Colony geometric complexity predicts the co-occurrence of coral photosymbiont genera

The endosymbiosis between tropical reef-building corals and dinoflagellate algae (family Symbiodiniaceae) underpins the healthy functioning of coral reef ecosystems. Although dominant host-symbiont pairings differ across spatial scales (e.g., bioregion, reef zone, and depth), corals often associate with multiple symbionts. Where diverse symbionts occur together, their local-scale ecology is poorly understood. Moreover, whilst coral morphological plasticity generates a structurally complex spatial habitat for endosymbiosis, the role of host geometry in facilitating symbiont co-occurrence is completely unexplored. Here, we integrated high-throughput sequencing of the ITS2 gene region with digital 3D photogrammetry to evaluate symbiont distribution within coral structural habitat and determine the influence of host morphology on symbiont community composition. Symbiont composition was characterised along a vertical gradient (coral apex to base) across 50 Hydnophora microconos colonies from Rarotonga, Cook Islands. We identified dominance by the genera Durusdinium and Cladocopium, with inter-genus co-occurrence recognised in 60% of coral colonies. The co-occurrence of two Cladocopium lineages (C3f and C3k) was validated based on congruence with the plastid minicircle psbA non-coding region (psbAncr). Geometric quantification from digital 3D reconstructions of coral colonies revealed that single symbiont taxon colonies were morphologically distinct, whilst multi-symbiont colonies exhibited a broader morphological range. Where Cladocopium-Durusdinium co-occurrence was identified, surface orientation indicated increased Durusdinium prevalence toward the base of coral colonies, corresponding to regions with the highest occlusion of modelled downwelling light. Collectively, these findings suggest that coral structural heterogeneity supports Symbiodiniaceae diversity and highlights the value of resolving microhabitat-level variation to understand symbiont co-occurrence.