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Reef health is currently primarily assessed using visual surveys of coral condition combined with measurements of water quality. However visible signs of compromised health often represent a very late stage in the stress response when little management action can be taken to mitigate impact. In contrast, microorganisms are very sensitive early indicators of ecosystem health because they are the first organisms to respond to any environmental perturbation. With support from the Qld Research Infrastructure Co-Investment Fund (QRICF) and in collaboration with the Integrated Marine Observing System (IMOS) and the Australian Institute of Marine Science (AIMS), we aim to construct the first GBR microbial genomics database (GMGD). The GMGD will provide the much-needed framework to ascertain the environmental relevance / ecosystem consequences of changes in microbial community structure and function following environmental perturbation. Initial sampling to populate the database will occur at existing long-term coral reef monitoring sites (AIMS Long Term Monitoring Program), which represent different coral community types reflecting longitudinal and cross-shelf environmental gradients. In addition, a sub-set of these inshore and offshore reef sites will be established as microbial observatories to capture changes in microbial activity associated with water quality and sea surface temperature. Considering how rapidly microorganisms respond to changing environmental conditions, the construction of GMGD would provide the basis for future development of sensitive diagnostic tools for use by management, regulatory and industry stakeholders as well as the broader marine research community.