Multiple techniques point to oxygenic phototrophs dominating the Isopora palifera skeletal microbiome

The limestone skeleton of Scleractinian corals is a complex and intricate environment consisting of an array of ecological microniches, which harbour a vast microbial community. In addition, recent studies have demonstrated that endolithic microbes play a variety of important ecological roles. Here, we use a combination of metabarcoding of the small subunit rRNA genes, microscopy and spectrophotometry to characterize the endolithic community of the coral Isopora palifera, one of the most common reef builders of the Great Barrier Reef. While a previous study suggested that the Isopora skeleton was dominated by anoxygenic phototrophs, our data show an abundance of chlorophyll a, highlighting the presence of oxygenic photosynthetic endolithic microbes. Proteobacteria, Bacteriodetes, Actinobacteria and Spirochaetes were consistently found, and the bacterial community was similar in shallow and deeper skeletal micro-samples. The micro-eukaryotic community was dominated by endolithic green algae, and the protist Labyrynthula, found at previously unreported high relative abundance.