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Nutrient levels in coastal environments have been increasing globally due to elevated inputs of sewage and terrigenous sediments carrying fertilizers. Yet, despite their immense filtering capacities, marine sponges appear to be less affected by elevated nutrients than sympatric benthic organisms, such as corals. While the molecular-level stress response of sponges to elevated seawater temperatures and other toxicants has been defined, this study represents the first global gene expression analysis of how sponges respond to elevated nit