Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Coral microbiome dynamics, functions and design in a changing world


Corals associate not only with dinoflagellates, which are their algal endosymbionts and which have been extensively studied over the past four decades, but also with a variety of other microorganisms. The coral microbiome includes dinoflagellates, viruses, fungi, archaea and bacteria, with knowledge of the latter growing rapidly. This Review focuses on the bacterial members of the coral microbiome and draws parallels with better-studied microbiomes in other biological systems. We synthesize current understanding of spatial, temporal and host-specific patterns in coral-associated bacterial communities, the drivers shaping these patterns, and the role of the microbiome in acclimatization and adaptation of the host to climate warming. We discuss how this knowledge can be harnessed to assist the future persistence of coral reefs and provide novel perspectives for the development of microbiome engineering and its implications for coral reef conservation and restoration.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Diversity of stony corals.
Fig. 2: Bacterial acquisition, community composition and diversity throughout the life of a coral.
Fig. 3: Coral microhabitats inhabited by the microbiota.
Fig. 4: Coral bleaching and the bacterial microbiome.
Fig. 5: Potential strategies for reconstructing synthetic microbiomes and genetically modified bacterial strains aimed at increasing the thermal tolerance of corals.


  1. 1.

    Sharshar, N., Banaszak, A. T., Lesser, M. P. & Amrami, D. Coral endolithic algae: life in a protected environment. Pac. Sci. 51, 167–173 (1997).

    Google Scholar 

  2. 2.

    Fine, M. & Loya, Y. Endolithic algae: an alternative source of photoassimilates during coral bleaching. Proc. R. Soc. Lond. B 269, 1205–1210 (2002).

    Google Scholar 

  3. 3.

    Schlichter, D., Zscharnack, B. & Krisch, H. Transfer of photoassimilates from endolithic algae to coral tissue. Naturwissenschaften 82, 561–564 (1995).

    CAS  Google Scholar 

  4. 4.

    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).

    PubMed  PubMed Central  Google Scholar 

  5. 5.

    Bentis, C. J., Kaufman, L. & Golubic, S. Endolithic fungi in reef-building corals (Order: Scleractinia) are common, cosmopolitan, and potentially pathogenic. Biol. Bull. 198, 254–260 (2000).

    CAS  PubMed  Google Scholar 

  6. 6.

    Wegley, L., Edwards, R., Rodriguez-Brito, B., Liu, H. & Rohwer, F. Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ. Microbiol. 9, 2707–2719 (2007). One of the first microbial metagenomic studies on coral showing that viruses, bacteria and fungi are abundant members of the coral microbiome.

    CAS  PubMed  Google Scholar 

  7. 7.

    Littman, R., Willis, B. L. & Bourne, D. G. Metagenomic analysis of the coral holobiont during a natural bleaching event on the Great Barrier Reef. Environ. Microbiol. Rep. 3, 651–660 (2011).

    CAS  PubMed  Google Scholar 

  8. 8.

    Amend, A. S., Barshis, D. J. & Oliver, T. A. Coral-associated marine fungi form novel lineages and heterogeneous assemblages. ISME J. 6, 1291–1301 (2012).

    CAS  PubMed  Google Scholar 

  9. 9.

    Wood-Charlson, E. M., Weynberg, K. D., Suttle, C. A., Roux, S. & Oppen, M. J. H. Metagenomic characterization of viral communities in corals: mining biological signal from methodological noise. Environ. Microbiol. 17, 3440–3449 (2015).

    PubMed  Google Scholar 

  10. 10.

    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 (2016).

    PubMed  PubMed Central  Google Scholar 

  11. 11.

    Thurber, R. V., Payet, J. P., Thurber, A. R. & Correa, A. M. Virus-host interactions and their roles in coral reef health and disease. Nat. Rev. Microbiol. 15, 205–216 (2017).

    CAS  PubMed  Google Scholar 

  12. 12.

    Huggett, M. J. & Apprill, A. Coral microbiome database: integration of sequences reveals high diversity and relatedness of coral-associated microbes. Environ. Microbiol. Rep. 11, 372–385 (2018).

    PubMed  Google Scholar 

  13. 13.

    Siboni, N., Ben-Dov, E., Sivan, A. & Kushmaro, A. Global distribution and diversity of coral-associated Archaea and their possible role in the coral holobiont nitrogen cycle. Environ. Microbiol. 10, 2979–2990 (2008).

    CAS  PubMed  Google Scholar 

  14. 14.

    Bahram, M., Anslan, S., Hildebrand, F., Bork, P. & Tedersoo, L. Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment. Environ. Microbiol. Rep. (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Spang, A., Caceres, E. F. & Ettema, T. J. Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science 357, eaaf3883 (2017).

    PubMed  Google Scholar 

  16. 16.

    Sharp, K. H., Distel, D. & Paul, V. J. Diversity and dynamics of bacterial communities in early life stages of the Caribbean coral Porites astreoides. ISME J. 6, 790–801 (2012). First evidence for vertical transmission of bacteria in a brooding coral from FISH and 16S rRNA gene sequencing.

    CAS  PubMed  Google Scholar 

  17. 17.

    Sharp, K. H., Ritchie, K. B., Schupp, P. J., Ritson-Williams, R. & Paul, V. J. Bacterial acquisition in juveniles of several broadcast spawning coral species. PLOS ONE 5, e10898 (2010).

    PubMed  PubMed Central  Google Scholar 

  18. 18.

    Johansson, M. E. & Hansson, G. C. in Mucins: Methods and Protocols Vol. 842 (eds McGuckin, M. A. & J Thornton, D.) 229–235 (Springer, 2012).

  19. 19.

    Chiu, H.-H., Mette, A., Shiu, J.-H. & Tang, S.-L. Bacterial distribution in the epidermis and mucus of the coral Euphyllia glabrescens by CARD-FISH. Zool. Stud. 51, 1332–1342 (2012).

    CAS  Google Scholar 

  20. 20.

    Zhou, G. et al. Microbiome dynamics in early life stages of the scleractinian coral Acropora gemmifera in response to elevated pCO2. Environ. Microbiol. 19, 3342–3352 (2017).

    CAS  PubMed  Google Scholar 

  21. 21.

    Leite, D. C. et al. Broadcast spawning coral Mussismilia hispida can vertically transfer its associated bacterial core. Front. Microbiol. 8, 176 (2017).

    PubMed  PubMed Central  Google Scholar 

  22. 22.

    Ricardo, G. F., Jones, R. J., Negri, A. P. & Stocker, R. That sinking feeling: suspended sediments can prevent the ascent of coral egg bundles. Sci. Rep. 6, 21567 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. 23.

    Ceh, J., van Keulen, M. & Bourne, D. G. Intergenerational transfer of specific bacteria in corals and possible implications for offspring fitness. Microb. Ecol. 65, 227–231 (2013).

    CAS  PubMed  Google Scholar 

  24. 24.

    Littman, R. A., Willis, B. L. & Bourne, D. G. Bacterial communities of juvenile corals infected with different Symbiodinium (dinoflagellate) clades. Mar. Ecol. Prog. Ser. 389, 45–59 (2009).

    Google Scholar 

  25. 25.

    Lema, K. A., Bourne, D. G. & Willis, B. L. Onset and establishment of diazotrophs and other bacterial associates in the early life history stages of the coral Acropora millepora. Mol. Ecol. 23, 4682–4695 (2014).

    CAS  PubMed  Google Scholar 

  26. 26.

    Epstein, H. E., Torda, G., Munday, P. L. & van Oppen, M. J. H. Parental and early life stage environments drive establishment of bacterial and dinoflagellate communities in a common coral. ISME J. 13, 1635–1638 (2019).

    CAS  PubMed  Google Scholar 

  27. 27.

    Hernandez-Agreda, A., Leggat, W., Bongaerts, P., Herrera, C. & Ainsworth, T. D. Rethinking the coral microbiome: simplicity exists within a diverse microbial biosphere. mBio 9, e00812–18 (2018). Coral 16S rRNA metabarcoding study proposing three components of the coral microbiome: the resident or individual microbiome (<3% of the taxa found within a species as a whole microbiome), the environmentally responsive community (>96%) and the core microbiome (~0.1%).

    PubMed  PubMed Central  Google Scholar 

  28. 28.

    de Vos, W. M. Fame and future of faecal transplantations — developing next-generation therapies with synthetic microbiomes. Microb. Biotechnol. 6, 316–325 (2013).

    PubMed  PubMed Central  Google Scholar 

  29. 29.

    Nyholm, S. V. & McFall-Ngai, M. The winnowing: establishing the squid–vibrio symbiosis. Nat. Rev. Microbiol. 2, 632–642 (2004).

    CAS  PubMed  Google Scholar 

  30. 30.

    Nyholm, S. V. & Graf, J. Knowing your friends: invertebrate innate immunity fosters beneficial bacterial symbioses. Nat. Rev. Microbiol. 10, 815–827 (2012).

    CAS  PubMed  Google Scholar 

  31. 31.

    Clúa, J., Roda, C., Zanetti, M. & Blanco, F. Compatibility between legumes and rhizobia for the establishment of a successful nitrogen-fixing symbiosis. Genes 9, 125 (2018).

    PubMed Central  Google Scholar 

  32. 32.

    Mansfield, K. M. & Gilmore, T. D. Innate immunity and cnidarian-Symbiodiniaceae mutualism. Dev. Comp. Immunol. 90, 199–209 (2018).

    PubMed  Google Scholar 

  33. 33.

    Puill-Stephan, E., Willis, B. L., Abrego, D., Raina, J. B. & van Oppen, M. J. H. Allorecognition maturation in the broadcast-spawning coral Acropora millepora. Coral Reefs 31, 1019–1028 (2012).

    Google Scholar 

  34. 34.

    Amsterdam, D. & Ostrov, B. E. The impact of the microbiome on immunosenescence. Immunol. Invest. 47, 801–811 (2018).

    CAS  PubMed  Google Scholar 

  35. 35.

    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).

    PubMed  PubMed Central  Google Scholar 

  36. 36.

    Pollock, F. J. et al. Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny. Nat. Commun. 9, 4921 (2018). Coral 16S rRNA gene metabarcoding study including 236 colonies representing 32 Australian scleractinian taxa showing that bacterial and archaeal communities in different coral compartments respond differently to host and environmental factors.

    PubMed  PubMed Central  Google Scholar 

  37. 37.

    Bythell, J. C., Brown, B. E. & Kirkwood, T. B. L. Do reef corals age? Biol. Rev. 93, 1192–1202 (2018).

    PubMed  Google Scholar 

  38. 38.

    Finkel, O. M., Castrillo, G., Paredes, S. H., González, I. S. & Dangl, J. L. Understanding and exploiting plant beneficial microbes. Curr. Opin. Plant Biol. 38, 155–163 (2017).

    PubMed  PubMed Central  Google Scholar 

  39. 39.

    Cong, J. & Zhang, X. How human microbiome talks to health and disease. Eur. J. Clin. Microbiol. Infect. Dis. 37, 1595–1601 (2018).

    PubMed  Google Scholar 

  40. 40.

    Sweet, M. J., Croquer, A. & Bythell, J. C. Bacterial assemblages differ between compartments within the coral holobiont. Coral Reefs 30, 39–52 (2011).

    Google Scholar 

  41. 41.

    Apprill, A., Weber, L. G. & Santoro, A. E. Distinguishing between microbial habitats unravels ecological complexity in coral microbiomes. mSystems 1, e00143–16 (2016).

    PubMed  PubMed Central  Google Scholar 

  42. 42.

    Agostini, S. et al. Biological and chemical characteristics of the coral gastric cavity. Coral Reefs 31, 147–156 (2012).

    Google Scholar 

  43. 43.

    Kramarsky-Winter, E. et al. The possible role of cyanobacterial filaments in coral black band disease pathology. Microb. Ecol. 67, 177–185 (2014).

    PubMed  Google Scholar 

  44. 44.

    Kimes, N. E., Van Nostrand, J. D., Weil, E., Zhou, J. & Morris, P. J. Microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased colonies. Environ. Microbiol. 12, 541–556 (2010).

    CAS  PubMed  Google Scholar 

  45. 45.

    Garren, M. & Azam, F. New method for counting bacteria associated with coral mucus. Appl. Environ. Microbiol. 76, 6128–6133 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. 46.

    Yang, S.-H. et al. Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera. Microbiome 7, 3 (2019).

    PubMed  PubMed Central  Google Scholar 

  47. 47.

    Wild, C., Niggl, W., Naumann, M. S. & Haas, A. F. Organic matter release by Red Sea coral reef organisms — potential effects on microbial activity and in situ O2 availability. Mar. Ecol. Prog. Ser. 411, 61–71 (2010).

    CAS  Google Scholar 

  48. 48.

    Coats, V. C. & Rumpho, M. E. The rhizosphere microbiota of plant invaders: an overview of recent advances in the microbiomics of invasive plants. Front. Microbiol. 5, 368 (2014).

    PubMed  PubMed Central  Google Scholar 

  49. 49.

    Lee, S. T. M., Davy, S. K., Tang, S.-L. & Kench, P. S. Mucus sugar content shapes the bacterial community structure in thermally stressed Acropora muricata. Front. Microbiol. 7, 371 (2016).

    PubMed  PubMed Central  Google Scholar 

  50. 50.

    Nakajima, R. et al. High inorganic phosphate concentration in coral mucus and its utilization by heterotrophic bacteria in a Malaysian coral reef. Mar. Ecol. 36, 835–841 (2015).

    CAS  Google Scholar 

  51. 51.

    Work, T. M. & Aeby, G. S. Microbial aggregates within tissues infect a diversity of corals throughout the Indo-Pacific. Mar. Ecol. Prog. Ser. 500, 1–9 (2014).

    Google Scholar 

  52. 52.

    Neave, M. J. et al. Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales. ISME J. 11, 186–200 (2016).

    PubMed  PubMed Central  Google Scholar 

  53. 53.

    van de Water, J. A. et al. The coral immune response facilitates protection against microbes during tissue regeneration. Mol. Ecol. 24, 3390–3404 (2015).

    PubMed  Google Scholar 

  54. 54.

    Ainsworth, T. D. et al. The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts. ISME J. 9, 2261–2274 (2015). Fluorescence in situ hybridization and 16S rRNA gene sequencing analyses show that certain bacteria are closely associated with in hospite microalgal symbionts, corals may have a core bacterial microbiome and different host compartments harbour distinct bacterial communities.

    CAS  Google Scholar 

  55. 55.

    Marcelino, V. R., van Oppen, M. J. H. & Verbruggen, H. Highly structured prokaryote communities exist within the skeleton of coral colonies. ISME J. 12, 300–303 (2017).

    PubMed  PubMed Central  Google Scholar 

  56. 56.

    Sunagawa, S., Woodley, C. M. & Medina, M. Threatened corals provide underexplored microbial habitats. PLOS ONE 5, e9554 (2010).

    PubMed  PubMed Central  Google Scholar 

  57. 57.

    Liang, J. et al. Distinct bacterial communities associated with massive and branching scleractinian corals and potential linkages to coral susceptibility to thermal or cold stress. Front. Microbiol. 8, 979 (2017).

    PubMed  PubMed Central  Google Scholar 

  58. 58.

    Diaz, J. M. et al. Species-specific control of external superoxide levels by the coral holobiont during a natural bleaching event. Nat. Commun. 7, 13801 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. 59.

    Chu, N. D. & Vollmer, S. V. Caribbean corals house shared and host-specific microbial symbionts over time and space. Environ. Microbiol. Rep. 8, 493–500 (2016).

    CAS  PubMed  Google Scholar 

  60. 60.

    Gardner, S. G. et al. Coral microbiome diversity reflects mass coral bleaching susceptibility during the 2016 El Niño heat wave. Ecol. Evol. 9, 938–956 (2018).

    Google Scholar 

  61. 61.

    Littman, R. A., Willis, B. L., Pfeffer, C. & Bourne, D. G. Diversities of coral-associated bacteria differ with location, but not species, for three acroporid corals on the Great Barrier Reef. FEMS Microbiol. Ecol. 68, 152–163 (2009).

    CAS  PubMed  Google Scholar 

  62. 62.

    Hernandez-Agreda, A., Leggat, W., Bongaerts, P. & Ainsworth, T. D. The microbial signature provides insight into the mechanistic basis of coral success across reef habitats. mBio 7, e00560–16 (2016).

    PubMed  PubMed Central  Google Scholar 

  63. 63.

    Hughes, T. P. et al. Global warming and recurrent mass bleaching of corals. Nature 543, 373–377 (2017).

    CAS  PubMed  Google Scholar 

  64. 64.

    Bourne, D., Iida, Y., Uthicke, S. & Smith-Keune, C. Changes in coral-associated microbial communities during a bleaching event. ISME J. 2, 350–363 (2008). Early 16S rRNA gene denaturing gradient gel electrophoresis and clone library study showing a shift in coral-associated bacteria during a summer heatwave but prior to visual signs of bleaching; the shift was characterized by an increase in Vibrio strains, followed by reversion to the pre-bleaching community once the temperatures returned to normal.

    CAS  PubMed  Google Scholar 

  65. 65.

    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). Coral 16S rRNA metabarcoding and experimental heat stress study showing that exposure to heat changes the bacterial microbiome in heat-sensitive but not in heat-tolerant colonies of the same species.

    CAS  PubMed  PubMed Central  Google Scholar 

  66. 66.

    Grottoli, A. G. et al. Coral physiology and microbiome dynamics under combined warming and ocean acidification. PLOS ONE 13, e0191156 (2018).

    PubMed  PubMed Central  Google Scholar 

  67. 67.

    Hadaidi, G. et al. Stable mucus-associated bacterial communities in bleached and healthy corals of Porites lobata from the Arabian seas. Sci. Rep. 7, 45362 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. 68.

    Tracy, A. M., Koren, O., Douglas, N., Weil, E. & Harvell, C. D. Persistent shifts in Caribbean coral microbiota are linked to the 2010 warm thermal anomaly. Environ. Microbiol. Rep. 7, 471–479 (2015).

    PubMed  Google Scholar 

  69. 69.

    Epstein, H. E., Torda, G. & van Oppen, M. J. H. Relative stability of the Pocillopora acuta microbiome throughout a thermal stress event. Coral Reefs 38, 373–386 (2019).

    Google Scholar 

  70. 70.

    Webster, N. et al. Host-associated coral reef microbes respond to the cumulative pressures of ocean warming and ocean acidification. Sci. Rep. 6, 19324 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  71. 71.

    Gajigan, A. P., Diaz, L. A. & Conaco, C. Resilience of the prokaryotic microbial community of Acropora digitifera to elevated temperature. Microbiologyopen 6, e00478 (2017).

    PubMed Central  Google Scholar 

  72. 72.

    Salerno, J. L., Reineman, D. R., Gates, R. D. & Rappé, M. S. The effect of a sublethal temperature elevation on the structure of bacterial communities associated with the coral Porites compressa. J. Mar. Biol. 2011, 969173 (2011).

    Google Scholar 

  73. 73.

    McDevitt-Irwin, J. M., Baum, J. K., Garren, M. & Vega Thurber, R. L. Responses of coral-associated bacterial communities to local and global stressors. Front. Mar. Sci. 4, 262 (2017).

    Google Scholar 

  74. 74.

    Zaneveld, J. R., McMinds, R. & Thurber, R. V. Stress and stability: applying the Anna Karenina principle to animal microbiomes. Nat. Microbiol. 2, 17121 (2017).

    CAS  PubMed  Google Scholar 

  75. 75.

    Morrow, K., Muller, E. & Lesser, M. in Coral Bleaching: Patterns, Processes, Causes and Consequences (eds van Oppen, M. J. H. & Lough, J. M.) 2nd edn 153–188 (Springer, 2018).

  76. 76.

    Niggl, W., Glas, M., Laforsch, C., Mayr, C. & Wild, C. in Proc. 11th Int. Coral Reef Symp. (ed. Riegl, B. & Dodge, R. E.) Vol. 2 905–911 (Nova Southeastern University National Coral Reef Institute, 2009).

  77. 77.

    Pinzón, J. H. et al. Whole transcriptome analysis reveals changes in expression of immune-related genes during and after bleaching in a reef-building coral. R. Soc. Open Sci. 2, 140214 (2015).

    PubMed  PubMed Central  Google Scholar 

  78. 78.

    Wooldridge, S. A. Breakdown of the coral-algae symbiosis: towards formalising a linkage between warm-water bleaching thresholds and the growth rate of the intracellular zooxanthellae. Biogeosciences 10, 1647–1658 (2013).

    Google Scholar 

  79. 79.

    Ritchie, K. B. Regulation of microbial populations by coral surface mucus and mucus-associated bacteria. Mar. Ecol. Prog. Ser. 322, 1–14 (2006).

    CAS  Google Scholar 

  80. 80.

    Bourne, D. G. & Munn, C. B. Diversity of bacteria associated with the coral Pocillopora damicornis from the Great Barrier Reef. Environ. Microbiol. 7, 1162–1174 (2005).

    CAS  PubMed  Google Scholar 

  81. 81.

    Ceh, J. et al. Nutrient cycling in early coral life stages: Pocillopora damicornis larvae provide their algal symbiont (Symbiodinium) with nitrogen acquired from bacterial associates. Ecol. Evol. 3, 2393–2400 (2013). Nanoscale secondary ion mass spectrometry study showing the incorporation and translocation of nitrogen from Vibrio and Alteromonas strains into coral larvae and specifically into the in hospite Symbiodiniaceae algae.

    Google Scholar 

  82. 82.

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

    PubMed  Google Scholar 

  83. 83.

    Meyer, J. L., Paul, V. J., Raymundo, L. J. & Teplitski, M. Comparative metagenomics of the polymicrobial Black Band disease of corals. Front. Microbiol. 8, 618 (2017).

    PubMed  PubMed Central  Google Scholar 

  84. 84.

    Den Uyl, P. A., Richardson, L. L., Jain, S. & Dick, G. J. Unraveling the physiological roles of the cyanobacterium Geitlerinema sp BBD and other lack Band Disease community members through genomic analysis of a mixed culture. PLOS ONE 11, e0157953 (2016).

    Google Scholar 

  85. 85.

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

    PubMed  PubMed Central  Google Scholar 

  86. 86.

    Lesser, M. P., Mazel, C. H., Gorbunov, M. Y. & Falkowski, P. G. Discovery of symbiotic nitrogen-fixing cyanobacteria in corals. Science 305, 997–1000 (2004). Microscopy and immunoblot experiments showing that cyanobacteria are present within coral tissues and express the nitrogen-fixing nitrogenase gene.

    CAS  PubMed  Google Scholar 

  87. 87.

    Lema, K. A. et al. Imaging the uptake of nitrogen-fixing bacteria into larvae of the coral Acropora millepora. ISME J. 10, 1804 (2016).

    CAS  PubMed  Google Scholar 

  88. 88.

    Tebben, J. et al. Induction of larval metamorphosis of the coral Acropora millepora by tetrabromopyrrole isolated from a Pseudoalteromonas bacterium. PLOS ONE 6, e19082 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  89. 89.

    Wichard, T. & Beemelmanns, C. Role of chemical mediators in aquatic interactions across the prokaryote–eukaryote boundary. J. Chem. Ecol. 44, 1008–1021 (2018).

    CAS  PubMed  Google Scholar 

  90. 90.

    Krediet, C. J., Ritchie, K. B., Alagely, A. & Teplitski, M. Members of native coral microbiota inhibit glycosidases and thwart colonization of coral mucus by an opportunistic pathogen. ISME J. 7, 980–990 (2013).

    CAS  PubMed  Google Scholar 

  91. 91.

    Certner, R. H. & Vollmer, S. V. Inhibiting bacterial quorum sensing arrests coral disease development and disease-associated microbes. Environ. Microbiol. 20, 645–657 (2018).

    CAS  PubMed  Google Scholar 

  92. 92.

    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).

    PubMed  Google Scholar 

  93. 93.

    Rau, G. H., McLeod, E. L. & Hoegh-Guldberg, O. The need for new ocean conservation strategies in a high-carbon dioxide world. Nat. Clim. Chang. 2, 720–724 (2012).

    Google Scholar 

  94. 94.

    West, A. G. et al. The microbiome in threatened species conservation. Biol. Conserv. 229, 85–98 (2019).

    Google Scholar 

  95. 95.

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

    CAS  PubMed  Google Scholar 

  96. 96.

    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).

    PubMed  PubMed Central  Google Scholar 

  97. 97.

    East, R. Soil science comes to life. Nature 501, S18–S19 (2013).

    CAS  PubMed  Google Scholar 

  98. 98.

    Daliri, E. B. M., Tango, C. N., Lee, B. H. & Oh, D. H. Human microbiome restoration and safety. Int. J. Med. Microbiol. 308, 487–497 (2018).

    PubMed  Google Scholar 

  99. 99.

    Correa-Garcia, S., Pande, P., Seguin, A., St-Arnaud, M. & Yergeau, E. Rhizoremediation of petroleum hydrocarbons: a model system for plant microbiome manipulation. Microb. Biotechnol. 11, 819–832 (2018).

    PubMed  PubMed Central  Google Scholar 

  100. 100.

    Peixoto, R. S., Rosado, P. M., de Assis Leite, D. C., Rosado, A. S. & Bourne, D. G. Beneficial microorganisms for corals (BMC): proposed mechanisms for coral health and resilience. Front. Microbiol. 8, 341 (2017).

    PubMed  PubMed Central  Google Scholar 

  101. 101.

    Lesser, M. P. Oxidative stress causes coral bleaching during exposure to elevated temperatures. Coral Reefs 16, 187–192 (1997). First study demonstrating that exposure of corals to exogenous antioxidants prevents bleaching during heat stress, indicating that oxidative stress underpins coral bleaching.

    Google Scholar 

  102. 102.

    Roethig, T. et al. Distinct bacterial communities associated with the coral model Aiptasia in aposymbiotic and symbiotic states with Symbiodinium. Front. Mar. Sci. 3, 234 (2016).

    Google Scholar 

  103. 103.

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

    Google Scholar 

  104. 104.

    Alagely, A., Krediet, C. J., Ritchie, K. B. & Teplitski, M. Signaling-mediated cross-talk modulates swarming and biofilm formation in a coral pathogen Serratia marcescens. ISME J. 5, 1609–1620 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  105. 105.

    Masson, F., Copete, S. C., Schüpfer, F., Garcia-Arraez, G. & Lemaitre, B. In vitro culture of the insect endosymbiont Spiroplasma poulsonii highlights bacterial genes involved in host-symbiont interaction. mBio 9, e00024–18 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  106. 106.

    Swainsbury, D. J. et al. Engineering of a calcium-ion binding site into the RC-LH1-PufX complex of Rhodobacter sphaeroides to enable ion-dependent spectral red-shifting. Biochim. Biophys. Acta 1858, 927–938 (2017).

    CAS  PubMed Central  Google Scholar 

  107. 107.

    Dalia, T. N. et al. Multiplex genome editing by natural transformation (MuGENT) for synthetic biology in Vibrio natriegens. ACS Synth. Biol. 6, 1650–1655 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  108. 108.

    Ito, R. et al. Widespread fosfomycin resistance in gram-negative bacteria attributable to the chromosomal fosA gene. mBio 8, e00749–17 (2017).

    PubMed  PubMed Central  Google Scholar 

  109. 109.

    Ducat, D. C., Way, J. C. & Silver, P. A. Engineering cyanobacteria to generate high-value products. Trends Biotechnol. 29, 95–103 (2017).

    Google Scholar 

  110. 110.

    Solé, R. Bioengineering the biosphere? Ecol. Complex. 22, 40–49 (2015).

    Google Scholar 

  111. 111.

    Chalker, B. & Taylor, D. Light-enhanced calcification, and the role of oxidative phosphorylation in calcification of the coral Acropora cervicornis. Proc. R. Soc. Lond. B 190, 323–331 (1975).

    CAS  PubMed  Google Scholar 

  112. 112.

    Muscatine, L. & Porter, J. W. Reef corals: mutualistic symbioses adapted to nutrient-poor environments. Bioscience 27, 454–460 (1977).

    Google Scholar 

  113. 113.

    Shade, A. & Handelsman, J. Beyond the Venn diagram: the hunt for a core microbiome. Environ. Microbiol. 14, 4–12 (2012).

    CAS  PubMed  Google Scholar 

  114. 114.

    Hernandez-Agreda, A., Gates, R. D. & Ainsworth, T. D. Defining the core microbiome in corals’ microbial soup. Trends Microbiol. 25, 125–140 (2016).

    PubMed  Google Scholar 

  115. 115.

    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).

    Google Scholar 

  116. 116.

    Hester, E. R., Barott, K. L., Nulton, J., Vermeij, M. J. & Rohwer, F. L. Stable and sporadic symbiotic communities of coral and algal holobionts. ISME J. 10, 1157 (2015).

    PubMed  PubMed Central  Google Scholar 

  117. 117.

    Brener-Raffalli, K. et al. Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato. Microbiome 6, 39 (2018).

    PubMed  PubMed Central  Google Scholar 

  118. 118.

    Chen, L. M., Garmaeva, S., Zhernakova, A., Fu, J. Y. & Wijmenga, C. A system biology perspective on environment–host–microbe interactions. Hum. Mol. Genet. 27, R187–R194 (2018).

    CAS  PubMed  Google Scholar 

  119. 119.

    Qin, Y., Druzhinina, I. S., Pan, X. & Yuan, Z. Microbially mediated plant salt tolerance and microbiome-based solutions for saline agriculture. Biotechnol. Adv. 34, 1245–1259 (2016).

    CAS  PubMed  Google Scholar 

Download references


M.J.H.v.O. acknowledges Australian Research Council Laureate Fellowship FL180100036. The authors acknowledge K. Fabricius and E. Matson, both at the Australian Institute of Marine Science, for taking photographs in figure 1 and K. Damjanovic, University of Queensland, for taking the photograph in figure 3.

Author information




Both authors contributed to all aspects of the article. M.J.H.v.O. wrote most of the manuscript.

Corresponding author

Correspondence to Madeleine J. H. van Oppen.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information

Nature Reviews Microbiology thanks R. Vega Thurber, C. Voolstra and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.


Robust and complex clades

The Scleractinia comprise two phylogenetic clades based on molecular evidence, the Complexa and the Robusta.


A correlation between host phylogenetic relatedness and multivariate community similarities of the associated microbiome (for example, composition and richness). Phylosymbiosis does not a priori imply co-evolution (although co-evolution can be one of the causes of phylosymbiosis) as it does not assume that microbial communities are stable or vertically transmitted from generation to generation.


Changes in microbiome composition frequently correlated with disease states, without inferring a causative link between the two and dysbiosis may not involve host features. Dysbiosis can potentially result in highly dissimilar microbial profiles among host individuals of the same species.

Designer microbiomes

Man-made, defined microbial communities of reduced complexity; they can include natural or genetically engineered microorganisms; synonym of synthetic microbiomes.

Minimal microbiome

The smallest but functionally indispensable subset of the total microbiome.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

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).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing