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Background  The coral is predominantly composed of the metabolically dependent coral host and the photosynthetic dinoflagellateSymbiodinium    sp . The system as a whole interacts with symbiotic eukaryotes, bacteria and viruses.Gemmocystis  cylindrus(cf. “type-N” symbiont) belonging to the obligatory parasitic phylum  Apicomplexa  ( Alveolata ) is ubiquitous in the Caribbean coral, but its presence in the Great Barrier Reef coral has yet to be documented. Approaches allowing identification of the healthy community from the pathogenic or saprobic organisms are needed for sustainable coral reef monitoring.    Methods & Principal Findings  We investigated the diversity of eukaryotes associated with a common reef-building corals from the southern Great Barrier Reef. We used three tag encoded 454 amplicon pyrosequencing assays targeting eukaryote small-subunit rRNA gene to demonstrate the presence of the apicomplexan type-N and a photosynthetic sister species to  Apicomplexa  -Chromeravelia    . Amplicon pyrosequencing revealed presence of the small-subunit rRNA genes of known eukaryotic pathogens (   Cryptosporidium    and    Cryptococcus   ). We therefore conducted bacterial tag encoded amplicon pyrosequencing assay for small-subunit rRNA gene to support effluent exposure of the coral. Bacteria of faecal origin ( Enterobacteriales ) formed 41% of total sequences in contrast to 0-2% of the coral-associated bacterial communities with and withoutC.  velia    , respectively.    Significance  This is the first time apicomplexan type-N has been detected in the Great Barrier Reef. Eukaryote tag encoded amplicon pyrosequencing assays demonstrate presence of apicomplexan type-N and  C. Velia  in total coral DNA. The data highlight the need for combined approaches for eukaryotic diversity studies coupled with bacterial community assessment to achieve a more realistic goals of defining the holobiont community and assessing coral disease. With increasing evidence of  Apicomplexa  in coral reef environments, it is important not only to understand the evolution of these organisms but also identify their potential as pathogens.

plos one

Combined Amplicon Pyrosequencing Assays Reveal Presence of the Apicomplexan “type-N” (cf. Gemmocystis cylindrus) and Chromera velia on the Great Barrier Reef, Australia