Exaiptasia diaphana core microbiome members are lost under climate change conditions despite host thermal tolerance

Abstract Acute and chronic exposure to elevated temperatures associated with Global Climate Change (GCC) threatens the structure and function of host-associated microbiomes, yet predicting microbial responses to heat stress remains challenging. We exposed two lines of the sea anemone, Exaiptasia diaphana , to acute and chronic thermal stress to quantify the impacts on cnidarian physiology and microbiome composition. Acute exposure caused rapid algal bleaching that was paired with pronounced shifts in bacteriome structure in both lines within 14 days of thermal exposure. Chronic exposure significantly affected the population structure, photo-physiology and bacteriome composition in only one host line, suggesting acclimation capacity depends on host-algal genetic backgrounds. Using 16S rRNA amplicon sequencing of 493 individuals sampled across 180 days, we found that sampling date explained nine-fold more variation in the microbiome composition than temperature exposure. Despite this temporal variation, we identified 16 indicator taxa that consistently changed in relative abundance under thermal stress. These taxa became central hubs in microbial association networks with increasing levels of thermal stress, suggesting they played key roles in bacteriome reorganization. As many of these taxa were present in other cnidarians, including reef-building corals, they may represent targets for conservation strategies that aim to enhance resilience on reefs.