation in BSC populations; their reproduction; and a novel approach to estimating fecundity in BSC. The retained catch from a novel small-mesh trap were compared with samples obtained using beam trawls and standard commercial round traps. I determined that the traps are more efficient at catching smaller crabs, and equally effective at catching larger size classes of crabs. In Wallis Lake, water temperature and conductivity had significant effects on abundance but there was no evidence that pulses of freshwater flow had a significant influence. Males were consistently located slightly further into the estuary compared to females, but there was no strong evidence of a spawning migration in response to low salinity. In Port Stephens, temperature and conductivity had significant effects on abundance, but the distribution of crabs within the estuary did not appear to be influenced by temperature, conductivity, or flow. The reproductive status of crabs in each estuary was highest in late winter, early spring and late summer. The highest proportion of egg-carrying (berried) females was in early spring to early summer periods in all estuaries. In Wallis Lake, the peaks in numbers of berried females were much shorter compared to Lake Macquarie and Port Stephens. I investigated a novel approach to streamline the egg count method whereby images of egg samples were digitised using a waterproofed flatbed scanner, followed by automated analysis of each image using customised computer macros. Overall, my study revealed nuanced effects of temperature and conductivity on fisheries production and on inter-annual and inter-site variation. Each estuary’s catchment and orientation to the ocean influenced their distribution and reproduction, contributing to the high variability in catch of this iconic species.
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(2021)ThesisPlanetary waves play a role in a large variety of oceanic and climate dynamics. In particular, Kelvin waves can provide rapid teleconnections from large-scale climate and weather events to remote regions of the globe. Kelvin waves may be partially responsible for linking climatic changes in Southern Ocean winds to increases in subsurface warming around Antarctica that can lead to glacial ice-melt and increases in global sea level rise. Kelvin waves may also link changes in Southern Ocean winds to increases in North Atlantic Deep Water (NADW) formation and an enhancement of the Atlantic Meridional Overturning Circulation (AMOC), which is responsible for circulating a vast amount of the ocean’s heat and nutrient content. However, the exact role of Kelvin waves in these processes is unclear. This thesis aims to further clarify the role that Kelvin waves play in these high-latitude climate processes. First, we use a suite of idealized models in order to better understand the dynamics of barotropic Kelvin waves around Antarctica. We find that super-inertial (high frequency) barotropic Kelvin waves are nearly completely scattered away from the Antarctic coastline due to a combination of coastal geometry and bathymetry. Sub-inertial (low frequency) barotropic Kelvin waves are mostly scattered away from the Antarctic coastline due to bathymetry, however a significant amount of barotropic Kelvin wave energy remains at the Antarctic coastline after one circumnavigation of the continent, enabling a gradual build-up of energy along the coast and the ability to sustain a barotropic Kelvin wave signal around Antarctica over time. Secondly, we perform a diagnostic study using theory and a range of varying resolution model simulations to quantify the amount of subsurface warming along the West Antarctic Peninsula caused by barotropic Kelvin waves via an induced bottom Ekman flow that advects warm Circumpolar Deep Water onto the Antarctic continental shelf. We find that barotropic Kelvin waves can account for a substantial amount of warming within one year, depending on the background temperature gradients and thickness of the bottom Ekman layer. Lastly, we explore the role of Kelvin waves in linking Southern Ocean wind-stress to NADW formation and the AMOC by analysing ensemble simulations from a fully-coupled ocean-sea-ice model at 1/4 degree horizontal resolution (50 vertical levels). We find first mode baroclinic Kelvin waves to propagate along a global coastal and equatorial waveguide from the Southern Ocean forcing region to the North Atlantic, where downwelling waves initiate an enhancement of the AMOC by making surface waters denser.