Environmental Factors Have a Stronger Influence on the Coral Holobiont in Comparison to Geographic Distance Along a 15,000‐km East‐to‐West Transect Through the Coral Triangle, Pacific and Indian Oceans

ABSTRACT Aim To determine the factors that structure coral‐associated microbial communities (bacteria and Symbiodiniaceae). These microbial communities play critical roles in reef ecosystem function, yet the relative importance of environmental versus geographic drivers in structuring these communities across large spatial scales remains poorly understood, particularly across broad Indo‐Pacific gradients that include biodiversity hotspots such as the Coral Triangle. Location Coral reefs across a ~15,000‐km east‐to‐west transect encompassing the Indian Ocean, Coral Triangle and South Pacific Ocean. Time Period Present day. Major Taxa Studied Coral host: Pocillopora acuta and its hosted Symbionts—Bacteria (16S rRNA gene) and Symbiodiniaceae (ITS2 region). Methods A total of 432 samples were collected, sequenced and processed to determine the composition of the hosted bacterial and Symbiodiniaceae communities. Biogeographic structuring and environmental associations were determined using alpha and beta diversity metrics, Mantel tests, distance‐based community dissimilarity and redundancy analysis. Results Significant differences in community composition and structure were detected between regions. Bacterial alpha diversity was relatively even across regions; however, community composition showed strong spatial turnover with a shift in bacterial and Symbiodiniaceae communities observed across the environmental gradient. Cooler Pacific reefs are characterized by Endozoicomonas‐ dominated bacterial communities and Cladocopium ‐dominated Symbiodiniaceae communities. In contrast, the warmer reefs of the Coral Triangle and western Indo‐Pacific have a higher abundance of opportunistic bacterial taxa, including Pseudoalteromonas , with Symbiodinaceae communities dominated by Durusdinium. Main Conclusion Bacterial and Symbiodiniaceae communities hosted by the coral P. acuta are structured primarily by environmental filtering, not by geographic distance. With communities primarily appearing to be structured by regionally specific and localized environmental conditions. These findings highlight the importance of local environmental conditions in structuring coral‐associated microbial assemblages across the Indo‐Pacific even when community members have the potential for long‐distance dispersal.