Strong Symbiodiniaceae influence on coral gene expression under ocean acidification and warming

Tropical coral reefs face unprecedented threats from ocean acidification and warming, driving alarming declines in reef communities worldwide. Yet environmental history and diverse symbiotic partnerships often shape how corals respond to environmental change. We investigated how the Caribbean coral Siderastrea siderea responds to simulated future ocean conditions by examining holobiont phenotypes, symbiotic communities, and gene expression profiles. After three months of exposure to various acidification and warming scenarios, S. siderea showed only moderate stress responses, with no shifts in algal symbiont or bacterial communities. Remarkably, even under the warmest temperature and lowest pH conditions, coral host gene expression patterns were primarily shaped by which Symbiodiniaceae genus they hosted, rather than experimental treatments. Corals predominantly hosting Durusdinium trenchii exhibited higher lipid content but reduced calcification rates compared to those hosting Cladocopium goreaui, suggesting different metabolic strategies based on which symbiont was predominant in the coral holobiont. While moderate treatment effects were observed, significant changes in holobiont phenotype and gene expression occurred mainly under extreme acidification conditions unlikely to be experienced within the next century. Under these extreme scenarios, we detected reduced growth rates and downregulation of calcification-related genes, indicating potential challenges for skeletal production in future oceans. These findings enhance our understanding of coral acclimatization strategies and emphasize how symbiotic relationships fundamentally shape coral responses to environmental change. As climate change intensifies, these molecular and physiological mechanisms may determine which coral species persist on future reefs.