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Marine environments, particularly coral reefs, are becoming increasingly threatened by localized impacts such as declining water quality from excess nutrients as well as global pressures related to human-induced climate change. Marine microorganisms are known to rapidly respond to a wide range of different environmental pressures and can act as early warning indicators of changes in the health of ocean ecosystems. Despite this, there is limited understanding of how microbes will respond to different environmental pressures. This ARC Discovery project will resolve this critical knowledge gap by developing a unique molecular platform for deriving quantitative stress thresholds for microbial communities inhabiting key reef habitats (seawater, sediments, invertebrates). Quantifying how reef microorganisms respond to a broad suite of environmental perturbations (temperature, nutrients, contaminants), will generate stress-response data that can be incorporated alongside eukaryotic data in environmental assessments, greatly improving the ecological relevance and reliability of risk and vulnerability assessments.