Kelly E. Speare

Microbiomes are essential features of holobionts, providing their hosts with key metabolic and functional traits like resistance to environmental disturbances and diseases. In scleractinian corals, questions remain about the microbiome's role in resistance and resilience to factors contributing to the ongoing global coral decline and whether microbes serve as a form of holobiont ecological memory. To test if and how coral microbiomes affect host health outcomes during repeated disturbances, we conducted a large‐scale (32 exclosures, 200 colonies, and 3 coral species sampled) and long‐term (28 months, 2018–2020) manipulative experiment on the forereef of Mo'orea, French Polynesia. In 2019 and 2020, this reef experienced the two most severe marine heatwaves on record for the site. Our experiment and these events afforded us the opportunity to test microbiome dynamics and roles in the context of coral bleaching and mortality resulting from these successive and severe heatwaves. We report unique microbiome responses to repeated heatwaves in Acropora retusa , Porites lobata , and Pocillopora spp., which included: microbiome acclimatization in A. retusa , and both microbiome resilience to the first marine heatwave and microbiome resistance to the second marine heatwave in Pocillopora spp. Moreover, observed microbiome dynamics significantly correlated with coral species‐specific phenotypes. For example, bleaching and mortality in A. retusa both significantly increased with greater microbiome beta dispersion and greater Shannon Diversity, while P. lobata colonies had different microbiomes across mortality prevalence. Compositional microbiome changes, such as changes to proportions of differentially abundant putatively beneficial to putatively detrimental taxa to coral health outcomes during repeated heat stress, also correlated with host mortality, with higher proportions of detrimental taxa yielding higher mortality in A. retusa . This study reveals evidence for coral species‐specific microbial responses to repeated heatwaves and, importantly, suggests that host‐dependent microbiome dynamics may provide a form of holobiont ecological memory to repeated heat stress.

The outcomes of species interactions can vary greatly in time and space with the outcomes of some interactions determined by priority effects. On coral reefs, benthic algae rapidly colonize disturbed substrate. In the absence of top‐down control from herbivorous fishes, these algae can inhibit the recruitment of reef‐building corals, leading to a persistent phase shift to a macroalgae‐dominated state. Yet, corals may also inhibit colonization by macroalgae, and therefore the effects of herbivores on algal communities may be strongest following disturbances that reduce coral cover. Here, we report the results from experiments conducted on the fore reef of Moorea, French Polynesia, where we: (1) tested the ability of macroalgae to invade coral‐dominated and coral‐depauperate communities under different levels of herbivory, (2) explored the ability of juvenile corals ( Pocillopora spp.) to suppress macroalgae, and (3) quantified the direct and indirect effects of fish herbivores and corallivores on juvenile corals. We found that macroalgae proliferated when herbivory was low but only in recently disturbed communities where coral cover was also low. When coral cover was <10%, macroalgae increased 20‐fold within 1 year under reduced herbivory conditions relative to high herbivory controls. Yet, when coral cover was high (50%), macroalgae were suppressed irrespective of the level of herbivory despite ample space for algal colonization. Once established in communities with low herbivory and low coral cover, macroalgae suppressed recruitment of coral larvae, reducing the capacity for coral replenishment. However, when we experimentally established small juvenile corals (2 cm diameter) following a disturbance, juvenile corals inhibited macroalgae from invading local neighborhoods, even in the absence of herbivores, indicating a strong priority effect in macroalgae–coral interactions. Surprisingly, fishes that initially facilitated coral recruitment by controlling algae had a net negative effect on juvenile corals via predation. Corallivores reduced the growth rates of corals exposed to fishes by ~30% relative to fish exclosures, despite increased competition with macroalgae within the exclosures. These results highlight that different processes are important for structuring coral reef ecosystems at different successional stages and underscore the need to consider multiple ecological processes and historical contingencies to predict coral community dynamics.