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Coral bacteria are highly dynamic and acutely affected by host health and environmental conditions. However, there is limited knowledge of how the dynamics of coral-associated bacterial communities and interactions among bacterial members change in response to dissolved inorganic nutrient stressors. Here, we used high-throughput sequencing of the 16S rRNA gene to examine dynamic changes in coral-associated bacterial communities under elevated ammonium stress. Short-term exposure to high levels of ammonium does not significantly harm cor