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1. High microbial diversity, functional redundancy, and prophage enrichment support the success of the yellow pencil coral, Madracis mirabilis, in Curaçao’s coral reefs

   https://doi.org/10.1128/msystems.01208-25  

   Wallace, Bailey A; Varona, Natascha S; Stiffler, Alexandra K; Vermeij, Mark_J A; Silveira, Cynthia (October 2025, mSystems)

   Adriaenssens, Evelien M (Ed.)

   ABSTRACT Coral reefs have undergone extensive coral loss and shifts in community composition worldwide. Despite this, some coral species appear naturally more resistant, such asMadracis mirabilis(hereinMadracis).Madracishas emerged as the dominant hard coral in Curaçao, comprising 26% of coral cover in reefs that declined by 78% between 1973 and 2015. Although life history traits and competitive mechanisms contribute toMadracis’s success, these factors alone may not fully explain it, as other species with similar traits have not shown comparable success. Here, we investigated the potential role of microbial communities in the success ofMadracison Curaçao reefs by leveraging a low-bias bacterial and viral enrichment method for metagenomic sequencing of coral samples, resulting in 77 unique bacterial metagenome-assembled genomes and 2,820 viral genomic sequences. Our analyses showed thatMadracis-associated bacterial and viral communities are 12% and 20% richer than the communities of five sympatric coral species combined. TheMadracis-associated bacterial community was dominated byRuegeriaandSphingomonas, genera that have previously been associated with coral health, defense against pathogens, and bioremediation. These communities also displayed higher functional redundancy, which is often associated with ecological resilience. The viral community exhibited a 50% enrichment of proviruses relative to other corals. These proviruses had the genomic capacity to laterally transfer genes involved in antibiotic resistance, central metabolism, and oxidative stress responses, potentially enhancing the adaptive capacity of theMadracismicrobiome and contributing toMadracis’s success on Curaçao’s reefs. IMPORTANCEUnderstanding why some coral species persist and thrive while most are in fast decline is critical.Madracis mirabilisis increasingly dominant on degraded reefs in Curaçao, yet the role of microbial communities in its success remains underexplored. This study highlights the potential role ofMadracis-associated bacterial and viral communities in supporting coral resilience and competitive success. By identifying key microbial partners and viral genes that may enhance host stress tolerance and defense against pathogens, we broaden the understanding of how the coral holobiont contributes to species persistence under environmental stress. These insights are valuable for predicting key microbial community players in reef interactions and may inform microbiome-based strategies to support coral conservation and restoration. 

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2. Heat-tolerant algal symbionts may prevent extirpation of the threatened elkhorn coral, Acropora palmata, in Florida during intensifying marine heatwaves

   https://doi.org/10.1007/s00338-025-02652-7  

   Karp, Richard F; Lepiz-Conejo, Fabrizio; Matsuda, Shayle B; Corbett, Bryce; Wen, Alexandra D; Unsworth, Joseph D; D’Alessandro, Martine; Nedimyer, Ken; Moura, Amelia; Muller, Erinn M; et al (June 2025, Coral Reefs)

   Abstract The elkhorn coral,Acropora palmata, was historically a major reef-building species in the Caribbean, but has suffered devastating declines in recent decades. Despite significant restoration efforts in Florida, the marine heatwave of 2023 caused severe bleaching and mortality to both wild and restored colonies. To understand the disastrous impacts, we evaluated the variation in heat tolerance among Florida’sA. palmatapopulation prior to the event. In 2022, we used rapid acute heat stress assays to assess the thermal tolerance of 172 adult colonies (125 unique genets) from four nurseries. We found variation in thermal tolerance (4.17°C range in ED50) that was attributed to nursery location (17.2% of variation), genet (25.9%), and symbiont abundance (15.6%). Algal symbiont type, however, was the strongest predictor of thermal performance, with the few (n = 10) colonies hostingDurusdiniumbeing, on average, 1.9°C more thermally tolerant than corals hostingSymbiodinium. This difference would have decreased the effective heat stress accumulation during the 2023 event by ~92%. Therefore, despite considerable variation in thermal tolerance among Florida’s elkhorn corals, hostingDurusdiniumappears to be the most effective mechanism for surviving such extreme heat stress. These findings suggest that restoration strategies that focus on rearing sexually derivedA. palmatarecruits withDurusdinium, followed by outplanting to suitable environments, may improve survival during future heatwaves. Combined with efforts to introduce additional elkhorn diversity from populations outside Florida, these approaches may be the most effective interventions to promote the continued survival of Florida’s elkhorn corals in the face of rapid climate change. 

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3. Removal of detritivore sea cucumbers from reefs increases coral disease

   https://doi.org/10.1038/s41467-024-45730-0  

   Clements, Cody S.; Pratte, Zoe A.; Stewart, Frank J.; Hay, Mark E. (February 2024, Nature Communications)

   Abstract Coral reefs are in global decline with coral diseases playing a significant role. This is especially true for Acroporid corals that represent ~25% of all Pacific coral species and generate much of the topographic complexity supporting reef biodiversity. Coral diseases are commonly sediment-associated and could be exacerbated by overharvest of sea cucumber detritivores that clean reef sediments and may suppress microbial pathogens as they feed. Here we show, via field manipulations in both French Polynesia and Palmyra Atoll, that historically overharvested sea cucumbers strongly suppress disease among corals in contact with benthic sediments. Sea cucumber removal increased tissue mortality ofAcropora pulchraby ~370% and colony mortality by ~1500%. Additionally, farmerfish that killAcropora pulchrabases to culture their algal gardens further suppress disease by separating corals from contact with the disease-causing sediment—functioning as mutualists rather than parasites despite killing coral bases. Historic overharvesting of sea cucumbers increases coral disease and threatens the persistence of tropical reefs. Enhancing sea cucumbers may enhance reef resilience by suppressing disease. 

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4. Microbiome ecological memory and responses to repeated marine heatwaves clarify variation in coral bleaching and mortality

   https://doi.org/10.1111/gcb.17088  

   Vompe, Alex_D; Epstein, Hannah_E; Speare, Kelly_E; Schmeltzer, Emily_R; Adam, Thomas_C; Burkepile, Deron_E; Sharpton, Thomas_J; Vega Thurber, Rebecca (December 2023, Global Change Biology)

   Abstract 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 inAcropora retusa,Porites lobata, andPocilloporaspp., which included: microbiome acclimatization inA. retusa, and both microbiome resilience to the first marine heatwave and microbiome resistance to the second marine heatwave inPocilloporaspp. Moreover, observed microbiome dynamics significantly correlated with coral species‐specific phenotypes. For example, bleaching and mortality inA. retusaboth significantly increased with greater microbiome beta dispersion and greater Shannon Diversity, whileP. lobatacolonies 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 inA. 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. 

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5. Coral bleaching resistance variation is linked to differential mortality and skeletal growth during recovery

   https://doi.org/10.1111/eva.13500  

   Walker, Nia S.; Nestor, Victor; Golbuu, Yimnang; Palumbi, Stephen R. (February 2023, Evolutionary Applications)

   Abstract The prevalence of global coral bleaching has focused much attention on the possibility of interventions to increase heat resistance. However, if high heat resistance is linked to fitness tradeoffs that may disadvantage corals in other areas, then a more holistic view of heat resilience may be beneficial. In particular, overall resilience of a species to heat stress is likely to be the product of both resistance to heat and recovery from heat stress. Here, we investigate heat resistance and recovery among individualAcropora hyacinthuscolonies in Palau. We divided corals into low, moderate, and high heat resistance categories based on the number of days (4–9) needed to reach significant pigmentation loss due to experimental heat stress. Afterward, we deployed corals back onto a reef in a common garden 6‐month recovery experiment that monitored chlorophylla, mortality, and skeletal growth. Heat resistance was negatively correlated with mortality during early recovery (0–1 month) but not late recovery (4–6 months), and chlorophyllaconcentration recovered in heat‐stressed corals by 1‐month postbleaching. However, moderate‐resistance corals had significantly greater skeletal growth than high‐resistance corals by 4 months of recovery. High‐ and low‐resistance corals on average did not exhibit skeletal growth within the observed recovery period. These data suggest complex tradeoffs may exist between coral heat resistance and recovery and highlight the importance of incorporating multiple aspects of resilience into future reef management programs. 

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