Living in the City: Symbiont stability and bacterial compositional and functional plasticity in Miami’s urban corals

Abstract Increasing urbanization and climate change pose significant threats to coral reefs, highlighting the need to understand the process underlying coral acclimatization in urban environments. Alterations in the microbiome composition represent a key mechanism by which corals adapt to varying environmental conditions. We compared endosymbionts and bacterial communities associated with Siderastrea siderea from urban and offshore Miami reef tracts across three seasons. We found two distinct genera of endosymbiotic Symbiodiniaceae algae, namely Cladocopium and Breviolum, consistently across sites and seasons, with Cladocopium predominating. The stable presence of these symbionts suggests host specificity in S. siderea and highlights the potential advantage of harboring multiple symbionts to enhance survival in diverse environments. In contrast, bacterial diversity exhibited variation across seasons and locations, with a small subset of microbes identified as a core microbiome demonstrating the remarkable plasticity of bacterial communities in response to environmental changes. Differential analysis revealed an increased abundance of Alteromonas and Synechococcus in urban corals, which may contribute to host nutrient acquisition, antibiotic production, and survival in polluted environments. Predicted functional profiles further demonstrated distinct metabolic reorganization of microbial communities between urban and offshore reefs, with urban corals enriched in pathways associated with stress response, pollutant degradation, and nutrient cycling. Together, these findings indicate that while algal symbionts remain stable, bacterial communities undergo both compositional and functional plasticity that likely supports coral persistence in highly urbanized environments.