Abstract
Dinoflagellates of the family Symbiodiniaceae are important symbionts of diverse marine animals and they also occupy different environmental niches on coral reefs. The link between diversity at ecosystem‐scale to microhabitats of Symbiodiniaceae within the coral holobiont is largely unknown. Using ITS2‐amplicon sequencing, we compared Symbiodiniaceae communities across four environments (seawater, near‐reef vs. distant sediments and turf algae) and two coral microhabitats (tissue, mucus) on a coral reef in the Red Sea. We found that coral and environmental habitats were both dominated by the genera Symbiodinium , Cladocopium and Durusdinium , but environmental habitats additionally harboured Fugacium , Gerakladium and Halluxium . Each environmental habitat harboured a distinct Symbiodiniaceae community. Nonetheless, 17 ITS2 sequences were shared among coral and environmental habitats and were also part of nearly half of the ITS2 type profiles in coral‐based communities. Tissues and mucus of 49 coral colonies from 17 genera had largely identical Symbiodiniaceae communities. Together with the large difference between environmental Symbiodiniaceae communities and those in the coral tissue and mucus, our results indicate a clear barrier between host‐associated and environmental Symbiodiniaceae communities marked by only few shared complete type profiles. Monitoring coral colonies after mucus sampling confirmed its suitability for long‐term monitoring of coral‐associated Symbiodiniaceae communities.