Host species identity drives temporally stable octocoral microbiomes in Florida

Octocorals are foundational components of Caribbean reef ecosystems, yet their bacterial microbiomes remain poorly characterized compared to scleractinian corals. We present an extensive 16S rRNA gene survey of western Atlantic octocoral microbiomes, characterizing 180 samples from four co-occurring South Florida species over three years: the encrusting species Briareum asbestinum and Erythropodium caribaeorum, and the branching species Eunicea flexuosa and Muricea muricata. Host species identity was the strongest predictor of microbiome composition, explaining 14.4% of bacterial community variation, while temporal and spatial factors contributed less than 2% each. Core microbiome analysis at three prevalence thresholds (80, 90 and 100%) revealed host-specific bacterial associations. All four species harbored largely host-specific Endozoicomonas ASVs as dominant core members, with encrusting species maintaining larger and more taxonomically diverse cores than branching species. Phylogenetic reconstruction placed the dominant Endozoicomonas ASVs among described Endozoicomonas species, three lineages related to E. euniceicola, which was described from Florida octocorals, while the dominant Mycoplasma ASVs were highly divergent from described type strains, suggesting undescribed octocoral-associated lineages. Differential abundance analysis identified only a few significant temporally or spatially variable ASVs, reinforcing overall community stability. These findings demonstrate strong host control over microbial associations and provide a phylogenetic framework for understanding octocoral-bacteria symbioses in the western Atlantic.