Published in Abstracts of International Coral Reef Symposium 2008 The Host as a Habitat Divided Nathan D. Olson, University of Hawaii at Hilo HI, USA Tracy Ainsworth, University of Queensland, Queensland, AUS Mali’o Kodis, University of Hawaii at Hilo, USA Ruth D. Gates, Hawaiian Institute of Marine Biology HI, USA Misaki Takabayashi, University of Hawaii at Hilo HI, USA Scleractinian corals are now viewed as complex holobiont systems comprising the animal host and a consortium of microbial symbionts. This conceptual shift has led us to consider the coral host as a habitat. When viewed as a habitat, the coral can be subdivided into three compartments or interacting systems; the endolith, tissue, and mucus. Microbes in these compartments are speculated to be linked to the rest of the holobiont community through nitrogen interdependency. In order to assess the identity and potential roles of symbiotic microbes in the nitrogen cycle of the coral holobiont, we examined the microbes present in each of these three compartments of Hawaiian corals of genus Montipora. The prevalence of endolithic fungi in Montipora capitata was analyzed across an environmental gradient present in Kaneohe Bay through the use of culturing techniques. The results indicate a mean prevalence of 75% (n = 120) with no statistically significant difference in prevalence at sites that cross the gradient. The mean prevalence of endolithic fungi is higher in Kaneohe Bay, Hawaii than reported for other reef systems. Within the coral tissue compartment, nifH sequence data obtained from M. capitata tissue indicates the presence of bacteria capable of nitrogen fixation belonging to the taxa Vibrio. Fluorescent in situ hybridization of tissue sections of M. capitata using probes specific to the bacterial genus Vibrio revealed that the bacteria are localized within the coral epidermal tissue layer. Lastly, the diversity of microbial ribotypes present in the mucus of M. patula was analyzed using molecular approaches. Collectively, these data contribute a more thorough characterization of the complexity of microbial communities in corals and allow for the generation of hypotheses regarding the role of each microbial member in the nitrogen cycling within the coral holobiont.