The Diversity, Distribution, and Temporal Stability of Coral ‘zooxanthellae’ on a Pacific Reef: from the Scale of Individual Colonies to Across the Host Community

The ecological and evolutionary consequences of partner fidelity and flexibility among coral–dinoflagellate mutualisms are widely debated. Resident symbionts can modulate the resilience of their hosts to environmental stressors, which explains, in part, why host–symbiont combinations differ over broad geographic ranges and across physical–environmental gradients in light and temperature. Therefore, flexibility in these mutualisms may influence the longevity of coral populations and communities subjected to ocean warming. However, despite decades of research, basic knowledge about these mutualisms remains incomplete, hindering the development of predictive ecological theory. In particular, few studies have investigated the long-term composition of symbiont populations within individual colonies. To further examine the extent to which coral colonies have stable relationships with specific symbionts over multiple years, diverse coral taxa (Scleractinia) from a West Indo-Pacific fore reef (Palau) were tagged and sampled at various intervals—ranging from six months to several years—over nine years' time. Symbiont identity was examined using multiple genetic markers that resolved symbiont diversity to species and individual genotypes (i.e., clonal strains). Members of the genus Cladocopium (formerly Symbiodinium Clade C) were prevalent across the host community. Generally, corals with open modes of symbiont acquisition harbored a host–generalist symbiont, while corals with vertical symbiont transmission were associated with co-evolved host-specific symbionts. Consistent with previous colony monitoring studies, symbiont populations in a majority of colonies were dominated by one species and one strain (based on multilocus genotyping) over multiple years. Thus, the distribution of symbiont diversity at the genus, species and clone level, comprising specific and stable partner combinations, scale predictably to reef habitat, host taxon, and individual colony. Recognizing these fundamental ecological patterns establishes a more comprehensive understanding of the population and community structure of these mutualisms.