Corals are fundamental ecosystem engineers, creating large, intricate reefs that support
diverse and abundant marine life. At the core of a healthy coral animal is a dynamic
relationship with microorganisms, including a mutually beneficial symbiosis with photosynthetic
dinoflagellates (Symbiodinium spp.) and enduring partnerships with an array of bacterial,
archaeal, fungal, protistan, and viral associates, collectively termed the coral holobiont.
The combined genomes of this coral holobiont form a coral hologenome, and genomic
interactions within the hologenome ultimately define the coral phenotype. Here we
integrate contemporary scientific knowledge regarding the ecological, host-specific,
and environmental forces shaping the diversity, specificity, and distribution of microbial
symbionts within the coral holobiont, explore physiological pathways that contribute
to holobiont fitness, and describe potential mechanisms for holobiont homeostasis.
Understanding the role of the microbiome in coral resilience, acclimation, and environmental
adaptation is a new frontier in reef science that will require large-scale collaborative