Heat accumulation on coral reefs mitigated by internal waves


Coral reefs are among the most species-rich, productive and economically valuable ecosystems on Earth but increasingly frequent pantropical coral bleaching events are threatening their persistence on a global scale. The 2015–2016 El Niño led to the hottest sea surface temperatures on record and widespread bleaching of shallow-water corals. However, the causes of spatial variation in bleaching are poorly understood, and near-surface estimates of heat stress, such as those inferred from satellites, cannot be generalized across the broad depth ranges occupied by corals. Here, using in situ temperatures recorded across reefs from the near surface to 30–50 m depths in the western, central and eastern Pacific, we show that during the peak of the 2015–2016 anomaly, temperature fluctuations associated with internal waves reduced cumulative heat exposure by up to 88%. The durations of severe thermal anomalies above 8 °C-days, at which point widespread coral bleaching and mortality are likely, were also decreased by >36% at some sites and were prevented entirely at others. The impact of internal waves across depths on coral reefs has the potential to create and support thermal refuges in which heat stress and coral bleaching risk may be modulated, but future effects depend on the response of internal wave climates to continued warming and strengthening ocean stratification.

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Fig. 1: In situ summertime water temperature variation across depths over three coral reefs in the Pacific Ocean.
Fig. 2: In situ water temperature variation relative to SST for observed and NIW time series.
Fig. 3: Internal waves decreased the duration and severity of thermal anomalies across depths and sites during the 2015–2016 El Niño.
Fig. 4: Heat accumulation across depths during the 2015–2016 El Niño with and without internal waves.

Data availability

Satellite SST observations can be accessed at https://coralreefwatch.noaa.gov/satellite/index.php. In situ data can be accessed at http://mcr.lternet.edu/data for the Moorea LTER site and at https://doi.pangaea.de/10.1594/PANGAEA.906191 for Iriomote and the Gulf of Chiriquí.

Code availability

The Matlab code used to produce the NIW data from observed temperature time series in this paper is available from the corresponding author on request.


  1. 1.

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

    Google Scholar 

  2. 2.

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

    Google Scholar 

  3. 3.

    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).

    Google Scholar 

  4. 4.

    Kahng, S. E. et al. Community ecology of mesophotic coral reef ecosystems. Coral Reefs 29, 255–275 (2010).

    Google Scholar 

  5. 5.

    Harris, P. T. et al. Submerged banks in the Great Barrier Reef, Australia, greatly increase available coral reef habitat. ICES J. Mar. Sci. 70, 284–293 (2013).

    Google Scholar 

  6. 6.

    Locker, S. D. et al. Geomorphology of mesophotic coral ecosystems: current perspectives on morphology, distribution, and mapping strategies. Coral Reefs 29, 329–345 (2010).

    Google Scholar 

  7. 7.

    Riegl, B. & Piller, W. E. Possible refugia for reefs in times of environmental stress. Int. J. Earth Sci. 92, 520–531 (2003).

    Google Scholar 

  8. 8.

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

    Google Scholar 

  9. 9.

    Penin, L., Adjeroud, M., Schrimm, M. & Lenihan, H. S. High spatial variability in coral bleaching around Moorea (French Polynesia): patterns across locations and water depths. C. R. Biol. 330, 171–181 (2007).

    Google Scholar 

  10. 10.

    Murakami, T. et al. Bleaching in vertically distributed corals in Amitori Bay of Iriomote Island. J. Jpn Soc. Civ. Eng. Ser. B3 73, I_881–I_886 (2017).

    Google Scholar 

  11. 11.

    Frade, P. R. et al. Deep reefs of the Great Barrier Reef offer limited thermal refuge during mass coral bleaching. Nat. Commun. 9, 3447 (2018).

    Google Scholar 

  12. 12.

    Baird, A. H. et al. A decline in bleaching suggests that depth can provide a refuge from global warming in most coral taxa. Mar. Ecol. Prog. Ser. 603, 257–264 (2018).

    Google Scholar 

  13. 13.

    Muir, P. R., Marshall, P. A., Abdulla, A. & Aguirre, J. D. Species identity and depth predict bleaching severity in reef-building corals: shall the deep inherit the reef? Proc. R. Soc. B 284, 20171551 (2017).

    Google Scholar 

  14. 14.

    Leichter, J. J., Helmuth, B. & Fischer, A. M. Variation beneath the surface: quantifying complex thermal environments on coral reefs in the Caribbean, Bahamas and Florida. J. Mar. Res. 64, 563–588 (2006).

    Google Scholar 

  15. 15.

    Leichter, J. J., Stokes, M. D., Hench, J. L., Witting, J. & Washburn, L. The island-scale internal wave climate of Moorea, French Polynesia. J. Geophys. Res. Oceans 117, C06008 (2012).

    Google Scholar 

  16. 16.

    Leichter, J. J., Stokes, M. D., Vilchis, L. I. & Fiechter, J. Regional synchrony of temperature variation and internal wave forcing along the Florida Keys reef tract. J. Geophys. Res. Oceans 119, 548–558 (2014).

    Google Scholar 

  17. 17.

    Wolanski, E. & Delesalle, B. Upwelling by internal waves, Tahiti, French-Polynesia. Cont. Shelf Res. 15, 357–368 (1995).

    Google Scholar 

  18. 18.

    Wolanski, E. & Pickard, G. L. Upwelling by internal tides and kelvin waves at the continental-shelf break on the Great Barrier Reef. Aust. J. Mar. Freshw. Res. 34, 65–80 (1983).

    Google Scholar 

  19. 19.

    Wall, M. et al. Large-amplitude internal waves benefit corals during thermal stress. Proc. R. Soc. B 282, 20140650 (2015).

    Google Scholar 

  20. 20.

    Sheppard, C. Large temperature plunges recorded by data loggers at different depths on an Indian Ocean atoll: comparison with satellite data and relevance to coral refuges. Coral Reefs 28, 399–403 (2009).

    Google Scholar 

  21. 21.

    van Woesik, R. et al. Climate-change refugia in the sheltered bays of Palau: analogs of future reefs. Ecol. Evol. 2, 2474–2484 (2012).

    Google Scholar 

  22. 22.

    Donner, S. D. An evaluation of the effect of recent temperature variability on the prediction of coral bleaching events. Ecol. Appl. 21, 1718–1730 (2011).

    Google Scholar 

  23. 23.

    Fitt, W. K., Brown, B. E., Warner, M. E. & Dunne, R. P. Coral bleaching: interpretation of thermal tolerance limits and thermal thresholds in tropical corals. Coral Reefs 20, 51–65 (2001).

    Google Scholar 

  24. 24.

    Hoegh-Guldberg, O. Climate change, coral bleaching and the future of the world’s coral reefs. Mar. Freshw. Res. 50, 839–866 (1999).

    Google Scholar 

  25. 25.

    Grottoli, A. G., Rodrigues, L. J. & Palardy, J. E. Heterotrophic plasticity and resilience in bleached corals. Nature 440, 1186–1189 (2006).

    Google Scholar 

  26. 26.

    Brown, B. E. Coral bleaching: causes and consequences. Coral Reefs 16, S129–S138 (1997).

    Google Scholar 

  27. 27.

    Glynn, P. W. & D’Croz, L. Experimental evidence for high temperature stress as the cause of El Niño-coincident coral mortality. Coral Reefs 8, 181–191 (1990).

    Google Scholar 

  28. 28.

    Coles, S. L. & Brown, B. E. Coral bleaching — capacity for acclimatization and adaptation. Adv. Mar. Biol. 46, 183–223 (2003).

    Google Scholar 

  29. 29.

    Marshall, P. A. & Baird, A. H. Bleaching of corals on the Great Barrier Reef: differential susceptibilities among taxa. Coral Reefs 19, 155–163 (2000).

    Google Scholar 

  30. 30.

    DeCarlo, T. M. & Harrison, H. B. An enigmatic decoupling between heat stress and coral bleaching on the Great Barrier Reef. PeerJ 7, e7473 (2019).

    Google Scholar 

  31. 31.

    Pisapia, C., Burn, D. & Pratchett, M. S. Changes in the population and community structure of corals during recent disturbances (February 2016-October 2017) on Maldivian coral reefs. Sci. Rep. 9, 8402 (2019).

    Google Scholar 

  32. 32.

    Loya, Y. et al. Coral bleaching: the winners and the losers. Ecol. Lett. 4, 122–131 (2001).

    Google Scholar 

  33. 33.

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

    Google Scholar 

  34. 34.

    Riegl, B. et al. Heat attenuation and nutrient delivery by localized upwelling avoided coral bleaching mortality in northern Galapagos during 2015/2016 ENSO. Coral Reefs 38, 773–785 (2019).

    Google Scholar 

  35. 35.

    Smith, T. B., Glynn, P. W., Maté, J. L., Toth, L. T. & Gyory, J. A depth refugium from catastrophic coral bleaching prevents regional extinction. Ecology 95, 1663–1673 (2014).

    Google Scholar 

  36. 36.

    Karnauskas, K. B. & Cohen, A. L. Equatorial refuge amid tropical warming. Nat. Clim. Change 2, 530–534 (2012).

    Google Scholar 

  37. 37.

    Klein, S. G. et al. Night-time temperature reprieves enhance the thermal tolerance of a symbiotic cnidarian. Front. Mar. Sci. 6, 453 (2019).

    Google Scholar 

  38. 38.

    Lesser, M. P., Slattery, M. & Mobley, C. D. Biodiversity and functional ecology of mesophotic coral reefs. Ann. Rev. Ecol. Evol. System. 49, 49–71 (2018).

    Google Scholar 

  39. 39.

    Glynn, P. W. Coral reef bleaching: facts, hypotheses and implications. Glob. Change Biol. 2, 495–509 (1996).

    Google Scholar 

  40. 40.

    Schramek, T. A., Colin, P. L., Merrifield, M. A. & Terrill, E. J. Depth-dependent thermal stress around corals in the tropical Pacific Ocean. Geophys. Res. Lett. 45, 9739–9747 (2018).

    Google Scholar 

  41. 41.

    Witman, J. D., Leichter, J. J., Genovese, S. J. & Brooks, D. A. Pulsed phytoplankton supply to the rocky subtidal zone: influence of internal waves. Proc. Natl Acad. Sci. USA 90, 1686–1690 (1993).

    Google Scholar 

  42. 42.

    Kleypas, J. A., McManus, J. W. & Menez, L. A. B. Environmental limits to coral reef development: where do we draw theline? Am. Zool. 39, 146–159 (1999).

    Google Scholar 

  43. 43.

    Guan, Y., Hohn, S. & Merico, A. Suitable environmental ranges for potential coral reef habitats in the tropical ocean. PLoS ONE 10, e0128831 (2015).

    Google Scholar 

  44. 44.

    Alford, M. H. et al. The formation and fate of internal waves in the South China Sea. Nature 521, 65–69 (2015).

    Google Scholar 

  45. 45.

    DeCarlo, T. M., Karnauskas, K. B., Davis, K. A. & Wong, G. T. F. Climate modulates internal wave activity in the Northern South China Sea. Geophys. Res. Lett. 42, 831–838 (2015).

    Google Scholar 

  46. 46.

    Reid, E. C. et al. Internal waves influence the thermal and nutrient environment on a shallow coral reef. Limnol. Oceanogr. 64, 1949–1965 (2019).

    Google Scholar 

  47. 47.

    Wyatt, A. S. J. High resolution in situ temperatures across coral reef slopes: Dongsha Atoll. PANGAEA https://doi.pangaea.de/10.1594/PANGAEA.907790 (2019).

  48. 48.

    Leichter, J. J., Wing, S. R., Miller, S. L. & Denny, M. W. Pulsed delivery of subthermocline water to Conch Reef (Florida Keys) by internal tidal bores. Limnol. Oceanogr. 41, 1490–1501 (1996).

    Google Scholar 

  49. 49.

    Leichter, J. J., Shellenbarger, G., Genovese, S. J. & Wing, S. R. Breaking internal waves on a Florida (USA) coral reef: a plankton pump at work? Mar. Ecol. Prog. Ser. 166, 83–97 (1998).

    Google Scholar 

  50. 50.

    Leichter, J. J. & Genovese, S. J. Intermittent upwelling and subsidized growth of the scleractinian coral Madracis mirabilis on the deep fore-reef slope of Discovery Bay, Jamaica. Mar. Ecol. Prog. Ser. 316, 95–103 (2006).

    Google Scholar 

  51. 51.

    Cai, W. et al. Increased variability of eastern Pacific El Niño under greenhouse warming. Nature 564, 201–206 (2018).

    Google Scholar 

  52. 52.

    Yamano, H., Sugihara, K. & Nomura, K. Rapid poleward range expansion of tropical reef corals in response to rising sea surface temperatures. Geophys. Res. Lett. 38, L04601 (2011).

    Google Scholar 

  53. 53.

    van Woesik, R. & McCaffrey, K. R. Repeated thermal stress, shading, and directional selection in the Florida Reef Tract. Front. Mar. Sci. 4, 182 (2017).

    Google Scholar 

  54. 54.

    Wessel, P. & Smith, W. H. F. GSHGG: A Global Self-consistent, Hierarchical, High-resolution Geography Database (SOEST, 2017); https://www.soest.hawaii.edu/pwessel/gshhg/

  55. 55.

    Wyatt, A. S. J. High resolution in situ temperatures across coral reef slopes: Manzamo, Okinawa, Japan. PANGAEA https://doi.pangaea.de/10.1594/PANGAEA.907831 (2019).

  56. 56.

    Maturi, E. et al. A new high-resolution sea surface temperature blended analysis. Bull. Am. Meteorol. Soc. 98, 1015–1026 (2017).

    Google Scholar 

  57. 57.

    Roberts-Jones, J., Fiedler, E. K. & Martin, M. J. Daily, global, high-resolution SST and Sea Ice Reanalysis for 1985–2007 using the OSTIA system. J. Clim. 25, 6215–6232 (2012).

    Google Scholar 

  58. 58.

    Kayanne, H., Suzuki, R. & Liu, G. Bleaching in the Ryukyu Islands in 2016 and associated degree heating week threshold. Galaxea 19, 17–18 (2017).

    Google Scholar 

  59. 59.

    Glynn, P. W., Maté, J. L., Baker, A. C. & Calderón, M. O. Coral bleaching and mortality in Panama and Ecuador during the 1997–1998 El Niño–Southern Oscillation Event: spatial/temporal patterns and comparisons with the 1982–1983 event. Bull. Mar. Sci. 69, 79–109 (2001).

    Google Scholar 

  60. 60.

    Forget, G. et al. ECCO version 4: an integrated framework for non-linear inverse modeling and global ocean state estimation. Geosci. Model Dev. 8, 3071–3104 (2015).

    Google Scholar 

  61. 61.

    Emery, W. J. & Thomson, R. E. Data Analysis Methods in Physical Oceanography (Elsevier, 2001).

  62. 62.

    Trauth, M. H. MATLAB Recipes for Earth Science 3rd edn (Springer, 2010).

  63. 63.

    Alessi, C. A. et al. CODE-2: Moored Array and Large-Scale Data Report Technical Report No. WHOI-85-35 (Woods Hole Oceanographic Institution, 1985).

  64. 64.

    Leichter, J. J., Deane, G. B. & Stokes, M. D. Spatial and temporal variability of internal wave forcing on a coral reef. J. Phys. Oceanogr. 35, 1945–1962 (2005).

    Google Scholar 

  65. 65.

    Liu, G., Strong, A. E. & Skirving, W. Remote sensing of sea surface temperatures during 2002 Barrier Reef coral bleaching. Eos 84, 137–141 (2003).

    Google Scholar 

  66. 66.

    Lough, J. M., Anderson, K. D. & Hughes, T. P. Increasing thermal stress for tropical coral reefs: 1871–2017. Sci. Rep. 8, 6079 (2018).

    Google Scholar 

  67. 67.

    Liu, G. et al. Predicting heat stress to inform reef management: NOAA Coral Reef Watch’s 4-month coral bleaching outlook. Front. Mar. Sci. 5, 57 (2018).

    Google Scholar 

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Logistical support in Iriomote was provided by T. Naruse, Dive Lateeq and Sera MarineTaxi, Shirahama, with funding provided by the Japan Society for the Promotion of Science (JSPS; grants nos. 15F15904 and 15K12183), the Japan Science and Technology Agency (CREST grant no. JPMJCR13A4), the Sumitomo Foundation (Environmental Research Grant) and the Nissei Foundation (Environmental Research Grant–Young Researcher). In Moorea, K. Sydel and C. Gotshalk assisted with access and processing of data from the Moorea Coral Reef (MCR) LTER Site, which is funded by the US National Science Foundation (NSF) under grant no. OCE 16-37396 (and earlier awards) as well as a gift from the Gordon and Betty Moore Foundation. Research in Moorea was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d’Accueil 2005–2018). This work represents a contribution of the MCR LTER Site. In Panama, data were obtained under NSF grant no. OCE-1535203, with permits from MiAmbiente. Participation by J.J.L. was also supported by the Center for International Collaboration at the Atmosphere Ocean Research Institute, The University of Tokyo. L.T.T. and R.B.A. were supported by NSF grant no. OCE-1535007. A.S.J.W. was partially supported by a Pathway-to-Position Fellowship from JSPS and L.T.T. was supported by the Coastal/Marine Hazards and Resources Program of the US Geological Survey. This is contribution no. 221 from the Institute for Global Ecology at the Florida Institute of Technology. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the US Government.

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The study was conceived and carried out by A.S.J.W. and J.J.L., who wrote the initial draft of the paper. All authors contributed to writing and editing subsequent drafts.

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Correspondence to Alex S. J. Wyatt.

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Wyatt, A.S.J., Leichter, J.J., Toth, L.T. et al. Heat accumulation on coral reefs mitigated by internal waves. Nat. Geosci. 13, 28–34 (2020). https://doi.org/10.1038/s41561-019-0486-4

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