Corals engage in symbioses with micro‐organisms that provide nutrients and protect the host. Where the prokaryotic microbes perform their symbiotic functions within a coral is, however, poorly understood. Here, we studied the tissue‐specific microbiota of the coral Corallium rubrum by dissecting its tissues from the skeleton and separating the white polyps from the red‐coloured coenenchyme, followed by 16S rRNA gene metabarcoding of the three fractions. Dissection was facilitated by incubating coral fragments in RNAlater, which caused tissues to detach from the skeleton. Our results show compartmentalisation of the microbiota. Specifically, Endozoicomonas, Parcubacteria and a Gammaproteobacteria were primarily located in polyps, whereas Nitrincolaceae and one Spirochaeta phylotype were found mainly in the coenenchyme. The skeleton‐associated microbiota was distinct from the microbiota in the tissues. Given the difference in tissue colour and microbiota of the polyps and coenenchyme, we analysed the microbiota of three colormorphs of C. rubrum (red, pink, white), finding that the main difference was a very low abundance of Spirochaeta in white colormorphs. While the functions of C. rubrum's symbionts are unknown, their localisation within the colony suggests that microhabitats exist, and the presence of Spirochaeta appears to be linked to the colour of C. rubrum. [ABSTRACT FROM AUTHOR]

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