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  • Review Article
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Extending the natural adaptive capacity of coral holobionts

Abstract

Anthropogenic climate change and environmental degradation destroy coral reefs, the ecosystem services they provide, and the livelihoods of close to a billion people who depend on these services. Restoration approaches to increase the resilience of corals are therefore necessary to counter environmental pressures relevant to climate change projections. In this Review, we examine the natural processes that can increase the adaptive capacity of coral holobionts, with the aim of preserving ecosystem functioning under future ocean conditions. Current approaches that centre around restoring reef cover can be integrated with emerging approaches to enhance coral stress resilience and, thereby, allow reefs to regrow under a new set of environmental conditions. Emerging approaches such as standardized acute thermal stress assays, selective sexual propagation, coral probiotics, and environmental hardening could be feasible and scalable in the real world. However, they must follow decision-making criteria that consider the different reef, environmental, and ecological conditions. The implementation of adaptive interventions tailored around nature-based solutions will require standardized frameworks, appropriate ecological risk–benefit assessments, and analytical routines for consistent and effective utilization and global coordination.

Key points

  • Coral reefs are degrading globally from anthropogenic climate change and local environmental impacts; deteriorated reefs are facing severe and widespread loss without active intervention.

  • Ongoing efforts aim to extend the natural adaptive capacity of reef-forming coral holobionts through incorporation of novel tools, methods, and environments to manipulate coral adaptive responses to survive under more extreme or variable conditions.

  • Emerging nature-based adaptive approaches spur novel intervention strategies that hold the promise to be feasible and scalable in the real world but must be tailored to address the diverse reef, environmental, and ecological conditions.

  • Implementing an adaptive intervention framework focused on naturally evolved solutions will require standardized methodology, appropriate ecological risk–benefit assessments, and analytical routines for consistent and effective utilization and global coordination.

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Fig. 1: The coral holobiont (metaorganism).
Fig. 2: Adaptive processes in the coral holobiont and their utilization in adaptive interventions.
Fig. 3: A scaled adaptive intervention framework.
Fig. 4: Research road map for extending the adaptive capacity of the coral holobiont.

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References

  1. Fisher, R. et al. Species richness on coral reefs and the pursuit of convergent global estimates. Curr. Biol. 25, 500–505 (2015).

    Article  Google Scholar 

  2. Costanza, R. et al. Changes in the global value of ecosystem services. Glob. Environ. Change 26, 152–158 (2014).

    Article  Google Scholar 

  3. Moberg, F. & Folke, C. Ecological goods and services of coral reef ecosystems. Ecol. Econ. 29, 215–233 (1999).

    Article  Google Scholar 

  4. Wilkinson, C. Status of Coral Reefs of the World: 2008 (Global Coral Reef Monitoring Network, 2008).

  5. Spalding, M. et al. Mapping the global value and distribution of coral reef tourism. Mar. Policy 82, 104–113 (2017).

    Article  Google Scholar 

  6. Hoegh-Guldberg, O. Climate change, coral bleaching and the future of the world’s coral reefs. Mar. Freshw. Res. 50, 839–866 (1999). This paper projects loss and degradation of coral reefs on a global scale before it became common knowledge.

    Google Scholar 

  7. Hughes, T. P. et al. Global warming transforms coral reef assemblages. Nature 556, 492–496 (2018).

    Article  Google Scholar 

  8. Porter, J. W. & Meier, O. W. Quantification of loss and change in Floridian reef coral populations. Am. Zool. 32, 625–640 (1992).

    Article  Google Scholar 

  9. Ruzicka, R. R. et al. Temporal changes in benthic assemblages on Florida Keys reefs 11 years after the 1997/1998 El Niño. Mar. Ecol. Prog. Ser. 489, 125–141 (2013).

    Article  Google Scholar 

  10. Somerfield, P. J. et al. Changes in coral reef communities among the Florida Keys, 1996–2003. Coral Reefs 27, 951–965 (2008).

    Article  Google Scholar 

  11. Lapointe, B. E., Brewton, R. A., Herren, L. W., Porter, J. W. & Hu, C. Nitrogen enrichment, altered stoichiometry, and coral reef decline at Looe Key, Florida Keys, USA: a 3-decade study. Mar. Biol. 166, 108 (2019).

    Article  Google Scholar 

  12. Suggett, D. J. & Smith, D. J. Coral bleaching patterns are the outcome of complex biological and environmental networking. Global Change Biol. https://doi.org/10.1111/gcb.14871 (2019).

    Article  Google Scholar 

  13. Hughes, T. P. et al. Spatial and temporal patterns of mass bleaching of corals in the Anthropocene. Science 359, 80–83 (2018).

    Article  Google Scholar 

  14. Lesser, M. P. in Coral Reefs: An Ecosystem in Transition (eds Dubinsky, Z. & Stambler, N.) 405–419 (Springer, 2011).

  15. Rädecker, N. et al. Heat stress destabilizes symbiotic nutrient cycling in corals. Proc. Natl Acad. Sci. USA 118, e2022653118 (2021). This paper demonstrates that algal symbionts cease photosynthate transfer to coral hosts under heat stress long before visual signs of bleaching (symbiont loss) become evident.

    Article  Google Scholar 

  16. Allen, M. R. et al. in Sustainable Development, and Efforts to Eradicate Poverty (eds Masson-Delmotte, V. et al.) 41–91 (IPCC, 2018).

  17. Gattuso, J.-P. et al. Contrasting futures for ocean and society from different anthropogenic CO2 emissions scenarios. Science 349, aac4722 (2015).

    Article  Google Scholar 

  18. Hughes, D. J. et al. Coral reef survival under accelerating ocean deoxygenation. Nat. Clim. Chang. 10, 296–307 (2020).

    Article  Google Scholar 

  19. Durack, P.J., Wijffels, S.E. & Matear, R.J. Ocean salinities reveal strong global water cycle intensification during 1950 to 2000. Science 336, 455-458 (2012).

    Article  Google Scholar 

  20. Morris, L. A., Voolstra, C. R., Quigley, K. M., Bourne, D. G. & Bay, L. K. Nutrient availability and metabolism affect the stability of coral–Symbiodiniaceae symbioses. Trends Microbiol. 27, 678–689 (2019).

    Article  Google Scholar 

  21. Muller, E. M., Sartor, C., Alcaraz, N. I. & van Woesik, R. Spatial Epidemiology of the Stony-Coral-Tissue-Loss Disease in Florida. Front. Mar. Sci. 7, 163 (2020).

    Article  Google Scholar 

  22. Hughes, T. P. et al. Climate change, human impacts, and the resilience of coral reefs. Science 301, 929–933 (2003).

    Article  Google Scholar 

  23. Nyström, M., Folke, C. & Moberg, F. Coral reef disturbance and resilience in a human-dominated environment. Trends Ecol. Evol. 15, 413–417 (2000).

    Article  Google Scholar 

  24. Wiedenmann, J. et al. Nutrient enrichment can increase the susceptibility of reef corals to bleaching. Nat. Clim. Chang. 3, 160–164 (2012).

    Article  Google Scholar 

  25. D’Angelo, C. & Wiedenmann, J. Impacts of nutrient enrichment on coral reefs: new perspectives and implications for coastal management and reef survival. Curr. Opin. Environ. Sust. 7, 82–93 (2014).

    Article  Google Scholar 

  26. Thurber, R. L. V. et al. Chronic nutrient enrichment increases prevalence and severity of coral disease and bleaching. Glob. Change Biol. 20, 544–554 (2014).

    Article  Google Scholar 

  27. Donovan, M. K. et al. Local conditions magnify coral loss after marine heatwaves. Science 372, 977–980 (2021).

    Article  Google Scholar 

  28. Climate change widespread, rapid, and intensifying. IPCC (9 August 2021); https://www.ipcc.ch/2021/08/09/ar6-wg1-20210809-pr.

  29. Radchuk, V. et al. Adaptive responses of animals to climate change are most likely insufficient. Nat. Commun. 10, 3109 (2019).

    Article  Google Scholar 

  30. Kleypas, J. et al. Designing a blueprint for coral reef survival. Biol. Conserv. 257, 109107 (2021).

    Article  Google Scholar 

  31. Gattuso, J.-P. et al. Ocean solutions to address climate change and Its effects on marine ecosystems. Front. Mar. Sci. 5, 337 (2018).

    Article  Google Scholar 

  32. Knowlton, N. et al. Rebuilding Coral Reefs: A Decadal Grand Challenge (International Coral Reef Society and Future Earth Coasts, 2021) https://doi.org/10.53642/NRKY9386.

  33. Hoegh-Guldberg, O., Kennedy, E. V., Beyer, H. L., McClennen, C. & Possingham, H. P. Securing a long-term future for coral reefs. Trends Ecol. Evol. 33, 936–944 (2018).

    Article  Google Scholar 

  34. Zoccola, D. et al. The World Coral Conservatory (WCC): a Noah’s ark for corals to support survival of reef ecosystems. PLoS Biol. 18, e3000823 (2020).

    Article  Google Scholar 

  35. Kleinhaus, K. et al. Science, diplomacy, and the Red Sea’s unique coral reef: it’s time for action. Front. Mar. Sci. 7, 90 (2020).

    Article  Google Scholar 

  36. van Oppen, M. J. H., Oliver, J. K., Putnam, H. M. & Gates, R. D. Building coral reef resilience through assisted evolution. Proc. Natl Acad. Sci. USA 112, 2307–2313 (2015).

    Article  Google Scholar 

  37. Baums, I. B. et al. Considerations for maximizing the adaptive potential of restored coral populations in the western Atlantic. Ecol. Appl. 29, e01978 (2019).

    Article  Google Scholar 

  38. Peixoto, R. S., Sweet, M. & Bourne, D. G. Customized medicine for corals. Front. Mar. Sci. 6, 686 (2019).

    Article  Google Scholar 

  39. Rinkevich, B. The active reef restoration toolbox is a vehicle for coral resilience and adaptation in a changing world. J. Mar. Sci. Eng. 7, 201 (2019).

    Article  Google Scholar 

  40. Boström-Einarsson, L. et al. Coral restoration — a systematic review of current methods, successes, failures and future directions. PLoS ONE 15, e0226631 (2020).

    Article  Google Scholar 

  41. Voolstra, C. R. et al. Standardized short-term acute heat stress assays resolve historical differences in coral thermotolerance across microhabitat reef sites. Glob. Chang. Biol. 26, 4328–4343 (2020). This paper highlights the potential of mobile acute heat stress assays to resolve fine-scale differences in coral thermotolerance, suitable for large-scale identification of resilient genotypes/reefs for conservation and restoration approaches.

    Article  Google Scholar 

  42. Parkinson, J. E. et al. Molecular tools for coral reef restoration: beyond biomarker discovery. Conserv. Lett. 13, e12687 (2020).

    Article  Google Scholar 

  43. Voolstra, C. R. et al. Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance. Mol. Ecol. https://doi.org/10.1111/mec.16064 (2021).

    Article  Google Scholar 

  44. Morikawa, M. K. & Palumbi, S. R. Using naturally occurring climate resilient corals to construct bleaching-resistant nurseries. Proc. Natl Acad. Sci. USA 116, 10586–10591 (2019).

    Article  Google Scholar 

  45. Sweet, M. & Brown, B. in Oceanography and Marine Biology — An Annual Review (eds Hughes R.N. et al.) 271–314 (CRC, 2016).

  46. Voolstra, C. R. & Ziegler, M. Adapting with microbial help: microbiome flexibility facilitates rapid responses to environmental change. Bioessays 42, e2000004 (2020). This paper proposes microbiome flexibility as a mechanism to aid adaptation to environmental change and posits that capacity for dynamic restructuring of the microbiome is host specific.

    Article  Google Scholar 

  47. Jaspers, C. et al. Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches. Zoology 133, 81–87 (2019).

    Article  Google Scholar 

  48. Torda, G. et al. Rapid adaptive responses to climate change in corals. Nat. Clim. Chang. 7, 627–636 (2017).

    Article  Google Scholar 

  49. Ziegler, M., Seneca, F. O., Yum, L. K., Palumbi, S. R. & Voolstra, C. R. Bacterial community dynamics are linked to patterns of coral heat tolerance. Nat. Commun. 8, 14213 (2017). This paper provides the first putative link between bacterial community composition and coral heat tolerance.

    Article  Google Scholar 

  50. Morgans, C. A., Hung, J. Y., Bourne, D. G. & Quigley, K. M. Symbiodiniaceae probiotics for use in bleaching recovery. Restor. Ecol. 28, 282–288 (2020).

    Article  Google Scholar 

  51. Liew, Y. J. et al. Intergenerational epigenetic inheritance in reef-building corals. Nat. Clim. Chang. 10, 254–259 (2020).

    Article  Google Scholar 

  52. Craggs, J. et al. Inducing broadcast coral spawning ex situ: closed system mesocosm design and husbandry protocol. Ecol. Evol. 7, 11066–11078 (2017).

    Article  Google Scholar 

  53. Camp, E. F., Schoepf, V. & Suggett, D. J. How can “super corals” facilitate global coral reef survival under rapid environmental and climatic change? Glob. Chang. Biol. 24, 2755–2757 (2018).

    Article  Google Scholar 

  54. Peixoto, R. S. et al. Coral probiotics: premise, promise, prospects. Annu. Rev. Anim. Biosci. 9, 265–288 (2021). This paper reviews coral probiotics and critical assessment of applicability.

    Article  Google Scholar 

  55. Doering, T. et al. Towards enhancing coral heat tolerance: a “microbiome transplantation” treatment using inoculations of homogenized coral tissues. Microbiome 9, 102 (2021).

    Article  Google Scholar 

  56. Howells, E. J. et al. Enhancing the heat tolerance of reef-building corals to future warming. Sci. Adv. 7 (2021).

  57. Devlin-Durante, M. K., Miller, M. W., Caribbean Acropora Research Group, Precht, W. F. & Baums, I. B. How old are you? Genet age estimates in a clonal animal. Mol. Ecol. 25, 5628–5646 (2016).

    Article  Google Scholar 

  58. Irwin, A. et al. Age and intraspecific diversity of resilient Acropora communities in Belize. Coral Reefs 36, 1111–1120 (2017).

    Article  Google Scholar 

  59. Palumbi, S. R., Barshis, D. J., Traylor-Knowles, N. & Bay, R. A. Mechanisms of reef coral resistance to future climate change. Science 344, 895–898 (2014). This paper demonstrates that acclimation and adaptation contribute to coral thermal tolerance and climate resistance at about equal contribution.

    Article  Google Scholar 

  60. Barott, K. L. et al. Coral bleaching response is unaltered following acclimatization to reefs with distinct environmental conditions. Proc. Natl Acad. Sci. USA 118, e2025435118 (2021).

    Article  Google Scholar 

  61. Thomas, L., López, E. H., Morikawa, M. K. & Palumbi, S. R. Transcriptomic resilience, symbiont shuffling, and vulnerability to recurrent bleaching in reef-building corals. Mol. Ecol. 28, 3371–3382 (2019).

    Article  Google Scholar 

  62. Bellantuono, A. J., Granados-Cifuentes, C., Miller, D. J., Hoegh-Guldberg, O. & Rodriguez-Lanetty, M. Coral thermal tolerance: tuning gene expression to resist thermal stress. PLoS ONE 7, e50685 (2012).

    Article  Google Scholar 

  63. Barshis, D. J. et al. Genomic basis for coral resilience to climate change. Proc. Natl Acad. Sci. USA 110, 1387–1392 (2013).

    Article  Google Scholar 

  64. Savary, R. et al. Fast and pervasive transcriptomic resilience and acclimation of extremely heat-tolerant coral holobionts from the northern Red Sea. Proc. Natl Acad. Sci. USA 118, e2023298118 (2021).

    Article  Google Scholar 

  65. Liew, Y. J. et al. Epigenome-associated phenotypic acclimatization to ocean acidification in a reef-building coral. Sci. Adv. 4, eaar8028 (2018).

    Article  Google Scholar 

  66. Durante, M. K., Baums, I. B., Williams, D. E., Vohsen, S. & Kemp, D. W. What drives phenotypic divergence among coral clonemates of Acropora palmata? Mol. Ecol. 28, 3208–3224 (2019).

    Article  Google Scholar 

  67. Rodríguez-Casariego, J. A. et al. Genome-Wide DNA Methylation Analysis Reveals a Conserved Epigenetic Response to Seasonal Environmental Variation in the Staghorn Coral Acropora cervicornis. Front. Mar. Sci. 7, 822 https://doi.org/10.3389/fmars.2020.560424 (2020).

  68. Putnam, H. M. & Gates, R. D. Preconditioning in the reef-building coral Pocillopora damicornis and the potential for trans-generational acclimatization in coral larvae under future climate change conditions. J. Exp. Biol. 218, 2365–2372 (2015).

    Article  Google Scholar 

  69. Putnam, H. M., Davidson, J. M. & Gates, R. D. Ocean acidification influences host DNA methylation and phenotypic plasticity in environmentally susceptible corals. Evol. Appl. 9, 1165–1178 (2016).

    Article  Google Scholar 

  70. Putnam, H. M., Ritson-Williams, R., Cruz, J. A., Davidson, J. M. & Gates, R. D. Environmentally-induced parental or developmental conditioning influences coral offspring ecological performance. Sci. Rep. 10, 13664 (2020).

    Article  Google Scholar 

  71. Drury, C. et al. Genomic variation among populations of threatened coral: Acropora cervicornis. BMC Genomics 17, 286 (2016).

    Article  Google Scholar 

  72. Bay, R. A., Rose, N. H., Logan, C. A. & Palumbi, S. R. Genomic models predict successful coral adaptation if future ocean warming rates are reduced. Sci. Adv. 3, e1701413 (2017).

    Article  Google Scholar 

  73. Prada, C. et al. Empty niches after extinctions increase population sizes of modern corals. Curr. Biol. 26, 3190–3194 (2016).

    Article  Google Scholar 

  74. Robitzch, V., Banguera-Hinestroza, E., Sawall, Y., Al-Sofyani, A. and Voolstra, C.R., 2015. Absence of genetic differentiation in the coral Pocillopora verrucosa along environmental gradients of the Saudi Arabian Red Sea. Front. Mar. Sci. 2, 5 (2015).

    Article  Google Scholar 

  75. Van Oppen, M. J. H., Souter, P., Howells, E. J., Heyward, A. & Berkelmans, R. Novel genetic diversity through somatic mutations: fuel for adaptation of reef corals? Diversity 3, 405–423 (2011).

    Article  Google Scholar 

  76. Vasquez Kuntz, K. L. et al. Juvenile corals inherit mutations acquired during the parent’s lifespan. Preprint at bioRxiv https://doi.org/10.1101/2020.10.19.345538 (2020).

    Article  Google Scholar 

  77. Matz, M. V., Treml, E. A., Aglyamova, G. V. & Bay, L. K. Potential and limits for rapid genetic adaptation to warming in a Great Barrier Reef coral. PLoS Genet. 14, e1007220 (2018).

    Article  Google Scholar 

  78. Guest, J. R. et al. Contrasting patterns of coral bleaching susceptibility in 2010 suggest an adaptive response to thermal stress. PLoS ONE 7, e33353 (2012).

    Article  Google Scholar 

  79. Coles, S. L. et al. Evidence of acclimatization or adaptation in Hawaiian corals to higher ocean temperatures. PeerJ 6, e5347 (2018).

    Article  Google Scholar 

  80. Sully, S., Burkepile, D. E., Donovan, M. K., Hodgson, G. & van Woesik, R. A global analysis of coral bleaching over the past two decades. Nat. Commun. 10, 1264 (2019).

    Article  Google Scholar 

  81. Camp, E. F. et al. The future of coral reefs subject to rapid climate change: lessons from natural extreme environments. Front. Mar. Sci. 5, 4 (2018).

    Article  Google Scholar 

  82. Oliver, T. A. & Palumbi, S. R. Do fluctuating temperature environments elevate coral thermal tolerance? Coral Reefs 30, 429–440 (2011).

    Article  Google Scholar 

  83. Morgan, K. M., Perry, C. T., Smithers, S. G., Johnson, J. A. & Daniell, J. J. Evidence of extensive reef development and high coral cover in nearshore environments: implications for understanding coral adaptation in turbid settings. Sci. Rep. 6, 29616 (2016).

    Article  Google Scholar 

  84. Middlebrook, R., Hoegh-Guldberg, O. & Leggat, W. The effect of thermal history on the susceptibility of reef-building corals to thermal stress. J. Exp. Biol. 211, 1050–1056 (2008).

    Article  Google Scholar 

  85. Brown, B. E., Dunne, R. P., Edwards, A. J., Sweet, M. J. & Phongsuwan, N. Decadal environmental ‘memory’ in a reef coral? Mar. Biol. 162, 479–483 (2015).

    Article  Google Scholar 

  86. Dixon, G., Liao, Y., Bay, L. K. & Matz, M. V. Role of gene body methylation in acclimatization and adaptation in a basal metazoan. Proc. Natl Acad. Sci. USA 115, 13342–13346 (2018).

    Article  Google Scholar 

  87. Humanes, A. et al. An experimental framework for selectively breeding corals for assisted evolution. Front. Mar. Sci. 8, 626 (2021).

    Article  Google Scholar 

  88. Dixon, G. B. et al. Genomic determinants of coral heat tolerance across latitudes. Science 348, 1460–1462 (2015). This paper demonstrates applicability of assisted evolution via selective breeding.

    Article  Google Scholar 

  89. van Oppen, M. J. H. et al. Shifting paradigms in restoration of the world’s coral reefs. Glob. Chang. Biol. 23, 3437–3448 (2017).

    Article  Google Scholar 

  90. Fukami, H. et al. Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals. Nature 427, 832–835 (2004).

    Article  Google Scholar 

  91. Voolstra, C. R. et al. Consensus guidelines for advancing coral holobiont genome and specimen voucher deposition. Front. Mar. Sci. 8, 1029 (2021).

    Article  Google Scholar 

  92. Seneca, F. O. & Palumbi, S. R. The role of transcriptome resilience in resistance of corals to bleaching. Mol. Ecol. 24, 1467–1484 (2015).

    Article  Google Scholar 

  93. Evensen, N. R., Fine, M., Perna, G., Voolstra, C. R. & Barshis, D. J. Remarkably high and consistent tolerance of a Red Sea coral to acute and chronic thermal stress exposures. Limnol. Oceanogr. https://doi.org/10.1002/lno.11715 (2021).

    Article  Google Scholar 

  94. Cleves, P. A., Strader, M. E., Bay, L. K., Pringle, J. R. & Matz, M. V. CRISPR/Cas9-mediated genome editing in a reef-building coral. Proc. Natl Acad. Sci. USA 115, 5235–5240 (2018).

    Article  Google Scholar 

  95. Cleves, P. A. et al. Reduced thermal tolerance in a coral carrying CRISPR-induced mutations in the gene for a heat-shock transcription factor. Proc. Natl Acad. Sci. USA 117, 28899–28905 (2020).

    Article  Google Scholar 

  96. Fuller, Z. L. et al. Population genetics of the coral Acropora millepora: toward genomic prediction of bleaching. Science 369, eaba4674 (2020).

    Article  Google Scholar 

  97. Yetsko, K. et al. Genetic differences in thermal tolerance among colonies of threatened coral Acropora cervicornis: potential for adaptation to increasing temperature. Mar. Ecol. Prog. Ser. 646, 45–68 (2020).

    Article  Google Scholar 

  98. Kenkel, C. D., Almanza, A. T. & Matz, M. V. Fine-scale environmental specialization of reef-building corals might be limiting reef recovery in the Florida Keys. Ecology 96, 3197–3212 (2015).

    Article  Google Scholar 

  99. D’Angelo, C. et al. Local adaptation constrains the distribution potential of heat-tolerant Symbiodinium from the Persian/Arabian Gulf. ISME J. 9, 2551–2560 (2015).

    Article  Google Scholar 

  100. Safaie, A. et al. High frequency temperature variability reduces the risk of coral bleaching. Nat. Commun. 9, 1671 (2018).

    Article  Google Scholar 

  101. Quigley, K. M., Bay, L. K. & van Oppen, M. J. H. Genome-wide SNP analysis reveals an increase in adaptive genetic variation through selective breeding of coral. Mol. Ecol. 29, 2176–2188 (2020).

    Article  Google Scholar 

  102. Craggs, J., Guest, J., Bulling, M. & Sweet, M. Ex situ co culturing of the sea urchin, Mespilia globulus and the coral Acropora millepora enhances early post-settlement survivorship. Sci. Rep. 9, 12984 (2019).

    Article  Google Scholar 

  103. Quigley, K. M. et al. Variability in fitness trade-offs amongst coral juveniles with mixed genetic backgrounds held in the wild. Front. Mar. Sci. 8, 161 (2021).

    Article  Google Scholar 

  104. LaJeunesse, T. C. et al. Systematic revision of Symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts. Curr. Biol. 28, 2570–2580.e6 (2018). This paper provides a revised coral symbiont taxonomy and shows that Symbiodiniaceae diversification coincides with the radiation of reef-building corals.

    Article  Google Scholar 

  105. Muscatine, L. The role of symbiotic algae in carbon and energy flux in reef corals. Coral Reefs 25, 75–87 (1990).

    Google Scholar 

  106. Trench, R. K. Microalgal–invertebrate symbiosis, a review. Endocytobiosis Cell Res. 9, 135–175 (1993).

    Google Scholar 

  107. Pogoreutz, C. et al. in Cellular Dialogues in the Holobiont (eds Bosch, T. C. G. & Hadfield, M. G.) 91–118 (CRC, 2020). https://doi.org/10.1201/9780429277375-7.

  108. Hume, B. C. C. et al. SymPortal: a novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling. Mol. Ecol. Resour. 19, 1063–1080 (2019).

    Article  Google Scholar 

  109. Decelle, J. et al. Worldwide occurrence and activity of the reef-building coral symbiont Symbiodinium in the open ocean. Curr. Biol. 28, 3625–3633.e3 (2018).

    Article  Google Scholar 

  110. Aranda, M. et al. Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle. Sci. Rep. 6, 39734 (2016).

    Article  Google Scholar 

  111. González-Pech, R. A., Bhattacharya, D., Ragan, M. A. & Chan, C. X. Genome evolution of coral reef symbionts as intracellular residents. Trends Ecol. Evol. 34, 799–806 (2019).

    Article  Google Scholar 

  112. Hume, B. C. C., Mejia-Restrepo, A., Voolstra, C. R. & Berumen, M. L. Fine-scale delineation of Symbiodiniaceae genotypes on a previously bleached central Red Sea reef system demonstrates a prevalence of coral host-specific associations. Coral Reefs 39, 583–601 (2020).

    Article  Google Scholar 

  113. Howells, E. J. et al. Corals in the hottest reefs in the world exhibit symbiont fidelity not flexibility. Mol. Ecol. 29, 899–911 (2020).

    Article  Google Scholar 

  114. Turnham, K. E., Wham, D. C., Sampayo, E. & LaJeunesse, T. C. Mutualistic microalgae co-diversify with reef corals that acquire symbionts during egg development. ISME J. https://doi.org/10.1038/s41396-021-01007-8 (2021).

    Article  Google Scholar 

  115. Grottoli, A. G. et al. The cumulative impact of annual coral bleaching can turn some coral species winners into losers. Glob. Chang. Biol. 20, 3823–3833 (2014).

    Article  Google Scholar 

  116. LaJeunesse, T. C., Smith, R. T., Finney, J. & Oxenford, H. Outbreak and persistence of opportunistic symbiotic dinoflagellates during the 2005 Caribbean mass coral ‘bleaching’ event. Proc. R. Soc. B Biol. Sci. 276, 4139–4148 (2009).

    Article  Google Scholar 

  117. Grégoire, V., Schmacka, F., Coffroth, M. A. & Karsten, U. Photophysiological and thermal tolerance of various genotypes of the coral endosymbiont Symbiodinium sp. (Dinophyceae). J. Appl. Phycol. 29, 1893–1905 (2017).

    Article  Google Scholar 

  118. Quigley, K. M., Baker, A. C., Coffroth, M. A., Willis, B. L. & van Oppen, M. J. H. in Coral Bleaching: Patterns, Processes, Causes and Consequences (eds van Oppen, M. J. H. & Lough, J. M.) 111–151 (Springer International, 2018).

  119. Ziegler, M., Arif, C. & Voolstra, C. R. in Coral Reefs of the Red Sea (eds Voolstra, C. R. & Berumen, M. L.) 69–89 (Springer International, 2019).

  120. Suggett, D. J., Warner, M. E. & Leggat, W. Symbiotic dinoflagellate functional diversity mediates coral survival under ecological crisis. Trends Ecol. Evol. 32, 735–745 (2017).

    Article  Google Scholar 

  121. Hume, B. C. C. et al. Ancestral genetic diversity associated with the rapid spread of stress-tolerant coral symbionts in response to Holocene climate change. Proc. Natl Acad. Sci. USA 113, 4416–4421 (2016).

    Article  Google Scholar 

  122. Ochsenkühn, M. A., Röthig, T., D’Angelo, C., Wiedenmann, J. & Voolstra, C. R. The role of floridoside in osmoadaptation of coral-associated algal endosymbionts to high-salinity conditions. Sci. Adv. 3, e1602047 (2017).

    Article  Google Scholar 

  123. Baumgarten, S. et al. Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. BMC Genomics 14, 704 (2013).

    Article  Google Scholar 

  124. Klein, S. G. et al. Symbiodinium mitigate the combined effects of hypoxia and acidification on a noncalcifying cnidarian. Glob. Chang. Biol. 23, 3690–3703 (2017).

    Article  Google Scholar 

  125. Liew, Y. J., Li, Y., Baumgarten, S., Voolstra, C. R. & Aranda, M. Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum. PLoS Genet. 13, e1006619 (2017).

    Article  Google Scholar 

  126. Warner, M. E. & Suggett, D. J. in The Cnidaria, Past, Present and Future: The World of Medusa and Her Sisters (eds Goffredo, S. & Dubinsky, Z.) 489–509 (Springer International, 2016).

  127. Levin, R. A. et al. Sex, scavengers, and chaperones: transcriptome secrets of divergent symbiodinium thermal tolerances. Mol. Biol. Evol. 33, 3032 (2016).

    Article  Google Scholar 

  128. Nand, A. et al. Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum. Nat. Genet. 53, 618–629 (2021).

    Article  Google Scholar 

  129. Buerger, P. et al. Heat-evolved microalgal symbionts increase coral bleaching tolerance. Sci. Adv. 6, eaba2498 (2020).

    Article  Google Scholar 

  130. Thornhill, D. J., Howells, E. J., Wham, D. C., Steury, T. D. & Santos, S. R. Population genetics of reef coral endosymbionts (Symbiodinium, Dinophyceae). Mol. Ecol. 26, 2640–2659 (2017).

    Article  Google Scholar 

  131. LaJeunesse, T. C. et al. Long-standing environmental conditions, geographic isolation and host–symbiont specificity influence the relative ecological dominance and genetic diversification of coral endosymbionts in the genus Symbiodinium. J. Biogeogr. 37, 785–800 (2010).

    Article  Google Scholar 

  132. Parkinson, J. E. et al. Gene expression variation resolves species and individual strains among coral-associated dinoflagellates within the genus Symbiodinium. Genome Biol. Evol. 8, 665–680 (2016).

    Article  Google Scholar 

  133. Baker, A. C. Flexibility and specificity in coral–algal symbiosis: diversity, ecology, and biogeography of Symbiodinium. Annu. Rev. Ecol. Evol. Syst. 34, 661–689 (2003).

    Article  Google Scholar 

  134. Boulotte, N. M. et al. Exploring the Symbiodinium rare biosphere provides evidence for symbiont switching in reef-building corals. ISME J. 10, 2693–2701 (2016).

    Article  Google Scholar 

  135. Ziegler, M., Eguíluz, V. M., Duarte, C. M. & Voolstra, C. R. Rare symbionts may contribute to the resilience of coral–algal assemblages. ISME J. 12, 161–172 (2018).

    Article  Google Scholar 

  136. Mies, M., Sumida, P. Y. G., Rädecker, N. & Voolstra, C. R. Marine Invertebrate Larvae Associated with Symbiodinium: A Mutualism from the Start? Front. Ecol. Evol. 5, 56 https://www.frontiersin.org/article/10.3389/fevo.2017.00056 (2017).

  137. Cumbo, V. R., Baird, A. H. & van Oppen, M. J. H. The promiscuous larvae: flexibility in the establishment of symbiosis in corals. Coral Reefs 32, 111–120 (2013).

    Article  Google Scholar 

  138. Quigley, K. M., Willis, B. L. & Bay, L. K. Heritability of the Symbiodinium community in vertically- and horizontally-transmitting broadcast spawning corals. Sci. Rep. 7, 8219 (2017).

    Article  Google Scholar 

  139. National Academies of Sciences, Engineering, and Medicine. A Research Review of Interventions to Increase the Persistence and Resilience of Coral Reefs (National Academies Press, 2019). This book reviews restoration interventions, detailing latest emerging technologies and approaches.

  140. Quigley, K. M., Randall, C. J., van Oppen, M. J. H. & Bay, L. K. Assessing the role of historical temperature regime and algal symbionts on the heat tolerance of coral juveniles. Biol. Open 9, bio047316 (2020).

    Article  Google Scholar 

  141. McIlroy, S. E. et al. The effects of Symbiodinium (Pyrrhophyta) identity on growth, survivorship, and thermal tolerance of newly settled coral recruits. J. Phycol. 52, 1114–1124 (2016).

    Article  Google Scholar 

  142. Thornhill, D. J., Daniel, M. W., LaJeunesse, T. C., Schmidt, G. W. & Fitt, W. K. Natural infections of aposymbiotic Cassiopea xamachana scyphistomae from environmental pools of Symbiodinium. J. Exp. Mar. Bio. Ecol. 338, 50–56 (2006).

    Article  Google Scholar 

  143. Coffroth, M. A., Lewis, C. F., Santos, S. R. & Weaver, J. L. Environmental populations of symbiotic dinoflagellates in the genus Symbiodinium can initiate symbioses with reef cnidarians. Curr. Biol. 16, R985–R987 (2006).

    Article  Google Scholar 

  144. Fujise, L. et al. Unlocking the phylogenetic diversity, primary habitats, and abundances of free-living Symbiodiniaceae on a coral reef. Mol. Ecol. 30, 343–360 (2021).

    Article  Google Scholar 

  145. Levin, R. A. et al. Engineering strategies to decode and enhance the genomes of coral symbionts. Front. Microbiol. 8, 1220 (2017).

    Article  Google Scholar 

  146. Chen, J. E., Barbrook, A. C., Cui, G., Howe, C. J. & Aranda, M. The genetic intractability of Symbiodinium microadriaticum to standard algal transformation methods. PLoS ONE 14, e0211936 (2019).

    Article  Google Scholar 

  147. Sheykhali, S. et al. Robustness to extinction and plasticity derived from mutualistic bipartite ecological networks. Sci. Rep. 10, 9783 (2020).

    Article  Google Scholar 

  148. Quigley, K. M., Bay, L. K. & Willis, B. L. Leveraging new knowledge of Symbiodinium community regulation in corals for conservation and reef restoration. Mar. Ecol. Prog. Ser. 600, 245–253 (2018).

    Article  Google Scholar 

  149. LaJeunesse, T. C. et al. Host–symbiont recombination versus natural selection in the response of coral–dinoflagellate symbioses to environmental disturbance. Proc. R. Soc. B: Biol. Sci. 277, 2925–2934 (2010).

    Article  Google Scholar 

  150. Poland, D. M. & Coffroth, M. A. Trans-generational specificity within a cnidarian–algal symbiosis. Coral Reefs 36, 119–129 (2017).

    Article  Google Scholar 

  151. Sampayo, E. M. et al. Coral symbioses under prolonged environmental change: living near tolerance range limits. Sci. Rep. 6, 36271 (2016).

    Article  Google Scholar 

  152. Abrego, D., van Oppen, M. J. H. & Willis, B. L. Onset of algal endosymbiont specificity varies among closely related species of Acropora corals during early ontogeny. Mol. Ecol. 18, 3532–3543 (2009).

    Article  Google Scholar 

  153. Pettay, D. T., Wham, D. C., Smith, R. T., Iglesias-Prieto, R. & LaJeunesse, T. C. Microbial invasion of the Caribbean by an Indo-Pacific coral zooxanthella. Proc. Natl Acad. Sci. USA 112, 7513–7518 (2015).

    Article  Google Scholar 

  154. Qin, Z. et al. Diversity of Symbiodiniaceae in 15 coral species from the Southern South China Sea: potential relationship with coral thermal adaptability. Front. Microbiol. 10, 2343 (2019).

    Article  Google Scholar 

  155. Claar, D. C. et al. Dynamic symbioses reveal pathways to coral survival through prolonged heatwaves. Nat. Commun. 11, 6097 (2020).

    Article  Google Scholar 

  156. Lim, E.-P. et al. Continuation of tropical Pacific Ocean temperature trend may weaken extreme El Niño and its linkage to the Southern Annular Mode. Sci. Rep. 9, 17044 (2019).

    Article  Google Scholar 

  157. Pollock, F. J. et al. Coral larvae for restoration and research: a large-scale method for rearing Acropora millepora larvae, inducing settlement, and establishing symbiosis. PeerJ 5, e3732 (2017).

    Article  Google Scholar 

  158. McFall-Ngai, M. et al. Animals in a bacterial world, a new imperative for the life sciences. Proc. Natl Acad. Sci. USA 110, 3229–3236 (2013).

    Article  Google Scholar 

  159. Bosch, T. C. G. & McFall-Ngai, M. J. Metaorganisms as the new frontier. Zoology 114, 185–190 (2011).

    Article  Google Scholar 

  160. Robbins, S. J. et al. A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nat. Microbiol. 4, 2090–2100 (2019).

    Article  Google Scholar 

  161. Bang, C. et al. Metaorganisms in extreme environments: do microbes play a role in organismal adaptation? Zoology 127, 1–19 (2018).

    Article  Google Scholar 

  162. Williams, A. D., Brown, B. E., Putchim, L. & Sweet, M. J. Age-related shifts in bacterial diversity in a reef coral. PLoS ONE 10, e0144902 (2015).

    Article  Google Scholar 

  163. Roder, C., Bayer, T., Aranda, M., Kruse, M. & Voolstra, C. R. Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences. Mol. Ecol. 24, 3501–3511 (2015).

    Article  Google Scholar 

  164. Sweet, M. J., Brown, B. E., Dunne, R. P., Singleton, I. & Bulling, M. Evidence for rapid, tide-related shifts in the microbiome of the coral Coelastrea aspera. Coral Reefs 36, 815–828 (2017).

    Article  Google Scholar 

  165. Ziegler, M. et al. Coral bacterial community structure responds to environmental change in a host-specific manner. Nat. Commun. 10, 3092 (2019).

    Article  Google Scholar 

  166. Reshef, L., Koren, O., Loya, Y., Zilber-Rosenberg, I. & Rosenberg, E. The coral probiotic hypothesis. Environ. Microbiol. 8, 2068–2073 (2006).

    Article  Google Scholar 

  167. Pogoreutz, C. et al. Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome. Ecol. Evol. 8, 2240–2252 (2018).

    Article  Google Scholar 

  168. Neave, M. J. et al. Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales. ISME J. 11, 186–200 (2017).

    Article  Google Scholar 

  169. Neave, M. J., Apprill, A., Ferrier-Pagès, C. & Voolstra, C. R. Diversity and function of prevalent symbiotic marine bacteria in the genus. Endozoicomonas. Appl. Microbiol. Biotechnol. 100, 8315–8324 (2016).

    Article  Google Scholar 

  170. Nissimov, J., Rosenberg, E. & Munn, C. B. Antimicrobial properties of resident coral mucus bacteria of Oculina patagonica. FEMS Microbiol. Lett. 292, 210–215 (2009).

    Article  Google Scholar 

  171. Sharp, K. H., Sneed, J. M., Ritchie, K. B., Mcdaniel, L. & Paul, V. J. Induction of larval settlement in the reef coral Porites astreoides by a cultivated marine roseobacter strain. Biol. Bull. 228, 98–107 (2015).

    Article  Google Scholar 

  172. Rosado, P. M. et al. Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation. ISME J. 13, 921–936 (2019).

    Article  Google Scholar 

  173. Sunagawa, S. et al. Bacterial diversity and white plague disease-associated community changes in the Caribbean coral Montastraea faveolata. ISME J. 3, 512–521 (2009).

    Article  Google Scholar 

  174. Ushijima, B., Smith, A., Aeby, G. S. & Callahan, S. M. Vibrio owensii induces the tissue loss disease Montipora white syndrome in the Hawaiian reef coral Montipora capitata. PLoS ONE 7, e46717 (2012).

    Article  Google Scholar 

  175. Mouchka, M. E., Hewson, I. & Harvell, C. D. Coral-associated bacterial assemblages: current knowledge and the potential for climate-driven impacts. Integr. Comp. Biol. 50, 662–674 (2010).

    Article  Google Scholar 

  176. Glasl, B., Herndl, G. J. & Frade, P. R. The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance. ISME J. 10, 2280–2292 (2016).

    Article  Google Scholar 

  177. Peixoto, R. S. et al. Beneficial Microorganisms for Corals (BMC): proposed mechanisms for coral health and resilience. Front. Microbiol. 8, 341 (2017).

    Article  Google Scholar 

  178. Mueller, E. A., Wisnoski, N. I., Peralta, A. L. & Lennon, J. T. Microbial rescue effects: how microbiomes can save hosts from extinction. Funct. Ecol. 34, 2055–2064 (2020).

    Article  Google Scholar 

  179. Leite, D. C. A. et al. Coral bacterial-core abundance and network complexity as proxies for anthropogenic pollution. Front. Microbiol. 9, 833 (2018).

    Article  Google Scholar 

  180. Fragoso Ados Santos, H. et al. Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota. Sci. Rep. 5, 18268 (2015).

    Article  Google Scholar 

  181. Silva, D. P. et al. Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites. Microbiome 9, 118 (2021).

    Article  Google Scholar 

  182. Welsh, R. M. et al. Alien vs. predator: bacterial challenge alters coral microbiomes unless controlled by Halobacteriovorax predators. PeerJ 5, e3315 (2017).

    Article  Google Scholar 

  183. Santoro, E. P. et al. Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality. Sci. Adv. 7, eabg3088 (2021).

    Article  Google Scholar 

  184. Assis, J. M. et al. Delivering Beneficial Microorganisms for Corals: rotifers as carriers of probiotic bacteria. Front. Microbiol. 11, 608506 (2020).

    Article  Google Scholar 

  185. Damjanovic, K., Blackall, L. L., Webster, N. S. & van Oppen, M. J. H. The contribution of microbial biotechnology to mitigating coral reef degradation. Microb. Biotechnol. 10, 1236–1243 (2017).

    Article  Google Scholar 

  186. van Oppen, M. J. H. & Blackall, L. L. Coral microbiome dynamics, functions and design in a changing world. Nat. Rev. Microbiol. 17, 557–567 (2019).

    Article  Google Scholar 

  187. Sweet, M. et al. Insights into the cultured bacterial fraction of corals. mSystems 6, e0124920 (2021).

    Article  Google Scholar 

  188. Brussaard, C. P. D., Baudoux, A.-C. & Rodríguez-Valera, F. in The Marine Microbiome: An Untapped Source of Biodiversity and Biotechnological Potential (eds Stal, L. J. & Cretoiu, M. S.) 155–183 (Springer International, 2016).

  189. Levin, R. A., Voolstra, C. R., Weynberg, K. D. & van Oppen, M. J. H. Evidence for a role of viruses in the thermal sensitivity of coral photosymbionts. ISME J. 11, 808–812 (2017).

    Article  Google Scholar 

  190. Messyasz, A. et al. Coral bleaching phenotypes associated with differential abundances of nucleocytoplasmic large DNA viruses. Front. Mar. Sci. https://doi.org/10.3389/fmars.2020.555474 (2020).

    Article  Google Scholar 

  191. Thurber, R. L. V. et al. Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. Proc. Natl Acad. Sci. USA 105, 18413–18418 (2008).

    Article  Google Scholar 

  192. Sweet, M. & Bythell, J. The role of viruses in coral health and disease. J. Invertebr. Pathol. 147, 136–144 (2017).

    Article  Google Scholar 

  193. Thurber, R. V., Payet, J. P., Thurber, A. R. & Correa, A. M. S. Virus–host interactions and their roles in coral reef health and disease. Nat. Rev. Microbiol. 15, 205–216 (2017). This paper reviews the role of viruses in coral holobiont biology.

    Article  Google Scholar 

  194. Frazão, N., Sousa, A., Lässig, M. & Gordo, I. Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut. Proc. Natl Acad. Sci. USA 116, 17906–17915 (2019).

    Article  Google Scholar 

  195. Lepage, P. et al. Dysbiosis in inflammatory bowel disease: a role for bacteriophages? Gut 57, 424–425 (2008).

    Article  Google Scholar 

  196. Barr, J. J. et al. Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc. Natl Acad. Sci. USA 110, 10771–10776 (2013).

    Article  Google Scholar 

  197. Silveira, C. B. & Rohwer, F. L. Piggyback-the-winner in host-associated microbial communities. NPJ Biofilms Microbiomes 2, 16010 (2016).

    Article  Google Scholar 

  198. Roach, T. N. F. et al. A multiomic analysis of in situ coral–turf algal interactions. Proc. Natl Acad. Sci. USA 117, 13588–13595 (2020).

    Article  Google Scholar 

  199. Cárdenas, A. et al. Coral-associated viral assemblages from the central Red Sea align with host species and contribute to holobiont genetic diversity. Front. Microbiol. 11, 572534 (2020).

    Article  Google Scholar 

  200. Bondy-Denomy, J. & Davidson, A. R. When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness. J. Microbiol. 52, 235–242 (2014).

    Article  Google Scholar 

  201. Weynberg, K. D., Voolstra, C. R., Neave, M. J., Buerger, P. & van Oppen, M. J. H. From cholera to corals: viruses as drivers of virulence in a major coral bacterial pathogen. Sci. Rep. 5, 17889 (2015).

    Article  Google Scholar 

  202. Silveira, C. B. et al. Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes. BMC Genomics 21, 126 (2020).

    Article  Google Scholar 

  203. Soffer, N., Brandt, M. E., Correa, A. M. S., Smith, T. B. & Thurber, R. V. Potential role of viruses in white plague coral disease. ISME J. 8, 271–283 (2014).

    Article  Google Scholar 

  204. Weynberg, K. D. et al. Prevalent and persistent viral infection in cultures of the coral algal endosymbiont Symbiodinium. Coral Reefs 36, 773–784 (2017).

    Article  Google Scholar 

  205. Brüwer, J. D., Agrawal, S., Liew, Y. J., Aranda, M. & Voolstra, C. R. Association of coral algal symbionts with a diverse viral community responsive to heat shock. BMC Microbiol. 17, 174 (2017).

    Article  Google Scholar 

  206. Jacquemot, L. et al. Therapeutic potential of a new jumbo phage that infects Vibrio coralliilyticus, a widespread coral pathogen. Front. Microbiol. 9, 2501 (2018).

    Article  Google Scholar 

  207. Efrony, R., Loya, Y., Bacharach, E. & Rosenberg, E. Phage therapy of coral disease. Coral Reefs 26, 7–13 (2007).

    Article  Google Scholar 

  208. Cohen, Y., Joseph Pollock, F., Rosenberg, E. & Bourne, D. G. Phage therapy treatment of the coral pathogen Vibrio coralliilyticus. Microbiologyopen 2, 64–74 (2013).

    Article  Google Scholar 

  209. Efrony, R., Atad, I. & Rosenberg, E. Phage therapy of coral white plague disease: properties of phage BA3. Curr. Microbiol. 58, 139–145 (2009).

    Article  Google Scholar 

  210. Atad, I., Zvuloni, A., Loya, Y. & Rosenberg, E. Phage therapy of the white plague-like disease of Favia favus in the Red Sea. Coral Reefs 31, 665–670 (2012).

    Article  Google Scholar 

  211. Sweet, M. J. & Bulling, M. T. On the importance of the microbiome and pathobiome in coral health and disease. Front. Mar. Sci. 4, 9 (2017).

    Article  Google Scholar 

  212. Pollock, F. J., Morris, P. J., Willis, B. L. & Bourne, D. G. The urgent need for robust coral disease diagnostics. PLoS Pathog. 7, e1002183 (2011).

    Article  Google Scholar 

  213. Lesser, M. P., Bythell, J. C., Gates, R. D., Johnstone, R. W. & Hoegh-Guldberg, O. Are infectious diseases really killing corals? Alternative interpretations of the experimental and ecological data. J. Exp. Mar. Bio. Ecol. 346, 36–44 (2007).

    Article  Google Scholar 

  214. Roder, C., Arif, C., Daniels, C., Weil, E. & Voolstra, C. R. Bacterial profiling of white plague disease across corals and oceans indicates a conserved and distinct disease microbiome. Mol. Ecol. 23, 965–974 (2014).

    Article  Google Scholar 

  215. Soffer, N., Zaneveld, J. & Vega Thurber, R. Phage–bacteria network analysis and its implication for the understanding of coral disease. Environ. Microbiol. 17, 1203–1218 (2015).

    Article  Google Scholar 

  216. Ubeda, C. et al. Antibiotic-induced SOS response promotes horizontal dissemination of pathogenicity island-encoded virulence factors in staphylococci. Mol. Microbiol. 56, 836–844 (2005).

    Article  Google Scholar 

  217. Cárdenas, A. et al. Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton. ISME J. 12, 59–76 (2018).

    Article  Google Scholar 

  218. Anthony, K. et al. New interventions are needed to save coral reefs. Nat. Ecol. Evol. 1, 1420–1422 (2017).

    Article  Google Scholar 

  219. Allard, S. M. et al. Introducing the mangrove microbiome initiative: identifying microbial research priorities and approaches to better understand, protect, and rehabilitate mangrove ecosystems. mSystems https://doi.org/10.1128/mSystems.00658-20 (2020).

    Article  Google Scholar 

  220. Zickfeld, K. et al. Long-term climate change commitment and reversibility: An EMIC intercomparison. J. Clim. 26, 5782–5809 (2013).

    Article  Google Scholar 

  221. Humanes, A. et al. A framework for selectively breeding corals for assisted evolution. Preprint at bioRxiv https://doi.org/10.1101/2021.02.23.432469 (2021).

    Article  Google Scholar 

  222. National Academies of Sciences, Engineering, and Medicine. A Decision Framework for Interventions to Increase the Persistence and Resilience of Coral Reefs (National Academies Press, 2019).

  223. Page, C. A., Muller, E. M. & Vaughan, D. E. Microfragmenting for the successful restoration of slow growing massive corals. Ecol. Eng. 123, 86–94 (2018).

    Article  Google Scholar 

  224. Schopmeyer, S. A. et al. Regional restoration benchmarks for Acropora cervicornis. Coral Reefs 36, 1047–1057 (2017).

    Article  Google Scholar 

  225. Suggett, D. J., Edmondson, J., Howlett, L. & Camp, E. F. Coralclip®: a low-cost solution for rapid and targeted out-planting of coral at scale. Restor. Ecol. 28, 289–296 (2020).

    Article  Google Scholar 

  226. Woesik, R. et al. Differential survival of nursery-reared Acropora cervicornis outplants along the Florida reef tract. Restor. Ecol. 29, e13302 (2021).

    Article  Google Scholar 

  227. Ware, M. et al. Survivorship and growth in staghorn coral (Acropora cervicornis) outplanting projects in the Florida Keys National Marine Sanctuary. PLoS ONE 15, e0231817 (2020).

    Article  Google Scholar 

  228. Ladd, M. C., Shantz, A. A., Bartels, E. & Burkepile, D. E. Thermal stress reveals a genotype-specific tradeoff between growth and tissue loss in restored Acropora cervicornis. Mar. Ecol. Prog. Ser. 572, 129–139 (2017).

    Article  Google Scholar 

  229. Goergen, E. A. & Gilliam, D. S. Outplanting technique, host genotype, and site affect the initial success of outplanted Acropora cervicornis. PeerJ 6, e4433 (2018).

    Article  Google Scholar 

  230. Chamberland, V. F. et al. New seeding approach reduces costs and time to outplant sexually propagated corals for reef restoration. Sci. Rep. 7, 18076 (2017).

    Article  Google Scholar 

  231. Craggs, J., Guest, J., Davis, M. & Sweet, M. Completing the life cycle of a broadcast spawning coral in a closed mesocosm. Invertebr. Reprod. Dev. 64, 244–247 (2020).

    Article  Google Scholar 

  232. Hock, K. et al. Connectivity and systemic resilience of the Great Barrier Reef. PLoS Biol. 15, e2003355 (2017).

    Article  Google Scholar 

  233. Quigley, K. M., Bay, L. K. & van Oppen, M. J. H. The active spread of adaptive variation for reef resilience. Ecol. Evol. 9, 11122–11135 (2019).

    Article  Google Scholar 

  234. Sangsawang, L. et al. 13C and 15N assimilation and organic matter translocation by the endolithic community in the massive coral Porites lutea. R. Soc. Open Sci. 4, 171201 (2017).

    Article  Google Scholar 

  235. Pernice, M. et al. Down to the bone: the role of overlooked endolithic microbiomes in reef coral health. ISME J. 14, 325–334 (2020).

    Article  Google Scholar 

  236. Kwong, W. K., Del Campo, J., Mathur, V., Vermeij, M. J. A. & Keeling, P. J. A widespread coral-infecting apicomplexan with chlorophyll biosynthesis genes. Nature 568, 103–107 (2019).

    Article  Google Scholar 

  237. Fine, M., Gildor, H. & Genin, A. A coral reef refuge in the Red Sea. Glob. Chang. Biol. 19, 3640–3647 (2013).

    Article  Google Scholar 

  238. Osman, E. O. et al. Thermal refugia against coral bleaching throughout the northern Red Sea. Glob. Chang. Biol. 24, e474–e484 (2018).

    Article  Google Scholar 

  239. Camp, E. F. et al. Corals exhibit distinct patterns of microbial reorganisation to thrive in an extreme inshore environment. Coral Reefs 39, 701–716 (2020).

    Article  Google Scholar 

  240. Grottoli, A. G. et al. Increasing comparability among coral bleaching experiments. Ecol. Appl. 31, e02262 (2021).

    Article  Google Scholar 

  241. Putnam, H. M., Barott, K. L., Ainsworth, T. D. & Gates, R. D. The vulnerability and resilience of reef-building corals. Curr. Biol. 27, R528–R540 (2017).

    Article  Google Scholar 

  242. Hagedorn, M. & Spindler, R. The reality, use and potential for cryopreservation of coral reefs. Adv. Exp. Med. Biol. 753, 317–329 (2014).

    Article  Google Scholar 

  243. Hagedorn, M. et al. Successful demonstration of assisted gene flow in the threatened coral Acropora palmata across genetically-isolated caribbean populations using cryopreserved sperm. Cold Spring Harb. Lab. https://doi.org/10.1101/492447 (2018).

    Article  Google Scholar 

  244. Hagedorn, M., Spindler, R. & Daly, J. Cryopreservation as a tool for reef restoration: 2019. Adv. Exp. Med. Biol. 1200, 489–505 (2019).

    Article  Google Scholar 

  245. Daly, J. et al. Successful cryopreservation of coral larvae using vitrification and laser warming. Sci. Rep. 8, 15714 (2018).

    Article  Google Scholar 

  246. Chakravarti, L. J., Beltran, V. H. & van Oppen, M. J. H. Rapid thermal adaptation in photosymbionts of reef-building corals. Glob. Chang. Biol. 23, 4675–4688 (2017).

    Article  Google Scholar 

  247. Quigley, K. M., Alvarez Roa, C., Torda, G., Bourne, D. G. & Willis, B. L. Co-dynamics of Symbiodiniaceae and bacterial populations during the first year of symbiosis with Acropora tenuis juveniles. Microbiologyopen 9, e959 (2020).

    Article  Google Scholar 

  248. Teplitski, M. & Ritchie, K. How feasible is the biological control of coral diseases? Trends Ecol. Evol. 24, 378–385 (2009).

    Article  Google Scholar 

Download references

Acknowledgements

C.R.V. acknowledges funding from the German Research Foundation (DFG) (grants 433042944 and 458901010). R.S.P. acknowledges funding from King Abdullah University of Science and Technology (grant FCC/1/1973-51-01). J.E.P. acknowledges funding from the University of South Florida Research & Innovation Internal Awards Program (grant 0142687). K.M.Q. acknowledges funding from the Australian Institute of Marine Science (AIMS). E.M.M. was supported by the Mote Eminent Scholarship and the National Science Foundation (NSF) (OCE-1452538). M.A. acknowledges funding from King Abdullah University of Science and Technology (grant FCC/1/1973-36-01).

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Researching data for article: C.R.V., R.P., J.E.P., K.M.Q., C.B.S., M.S., M.A.; substantial contribution to discussion of content: C.R.V., D.J.S., R.P., J.E.P., K.M.Q., C.B.S., D.G.B., M.A.; writing: C.R.V., D.J.S., R.P., J.E.P., K.M.Q., C.B.S., D.G.B., M.A.; review/editing manuscript before submission: C.R.V., D.J.S., R.P., J.E.P., K.M.Q., C.B.S., M.S., E.M.M., D.J.B., D.G.B., M.A.

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Correspondence to Christian R. Voolstra.

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Nature Reviews Earth & Environment thanks D. Huang, who co-reviewed with E. Bollati; J. Wiedenmann; S.-L. Tang; and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Glossary

Coral bleaching

Discolouration of coral tissue due to the loss of microalgal symbionts triggered by climate change-induced ocean warming and thermal stress anomalies.

Assisted evolution

Human interventions aimed at speeding up natural evolutionary processes to increase the rate of adaptation of threatened species.

Adaptive capacity

The ability of coral holobionts to respond and adjust to environmental stress.

Acclimation

The physiological process of becoming accustomed to a new condition.

Environmental adaptation

The process of (meta-)organismal change used more broadly to denote adjustment to prevailing environmental conditions, for example in the context of host microbiome changes

Evolutionary adaptation

The process of genetic change through which populations become better attuned to their environment over generations.

Restoration

The action of returning something to a former condition, for instance through reinstatement of the original functional or genetic diversity.

Environmental hardening

The preconditioning of coral colonies to elevated temperatures as a means to increase tolerance to future heat stress events (can also apply to other stressors).

Microhabitats

A small area that differs from the surrounding habitat, with unique conditions that could select for unique genotypes that might not be found in the remainder of the area.

Beneficial Microorganisms for Corals

(BMCs). Umbrella term to define (microbial) symbionts that promote coral health and can be used as probiotics.

Coral probiotics

Live microorganisms to benefit coral host health.

Coral prebiotics

Molecules that modulate bacterial (microbial) association to benefit coral host health.

Lysis

A common outcome of viral infections, whereby cells are actively induced by viruses to release newly assembled viruses that can then infect other cells.

Genetically modified organisms

(GMOs). Organisms whose genomes are engineered to produce specific traits of interest.

Environmental rehabilitation

The action of restoring to an improved condition to allow species and ecosystems to thrive under altered environmental conditions.

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Voolstra, C.R., Suggett, D.J., Peixoto, R.S. et al. Extending the natural adaptive capacity of coral holobionts. Nat Rev Earth Environ 2, 747–762 (2021). https://doi.org/10.1038/s43017-021-00214-3

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