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Corals host diverse microbial communities that are involved in acclimatization, pathogen defense, and nutrient cycling. Surveys of coral-associated microbes have been particularly directed toward  Symbiodinium  and bacteria. However, a holistic understanding of the total microbiome has been hindered by a lack of analyses bridging taxonomically disparate groups. Using high-throughput amplicon sequencing, we simultaneously characterized the  Symbiodinium , bacterial, and fungal communities associated with the Caribbean coral  Siderastrea siderea  collected from two depths (17 and 27 m) on Conch reef in the Florida Keys.  S. siderea  hosted an exceptionally diverse  Symbiodinium  community, structured differently between sampled depth habitats. While dominated at 27 m by a  Symbiodinium  belonging to clade C, at 17 m  S. siderea  primarily hosted a mixture of clade B types. Most fungal operational taxonomic units were distantly related to available reference sequences, indicating the presence of a high degree of fungal novelty within the  S. siderea  holobiont and a lack of knowledge on the diversity of fungi on coral reefs. Network analysis showed that co-occurrence patterns in the  S. siderea  holobiont were prevalent among bacteria, however, also detected between fungi and bacteria. Overall, our data show a drastic shift in the associated  Symbiodinium  community between depths on Conch Reef, which might indicate that alteration in this community is an important mechanism facilitating local physiological adaptation of the  S. siderea  holobiont. In contrast, bacterial and fungal communities were not structured differently between depth habitats.

Inter-domain microbial diversity within the coral holobiontSiderastrea sidereafrom two depth habitats