Low-abundance taxa drive host microbiome response to temperature stress

Global climate change (GCC) will lead to the deterioration of host and microbiome health, posing a significant threat to complex symbioses. To gauge the reproducibility of thermal warming associated with GCC and the time scales on which it occurs, we monitored shifts in the Exaiptasia microbiome in 24 populations of the model cnidarian Exaiptasia diaphana over the course of six months. We identified a small cohort of temperature-sensitive amplicon sequence variants (ASVs) that reproducibly declined with increases in temperature before changes in host fitness occurred. After comparing these ASVs to global datasets, we found that the heat-impacted ASVs from our experiment were also present in many other cnidarian species, highlighting their potential as widespread indicators of thermal stress. Overall, we find that fewer than 1% of the microbiome within E. diaphana are heat indicator taxa, suggesting that a small but consistent group of ASVs signals the early stages of thermal stress.