Self-supervised feature learning for rapid processing of marine imagery. Fast and reliable quantitative estimates of marine environmental health are needed for scientific studies, design and management of protected areas, and regulatory compliance of industrial activity in the ocean. Australia is collecting seafloor images at increasing rates but expert annotations are not keeping up, meaning that typical machine learning approaches struggle. This project will develop self-supervised techniques ....Self-supervised feature learning for rapid processing of marine imagery. Fast and reliable quantitative estimates of marine environmental health are needed for scientific studies, design and management of protected areas, and regulatory compliance of industrial activity in the ocean. Australia is collecting seafloor images at increasing rates but expert annotations are not keeping up, meaning that typical machine learning approaches struggle. This project will develop self-supervised techniques that use large amounts of unlabeled data to enhance performance. Our design takes advantage of additional information available for marine imagery such as geolocation and remote sensing context. We will explore how these representations can guide additional sampling and improve performance in classification tasks.Read moreRead less
Can cyanobacteria use organic nutrients to thrive in future oceans? Marine cyanobacteria are central to regulating the global climate and underpin entire marine food webs. Though they possess genes necessary to uptake diverse organic nutrients, we know very little about whether and how organic nutrients shape the physiology and ecology of cyanobacteria. Using our innovative high-throughput approach, this project aims to systematically characterise organic nutrient uptake in picocyanobacteria. O ....Can cyanobacteria use organic nutrients to thrive in future oceans? Marine cyanobacteria are central to regulating the global climate and underpin entire marine food webs. Though they possess genes necessary to uptake diverse organic nutrients, we know very little about whether and how organic nutrients shape the physiology and ecology of cyanobacteria. Using our innovative high-throughput approach, this project aims to systematically characterise organic nutrient uptake in picocyanobacteria. Our molecules-to-ecosystems approach expects to transform our understanding of alternate nutrient acquisition in cyanobacteria and how it may shape populations of these important photosynthetic organisms in a rapidly-changing ocean landscape. Read moreRead less
eGenomics - Next generation biomonitoring of threatened species. DNA is the molecule of life and exists everywhere in the environment as a largely untapped source of information on evolution, biodiversity, and ecosystem health. Our overriding aim is to start mining that information to benefit threatened species. Based on optimized ancient DNA methods, powerful sequencing technology, whole genome analyses, and RNA profiling, we present a novel and holistic framework for genetic biomonitoring. In ....eGenomics - Next generation biomonitoring of threatened species. DNA is the molecule of life and exists everywhere in the environment as a largely untapped source of information on evolution, biodiversity, and ecosystem health. Our overriding aim is to start mining that information to benefit threatened species. Based on optimized ancient DNA methods, powerful sequencing technology, whole genome analyses, and RNA profiling, we present a novel and holistic framework for genetic biomonitoring. In two parallel model systems we will study corals and reptiles to improve environmental detection while simultaneously obtaining information on their population health. This will foster more efficient conservation of endangered species that are of tremendous importance to our marine and terrestrial ecosystems.Read moreRead less
Quantifying kelp carbon and nutrient flows for nature-based solutions . This fellowship aims to resolve carbon removal and nutrient mitigation potential of Australia’s kelp forests now and in future. It will create new understanding of the ecosystem services provided by the Great Southern Reef, and the capacity of kelp forests to provide nature-based solutions to reduce emissions and improve coastal water quality. Using a combination of global models and ecological experiments on kelp forests an ....Quantifying kelp carbon and nutrient flows for nature-based solutions . This fellowship aims to resolve carbon removal and nutrient mitigation potential of Australia’s kelp forests now and in future. It will create new understanding of the ecosystem services provided by the Great Southern Reef, and the capacity of kelp forests to provide nature-based solutions to reduce emissions and improve coastal water quality. Using a combination of global models and ecological experiments on kelp forests and their replacement ecosystem states, the fellowship will predict changes in function with warming. This information is critical to determine net ecosystem mitigation potential and will significantly advance our understanding of the potential of kelp forests to generate co-benefits while conserving biodiversity. Read moreRead less
Resolving the threat of ocean deoxygenation to coral resilience. This project aims to uncover the role low oxygen plays in shaping healthy corals over space and time. Climate change and land use development are rapidly deoxygenating shallow water coral reefs, yet we have no knowledge of how less oxygen availability affects critical life history factors that govern coral resilience: growth, reproduction, and stress tolerance. This project unites a multidisciplinary team of experts to, for the fir ....Resolving the threat of ocean deoxygenation to coral resilience. This project aims to uncover the role low oxygen plays in shaping healthy corals over space and time. Climate change and land use development are rapidly deoxygenating shallow water coral reefs, yet we have no knowledge of how less oxygen availability affects critical life history factors that govern coral resilience: growth, reproduction, and stress tolerance. This project unites a multidisciplinary team of experts to, for the first time, couple advanced oxygen sensing, metabolic physiology, coral reproductive and stress biology to transform our understanding of oxygen thresholds that are diagnostic of reduced coral competitive fitness across life stages (adults, juveniles, larvae), needed to improve coral reef ecosystem management.Read moreRead less
Modern statistical methods for clustering community ecology data. This project will develop statistical methods and software for clustering community ecology data, and use them to analyse systematic survey and citizen science program data collected along the Great Barrier Reef. By doing so, the project will address the dearth of statistical classification techniques for high-dimensional, multi-response data with complex relationships. When the resultant clustering methods are used to construct b ....Modern statistical methods for clustering community ecology data. This project will develop statistical methods and software for clustering community ecology data, and use them to analyse systematic survey and citizen science program data collected along the Great Barrier Reef. By doing so, the project will address the dearth of statistical classification techniques for high-dimensional, multi-response data with complex relationships. When the resultant clustering methods are used to construct bioregions and characterise species’ environmental responses, they should significantly enhance evaluations of the impact of human activity and environmental change on coral diversity. Ultimately, these evaluations can underpin future decisions in the conservation and management of the Great Barrier Reef.Read moreRead less
Resolving the role of kelp in blue carbon cycles to enable management. We aim to uncover how kelp forests contribute to carbon storage, biodiversity enhancement and nutrient mitigation in Australia. We will combine mapping and modelling to identify local variation in kelp carbon stocks and sequestration potential and verify kelp carbon export to deep ocean sinks through genetic tracing in seawater and sediments. Co-benefits will be identified through nutrient experiments and reef surveys. We wil ....Resolving the role of kelp in blue carbon cycles to enable management. We aim to uncover how kelp forests contribute to carbon storage, biodiversity enhancement and nutrient mitigation in Australia. We will combine mapping and modelling to identify local variation in kelp carbon stocks and sequestration potential and verify kelp carbon export to deep ocean sinks through genetic tracing in seawater and sediments. Co-benefits will be identified through nutrient experiments and reef surveys. We will also assess the risk that calcification and production of halogenic gas within the kelp forest could offset its climate mitigation potential. Project outcomes will enable management to consider kelp ecosystem services broadly and optimize our capacity to meet current emission reduction and biodiversity commitments.Read moreRead less
Origin and evolution of animal-bacterial symbiosis. This project seeks to understand how interactions between animals and their microbial symbionts – the holobiont – evolved, and how they are influenced by the environment over an animal's life. Using a homegrown Australian model, a sea sponge from the Great Barrier Reef, and advanced multi-omic approaches (genomics plus cell biology), this project aims to uncover the mechanisms underlying the establishment and maintenance of the holobiont throug ....Origin and evolution of animal-bacterial symbiosis. This project seeks to understand how interactions between animals and their microbial symbionts – the holobiont – evolved, and how they are influenced by the environment over an animal's life. Using a homegrown Australian model, a sea sponge from the Great Barrier Reef, and advanced multi-omic approaches (genomics plus cell biology), this project aims to uncover the mechanisms underlying the establishment and maintenance of the holobiont through development, and under changing ecological and environmental conditions. Because of the evolutionary position of sponges, outcomes of this project expect to reveal cardinal rules governing animal-microbe interactions that are fundamental to the health and conservation of most animals and ecosystems.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE230100284
Funder
Australian Research Council
Funding Amount
$438,547.00
Summary
Adaptation potential of Australia’s coral reefs to a changing climate. Oceans are changing. Coral reefs are wonders of high socio-economic value threatened by climate extremes. This project aims to identify reefs that support the most fundamental biological processes for ecosystem-scale resilience: dispersal, symbioses, and adaptation. To urgently prepare against extinction, this project expects to deliver ground-breaking estimates of coral evolution by integrating genomics and innovative diseas ....Adaptation potential of Australia’s coral reefs to a changing climate. Oceans are changing. Coral reefs are wonders of high socio-economic value threatened by climate extremes. This project aims to identify reefs that support the most fundamental biological processes for ecosystem-scale resilience: dispersal, symbioses, and adaptation. To urgently prepare against extinction, this project expects to deliver ground-breaking estimates of coral evolution by integrating genomics and innovative disease models. Expected outcomes include the discovery of reefs that can survive extremes and repopulate other reefs, providing benefits in optimized capabilities to protect resilient and vulnerable reefs to sustain future ecosystem services and boosting Australia as a global leader in the conservation genomics revolution.Read moreRead less
Improved management of marine habitats by learning from historical change. This project aims to greatly improve the cost-effectiveness of actions to protect and restore shallow subtidal marine habitats by quantifying the severity and distribution of recent human impacts. Environmental change will be quantified as the difference between contemporary and historical assemblages encompassing thousands of invertebrate species, and by reading historical chronicles coded by mollusc shells layered in se ....Improved management of marine habitats by learning from historical change. This project aims to greatly improve the cost-effectiveness of actions to protect and restore shallow subtidal marine habitats by quantifying the severity and distribution of recent human impacts. Environmental change will be quantified as the difference between contemporary and historical assemblages encompassing thousands of invertebrate species, and by reading historical chronicles coded by mollusc shells layered in sediments. The roles of different stressors (warming, dredging, eutrophication, introduced species, sediment runoff) will be distinguished. Expected outcomes include continental-scale understanding of factors that facilitate ecosystem decline and recovery, and of sites and species traits most affected by ongoing threats.Read moreRead less