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In a time of unprecedented ecological change, understanding natural biophysical relationships between reef resilience and physical drivers is of increasing importance. This study evaluates how wave forcing structures coral reef benthic community composition and recovery trajectories after the major 2015/2016 bleaching event in the remote Chagos Archipelago, Indian Ocean. Benthic cover and substrate rugosity were quantified from digital imagery at 23 fore reef sites around a small coral atoll (Salomon) in 2020 and compared to data from a similar survey in 2006 and opportunistic surveys in intermediate years. Cluster analysis and principal component analysis show strong separation of community composition between exposed (modelled wave exposure > 1000 J m−3) and sheltered sites (−3) in 2020. This difference is driven by relatively high cover of Porites sp., other massive corals, encrusting corals, soft corals, rubble and dead table corals at sheltered sites versus high cover of pavement and sponges at exposed sites. Total coral cover and rugosity were also higher at sheltered sites. Adding data from previous years shows benthic community shifts from distinct exposure-driven assemblages and high live coral cover in 2006 towards bare pavement, dead Acropora tables and rubble after the 2015/2016 bleaching event. The subsequent recovery trajectories at sheltered and exposed sites are surprisingly parallel and lead communities towards their respective pre-bleaching communities. These results demonstrate that in the absence of human stressors, community patterns on fore reefs are strongly controlled by wave exposure, even during and after widespread coral loss from bleaching events.

Emerging evidence indicates that individual stressors can modify the coral microbiome; however, few studies have examined the impacts of multiple stressors through natural climatic events. During periods of low and high heat stress associated with the 2015–2016 El Nino, we tracked the microbiomes of two coral species (Porites lobata and Montipora aequituberculata) across sites on Kiritimati (Christmas) Island with different levels of local disturbance (i.e. subsistence fishing, pollution, dredging). At low heat stress, local disturbance was associated with increased microbial alpha diversity (i.e. number of microbial OTUs and their relative abundance) in both species and increased beta diversity (i.e. coral to coral variation in microbial community composition) in P. lobata. High levels of thermal stress subsequently elevated microbial beta diversity in both species at the low disturbance sites up to the level experienced at the high disturbance sites under low heat stress, illustrating that each stressor can destabilize the coral microbiome. However, with high heat stress microbial alpha diversity was no longer significantly different between disturbance levels for either species. Survival of P. lobata throughout the entire El Nino event was greater at low disturbance sites than high ones (40% vs. 15%), suggesting that protection from local stressors may enhance survival of stress-tolerant corals. However, no M. aequituberculata tracked in this study survived the thermal anomaly. Whether enhanced survivorship can be directly attributed to lower microbial diversity, however, remains to be tested. Overall, we found that, rather than acting synergistically, multiple stressors either acted antagonistically to one another (alpha diversity for both coral species, beta diversity for P. lobata) or exhibited dominance (beta diversity for M. aequituberculata), suggesting that multiple stressors cause various interaction outcomes on the coral microbiome and highlighting the need for future research to evaluate these interactions and their consequences for coral resilience.