1932

Abstract

The interaction of coral reefs, both chemically and physically, with the surrounding seawater is governed, at the smallest scales, by turbulence. Here, we review recent progress in understanding turbulence in the unique setting of coral reefs—how it influences flow and the exchange of mass and momentum both above and within the complex geometry of coral reef canopies. Flow above reefs diverges from canonical rough boundary layers due to their large and highly heterogeneous roughness and the influence of surface waves. Within coral canopies, turbulence is dominated by large coherent structures that transport momentum both into and away from the canopy, but it is also generated at smaller scales as flow is forced to move around branches or blades, creating wakes. Future work interpreting reef-related observations or numerical models should carefully consider the influence that spatial variation has on momentum and scalar flux.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-marine-042120-071823
2021-01-03
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/marine/13/1/annurev-marine-042120-071823.html?itemId=/content/journals/10.1146/annurev-marine-042120-071823&mimeType=html&fmt=ahah

Literature Cited

  1. Amador A, Arzeno IB, Giddings SN, Merrifield MA, Pawlak G 2020. Cross-shore structure of tidally-driven alongshore flow over rough bathymetry. J. Geophys. Res. Oceans 125:e2020JC016264
    [Google Scholar]
  2. Arzeno IB, Collignon A, Merrifield M, Giddings SN, Pawlak G 2018. An alongshore momentum budget over a fringing tropical fore-reef. J. Geophys. Res. Oceans 123:7839–55
    [Google Scholar]
  3. Asher S, Niewerth S, Koll K, Shavit U 2016. Vertical variations of coral reef drag forces. J. Geophys. Res. Oceans 121:3549–63
    [Google Scholar]
  4. Asher S, Shavit U. 2019. The effect of water depth and internal geometry on the turbulent flow inside a coral reef. J. Geophys. Res. Oceans 124:3508–22
    [Google Scholar]
  5. Atkinson MJ. 1992. Productivity of Enewetk Atoll reef flats predicted from mass transfer relationships. Cont. Shelf Res. 12:799–807
    [Google Scholar]
  6. Atkinson MJ, Bilger RW. 1992. Effects of water velocity on phosphate uptake in coral reef-hat communities. Limnol. Oceanogr. 37:273–79
    [Google Scholar]
  7. Bailey SC, Vallikivi M, Hultmark M, Smits AJ 2014. Estimating the value of von Kármán's constant in turbulent pipe flow. J. Fluid Mech. 749:79–98
    [Google Scholar]
  8. Bandet M. 2009. Dynamics of wave-induced boundary layers over very rough boundaries: field observations over a stretch of coral reef PhD Thesis, Univ. Hawaii Honolulu:
  9. Belcher SE, Harman IN, Finnigan JJ 2012. The wind in the willows: flows in forest canopies in complex terrain. Annu. Rev. Fluid Mech. 44:479–504
    [Google Scholar]
  10. Bilger RW, Atkinson MJ. 1992. Anomalous mass transfer of phosphate on coral reef flats. Limnol. Oceanogr. 37:261–72
    [Google Scholar]
  11. Böhm M, Finnigan JJ, Raupach MR, Hughes D 2013. Turbulence structure within and above a canopy of bluff elements. Bound. Layer Meteorol. 146:393–419
    [Google Scholar]
  12. Bozec YM, Alvarez-Filip L, Mumby PJ 2015. The dynamics of architectural complexity on coral reefs under climate change. Glob. Change Biol. 21:223–35
    [Google Scholar]
  13. Burke L, Reytar K, Spalding M, Perry A 2011. Reefs at risk revisited Rep., World Resour. Inst Washington, DC:
  14. Chang S, Elkins C, Alley M, Eaton J, Monismith S 2009. Flow inside a coral colony measured using magnetic resonance velocimetry. Limnol. Oceanogr. 54:1819–27
    [Google Scholar]
  15. Chang S, Elkins C, Eaton JK, Monismith S 2013. Local mass transfer measurements for corals and other complex geometries using gypsum dissolution. Exp. Fluids 54:1563
    [Google Scholar]
  16. Chang S, Iaccarino G, Ham F, Elkins C, Monismith S 2014. Local shear and mass transfer on individual coral colonies: computations in unidirectional and wave-driven flows. J. Geophys. Res. Oceans 119:2599–619
    [Google Scholar]
  17. Chirayath V, Earle SA. 2016. Drones that see through waves-preliminary results from airborne fluid lensing for centimeter-scale aquatic conservation. Aquat. Conserv. Mar. Freshw. Ecosyst. 26:237–50
    [Google Scholar]
  18. Christoffersen JB, Jonsson IC. 1985. Bed friction and dissipation in a combined current and wave motion. Ocean Eng 12:387–423
    [Google Scholar]
  19. Claussen M. 1990. Area-averaging of surface fluxes in a neutrally stratified, horizontally inhomogeneous atmospheric boundary layer. Atmos. Environ. A 24:1349–60
    [Google Scholar]
  20. Coles D. 1956. The law of the wake in the turbulent boundary layer. J. Fluid Mech. 1:191–226
    [Google Scholar]
  21. Davis KA, Arthur RS, Reid EC, Rogers JS, Fringer OB et al. 2020. Fate of internal waves on a shallow shelf. J. Geophys. Res. Oceans. 125:e2019JC015377
    [Google Scholar]
  22. Davis KA, Leichter JJ, Hench JL, Monismith SG 2008. Effects of western boundary current dynamics on the internal wave field of the Southeast Florida shelf. J. Geophys. Res. Oceans 113:C09010
    [Google Scholar]
  23. Davis KA, Monismith SG. 2011. The modification of bottom boundary layer turbulence and mixing by internal waves shoaling on a barrier reef. J. Phys. Oceanogr. 41:2223–41
    [Google Scholar]
  24. Dawson DA, Trass O. 1972. Mass transfer at rough surfaces. Int. J. Heat Mass Transf. 15:1317–36
    [Google Scholar]
  25. D'elia CF, Wiebe WJ. 1990. Biogeochemical nutrient cycles in coral-reef ecosystems. Ecosyst. World 25:49–74
    [Google Scholar]
  26. Dipprey DF, Sabersky RH. 1963. Heat and momentum transfer in smooth and rough tubes at various Prandtl numbers. Int. J. Heat Mass Transf. 6:329–53
    [Google Scholar]
  27. Dixen M, Hatipoglu F, Sumer BM, Fredsøe J 2008. Wave boundary layer over a stone-covered bed. Coast. Eng. 55:1–20
    [Google Scholar]
  28. Duvall MS, Hench JL, Rosman JH 2019. Collapsing complexity: quantifying multiscale properties of reef topography. J. Geophys. Res. Oceans 124:5021–38
    [Google Scholar]
  29. Dvorak FA. 1969. Calculation of turbulent boundary layers on rough surfaces in pressure gradients. AIAA J 7:1752–59
    [Google Scholar]
  30. Falter JL, Atkinson MJ, Coimbra CF 2005. Effects of surface roughness and oscillatory flow on the dissolution of plaster forms: evidence for nutrient mass transfer to coral reef communities. Limnol. Oceanogr. 50:246–54
    [Google Scholar]
  31. Falter JL, Atkinson MJ, Lowe RJ, Monismith SG, Koseff JR 2007. Effects of nonlocal turbulence on the mass transfer of dissolved species to reef corals. Limnol. Oceanogr. 52:274–85
    [Google Scholar]
  32. Falter JL, Atkinson MJ, Merrifield M 2004. Mass-transfer limitation of nutrient uptake by a wave-dominated reef flat community. Limnol. Oceanogr. 49:1820–31
    [Google Scholar]
  33. Falter JL, Lowe RJ, Atkinson MJ, Cuet P 2012. Seasonal coupling and de-coupling of net calcification rates from coral reef metabolism and carbonate chemistry at Ningaloo Reef, Western Australia. J. Geophys. Res. Oceans 117:C05003
    [Google Scholar]
  34. Falter JL, Lowe RJ, Zhang Z 2016. Toward a universal mass-momentum transfer relationship for predicting nutrient uptake and metabolite exchange in benthic reef communities. Geophys. Res. Lett. 43:9764–72
    [Google Scholar]
  35. Falter JL, Lowe RJ, Zhang Z, McCulloch M 2013. Physical and biological controls on the carbonate chemistry of coral reef waters: effects of metabolism, wave forcing, sea level, and geomorphology. PLOS ONE 8:e53303
    [Google Scholar]
  36. Feddersen F, Guza RT, Elgar S, Herbers THC 2000. Velocity moments in alongshore bottom stress parameterizations. J. Geophys. Res. Oceans 105:8673–86
    [Google Scholar]
  37. Ferrari R, McKinnon D, He H, Smith RN, Corke P et al. 2016. Quantifying multiscale habitat structural complexity: a cost-effective framework for underwater 3D modelling. Remote Sens 8:113
    [Google Scholar]
  38. Ferrario F, Beck M, Storlazzi C, Micheli F, Shepard C, Airoldi L 2014. The effectiveness of coral reefs for coastal hazard risk reduction and adaptation. Nat. Commun. 5:3794
    [Google Scholar]
  39. Finnigan JJ. 2000. Turbulence in plant canopies. Annu. Rev. Fluid Mech. 32:519–71
    [Google Scholar]
  40. Finnigan JJ, Shaw RH, Patton EG 2009. Turbulence structure above a vegetation canopy. J. Fluid Mech. 637:387–424
    [Google Scholar]
  41. Flack KA, Schultz MP. 2010. Review of hydraulic roughness scales in the fully rough regime. J. Fluids Eng. 132:041203
    [Google Scholar]
  42. Flack KA, Schultz MP, Shapiro TA 2005. Experimental support for Townsend's Reynolds number similarity hypothesis on rough walls. Phys. Fluids 17:035102
    [Google Scholar]
  43. Fredsøe J, Deigaard R. 1992. Mechanics of Coastal Sediment Transport Singapore: World Sci.
  44. Genin A, Monismith SG, Reidenbach MA, Yahel G, Koseff JR 2009. Intense benthic grazing of phytoplankton in a coral reef. Limnol. Oceanogr. 54:938–51
    [Google Scholar]
  45. Gerritsen F. 1981. Wave attenuation and wave set-up on a coastal reef Tech. Rep., Univ. Hawaii Honolulu:
  46. Ghisalberti M, Nepf HM. 2002. Mixing layers and coherent structures in vegetated aquatic flows. J. Geophys. Res. Oceans 107:3–111
    [Google Scholar]
  47. Ghisalberti M, Nepf HM. 2006. The structure of the shear layer in flows over rigid and flexible canopies. Environ. Fluid Mech. 6:277–301
    [Google Scholar]
  48. Goldstein RJ, Karni J. 1984. The effect of a wall boundary-layer on local mass transfer from a cylinder in crossflow. ASME J. Heat Transf. 106:260–67
    [Google Scholar]
  49. Graham NAJ, Nash KL. 2013. The importance of structural complexity in coral reef ecosystems. Coral Reefs 32:315–26
    [Google Scholar]
  50. Grant WD, Madsen OS. 1979. Combined wave and current interaction with a rough bottom. J. Geophys. Res. Oceans 84:1797–807
    [Google Scholar]
  51. Grant WD, Madsen OS. 1986. The continental shelf bottom boundary layer. Annu. Rev. Fluid Mech. 18:265–305
    [Google Scholar]
  52. Gratwicke B, Speight MR. 2005. Effects of habitat complexity on Caribbean marine fish assemblages. Mar. Ecol. Prog. Ser. 292:301–10
    [Google Scholar]
  53. Green A. 2002. Status of coral reefs on the main volcanic islands of American Samoa: a resurvey of long term monitoring sites (benthic communities, fish communities, and key macroinvertebrates) Rep., Dep. Mar. Wildl. Resour., Pago Pago, Am Samoa:
  54. Gregg MC, D'Asaro EA, Riley JJ, Kunze E 2018. Mixing efficiency in the ocean. Annu. Rev. Mar. Sci. 10:443–73
    [Google Scholar]
  55. Gruber RK, Lowe RJ, Falter JL 2019. Tidal and seasonal forcing of dissolved nutrient fluxes in reef communities. Biogeosciences 16:1921–35
    [Google Scholar]
  56. Guo J, Julien PY. 2006. Application of modified log-wake law in open-channels. World Environmental and Water Resource Congress 2006: Examining the Confluence of Environmental and Water Concerns R Graham Reston, VA: Am. Soc. Civil Eng https://doi.org/10.1061/40856(200)71
    [Crossref] [Google Scholar]
  57. Harborne AR, Mumby PJ, Ferrari R 2012. The effectiveness of different meso-scale rugosity metrics for predicting intra-habitat variation in coral-reef fish assemblages. Environ. Biol. Fish 94:431–42
    [Google Scholar]
  58. Hearn CJ. 1999. Wave-breaking hydrodynamics within coral reef systems and the effect of changing relative sea level. J. Geophys. Res. Oceans 104:30007–19
    [Google Scholar]
  59. Hearn CJ, Atkinson M, Falter J 2001. A physical derivation of nutrient-uptake rates in coral reefs: effects of roughness and waves. Coral Reefs 20:347–56
    [Google Scholar]
  60. Heathershaw AD, Simpson JH. 1978. The sampling variability of the Reynolds stress and its relation to boundary shear stress and drag coefficient measurements. Estuar. Coast. Shelf Sci. 6:263–74
    [Google Scholar]
  61. Hench JL, Rosman JH. 2013. Observations of spatial flow patterns at the coral colony scale on a shallow reef flat. J. Geophys. Res. Oceans 118:1142–56
    [Google Scholar]
  62. Holbrook SJ, Brooks AJ, Schmitt RJ 2002. Variation in structural attributes of patch-forming corals and in patterns of abundance of associated fishes. Mar. Freshw Res. 53:1045–53
    [Google Scholar]
  63. Huang ZC, Lenain L, Melville WK, Middleton JH, Reineman B et al. 2012. Dissipation of wave energy and turbulence in a shallow coral reef lagoon. J. Geophys. Res. Oceans 117:4063–71
    [Google Scholar]
  64. Hughes TP, Kerry JT, Álvarez-Noriega M, Álvarez-Romero J, Anderson KD et al. 2017. Global warming and recurrent mass bleaching of corals. Nature 543:373–77
    [Google Scholar]
  65. Ivey GN, Winters KB, Koseff JR 2008. Density stratification, turbulence, but how much mixing. ? Annu. Rev. Fluid Mech. 40:169–84
    [Google Scholar]
  66. Jackson PS. 1981. On the displacement height in the logarithmic velocity profile. J. Fluid Mech. 1111981:15–25
    [Google Scholar]
  67. Jaramillo S, Pawlak G. 2011. AUV-based bed roughness mapping over a tropical reef. Coral Reefs 30:11–23
    [Google Scholar]
  68. Jiménez J. 2004. Turbulent flows over rough walls. Annu. Rev. Fluid Mech. 36:173–96
    [Google Scholar]
  69. Jiménez J. 2012. Cascades in wall-bounded turbulence. Annu. Rev. Fluid Mech. 44:27–45
    [Google Scholar]
  70. Jones NL, Monismith SG. 2008. The influence of whitecapping waves on the vertical structure of turbulence in a shallow estuarine embayment. J. Phys. Oceanogr. 38:1563–80
    [Google Scholar]
  71. Jonsson IG. 1967. Wave boundary layers and friction factors. Coastal Engineering 1966127–48 Reston, VA: Am. Soc. Civil Eng.
    [Google Scholar]
  72. Kaimal JC, Wyngaard JC, Izumi Y, Coté OR 1972. Spectral characteristics of surface layer turbulence. Q. J. R. Meteorol. Soc. 98:563–89
    [Google Scholar]
  73. Kamphuis JW. 1975. Friction factor under oscillatory waves. J. Waterw. Harb. Coast. Eng. Div. 101:135–44
    [Google Scholar]
  74. Leichter JJ, Helmuth B, Fischer AM 2006. Variation beneath the surface: quantifying complex thermal environments on coral reefs in the Caribbean, Bahamas and Florida. J. Mar. Res. 64:563–88
    [Google Scholar]
  75. Leichter JJ, Wing SR, Miller SL, Denny MW 1996. Pulsed delivery of subthermocline water to Conch Reef (Florida Keys) by internal tidal bores. Limnol. Oceanogr. 41:1490–501
    [Google Scholar]
  76. Lentz SJ, Churchill JH, Davis KA 2018. Coral reef drag coefficients—surface gravity wave enhancement. J. Phys. Oceanogr. 48:1555–66
    [Google Scholar]
  77. Lentz SJ, Churchill JH, Davis KA, Farrar JT, Pineda J, Starczak V 2016. The characteristics and dynamics of wave-driven flow across a platform coral reef in the Red Sea. J. Geophys. Res. Oceans 121:1360–76
    [Google Scholar]
  78. Lentz SJ, Davis KA, Churchill JH, DeCarlo TM 2017. Coral reef drag coefficients-water depth dependence. J. Phys. Oceanogr. 47:1061–75
    [Google Scholar]
  79. Leonardi S, Orlandi P, Smalley RJ, Djenidi L, Antonia RA 2003. Direct numerical simulations of turbulent channel flow with transverse square bars on one wall. J. Fluid Mech. 491:229–38
    [Google Scholar]
  80. Lesser MP. 1997. Oxidative stress causes coral bleaching during exposure to elevated temperatures. Coral Reefs 16:187–92
    [Google Scholar]
  81. Long CE, Wiberg PL, Nowell AR 1993. Evaluation of von Karman's constant from integral flow parameters. J. Hydraul. Eng. 119:1182–90
    [Google Scholar]
  82. Long MH, Rheuban JE, McCorkle DC, Burdige DJ, Zimmerman RC 2019. Closing the oxygen mass balance in shallow coastal ecosystems. Limnol. Oceanogr. 64:2694–708
    [Google Scholar]
  83. Longuet-Higgins MS, Stewart R. 1962. Radiation stress and mass transport in gravity waves with application to ‘surf beats. .’ J. Fluid Mech. 13:481–504
    [Google Scholar]
  84. Lowe RJ, Falter JL. 2015. Oceanic forcing of coral reefs. Annu. Rev. Mar. Sci. 7:43–66
    [Google Scholar]
  85. Lowe RJ, Falter JL, Bandet MD, Pawlak G, Atkinson MJ et al. 2005a. Spectral wave dissipation over a barrier reef. J. Geophys. Res. Oceans 110:C04001
    [Google Scholar]
  86. Lowe RJ, Falter JL, Koseff JR, Monismith SG, Atkinson MJ 2007. Spectral wave flow attenuation within submerged canopies: implications for wave energy dissipation. J. Geophys. Res. Oceans 112:C05018
    [Google Scholar]
  87. Lowe RJ, Koseff JR, Monismith SG 2005b. Oscillatory flow through submerged canopies: 1. Velocity structure. J. Geophys. Res. Oceans 110:C10016
    [Google Scholar]
  88. Lowe RJ, Koseff JR, Monismith SG, Falter JL 2005c. Oscillatory flow through submerged canopies: 2. Canopy mass transfer. J. Geophys. Res. Oceans 110:C10017
    [Google Scholar]
  89. Lowe RJ, Shavit U, Falter JL, Koseff JR, Monismith SG 2008. Modeling flow in coral communities with and without waves: a synthesis of porous media and canopy flow approaches. Limnol. Oceanogr. 53:2668–80
    [Google Scholar]
  90. Lueck RG, Lu Y. 1997. The logarithmic layer in a tidal channel. Cont. Shelf Res. 17:1785–801
    [Google Scholar]
  91. Lugo-Fernandez A, Roberts HH, Wiseman WJ, Carter BL 1998. Water level and currents of tidal and infragravity periods at Tague Reef, St. Croix (USVI). Coral Reefs 17:343–49
    [Google Scholar]
  92. Luhar M, Rominger J, Nepf H 2008. Interaction between flow, transport, and vegetation spatial structure. Environ. Fluid. Mech. 8:423–39
    [Google Scholar]
  93. Madsen OS. 1994. Spectral wave-current bottom boundary layer flows. Coastal Engineering 1994 BL Edge 623–34 Reston, VA: Am. Soc. Civ. Eng.
    [Google Scholar]
  94. Mahrt L. 1987. Grid-averaged surface fluxes. Mon. Weath. Rev. 115:1550–60
    [Google Scholar]
  95. Mahrt L. 2000. Surface heterogeneity and vertical structure of the boundary layer. Bound. Layer Meteorol. 96:33–62
    [Google Scholar]
  96. Mason PJ. 1988. The formation of areally averaged roughness lengths. Q. J. R. Meteorol. Soc. 114:399–420
    [Google Scholar]
  97. McClanahan TR, Maina J, Moothien-Pillay R, Baker AC 2005. Effects of geography, taxa, water flow, and temperature variation on coral bleaching intensity in Mauritius. Mar. Ecol. Prog. Ser. 71:130–34
    [Google Scholar]
  98. McDonald CB, Koseff JR, Monismith SG 2006. Effects of the depth to coral height ratio on drag coefficients for unidirectional flow over coral. Limnol. Oceanogr. 51:1294–301
    [Google Scholar]
  99. Molina L, Pawlak G, Wells JR, Monismith SG, Merrifield MA 2014. Diurnal cross-shore thermal exchange on a tropical forereef. J. Geophys. Res. Oceans 119:6101–20
    [Google Scholar]
  100. Moltchanov S, Bohbot-Raviv Y, Duman T, Shavit U 2015. Canopy edge flow: a momentum balance analysis. Water Resour. Res. 51:2081–95
    [Google Scholar]
  101. Monismith SG. 2007. Hydrodynamics of coral reefs. Annu. Rev. Fluid Mech. 39:37–55
    [Google Scholar]
  102. Monismith SG, Davis KA, Shellenbarger GG, Hench JL, Nidzieko NJ et al. 2010. Flow effects on benthic grazing on phytoplankton by a Caribbean reef. Limnol. Oceanogr. 55:1881–92
    [Google Scholar]
  103. Monismith SG, Genin A, Reidenbach MA, Yahel G, Koseff JR 2006. Thermally driven exchanges between a coral reef and the adjoining ocean. J. Phys. Oceanogr. 36:1332–47
    [Google Scholar]
  104. Monismith SG, Herdman LM, Ahmerkamp S, Hench JL 2013. Wave transformation and wave-driven flow across a steep coral reef. J. Phys. Oceanogr. 43:1356–79
    [Google Scholar]
  105. Monismith SG, Koseff JR, White BL 2018. Mixing efficiency in the presence of stratification: Is it constant. ? Geophys. Res. Lett. 45:5627–34
    [Google Scholar]
  106. Monismith SG, Rogers JS, Koweek D, Dunbar RB 2015. Frictional wave dissipation on a remarkably rough reef. Geophys. Res. Lett. 42:4063–71
    [Google Scholar]
  107. Nakamura T, van Woesik R 2001. Water-flow rates and passive diffusion partially explain differential survival of corals during the 1998 bleaching event. Mar. Ecol. Prog. Ser. 212:301–4
    [Google Scholar]
  108. Nakamura T, van Woesik R, Yamasaki H 2005. Photoinhibition of photosynthesis is reduced by water flow in the reef-building coral Acropora digitifera. Mar. Ecol. Prog. Ser 301:109–18
    [Google Scholar]
  109. Napoli E, Armenio V, DeMarchis M 2008. The effect of the slope of irregularly distributed roughness elements on turbulent wall-bounded flows. J. Fluid Mech. 613:385–94
    [Google Scholar]
  110. Nelson RC. 1996. Hydraulic roughness of coral reef platforms. Appl. Ocean Res. 18:265–74
    [Google Scholar]
  111. Nepf HM. 2012. Flow and transport in regions with aquatic vegetation. Annu. Rev. Fluid Mech. 44:123–42
    [Google Scholar]
  112. Nepf HM, Vivoni ER. 2000. Flow structure in depth-limited, vegetated flow. J. Geophys. Res. Oceans 105:28547–57
    [Google Scholar]
  113. Nezu I, Nakagawa H. 1993. Turbulence in Open-Channel Flows Rotterdam, Neth: Balkema
  114. Nielsen P. 1992. Coastal Bottom Boundary Layers and Sediment Transport Singapore: World Sci.
  115. Nikuradse J. 1933. Stromungsgesetze in rauhen Rohren Düsseldorf, Ger: Ver. Dtsch. Ing.
  116. Nunes V, Pawlak G. 2008. Observations of bed roughness of a coral reef. J. Coast. Res. 24:SP239–50
    [Google Scholar]
  117. Pan Y, Banerjee S. 1995. A numerical study of free-surface turbulence in channel flow. Phys. Fluids 7:1649–64
    [Google Scholar]
  118. Pawlak G, MacCready P. 2002. Oscillatory flow across an irregular boundary. J. Geophys. Res. Oceans 107:4–117
    [Google Scholar]
  119. Péquignet A-C, Becker JM, Merrifield MA, Boc SJ 2011. The dissipation of wind wave energy across a fringing reef at Ipan. Coral Reefs 30:71–82
    [Google Scholar]
  120. Perry AE, Schofield WH, Joubert PN 1969. Rough wall turbulent boundary layers. J. Fluid Mech. 37:383–413
    [Google Scholar]
  121. Pomeroy AW, Lowe RJ, Symonds G, Van Dongeren AR, Moore C 2012. The dynamics of infragravity wave transformation over a fringing reef. J. Geophys. Res. Oceans 117:C11022
    [Google Scholar]
  122. Pomeroy AW, Lowe RJ, Van Dongeren AR, Ghisalberti M, Bodde W, Roelvink D 2015. Spectral wave-driven sediment transport across a fringing reef. Coast. Eng. 98:78–94
    [Google Scholar]
  123. Pope SB. 2000. Turbulent Flows Cambridge, UK: Cambridge Univ. Press
  124. Rajagopalan K. 2010. Large eddy simulation of turbulent boundary layers over rough bathymetry PhD Thesis, Univ. Hawaii Honolulu:
  125. Raupach MR. 1992. Drag and drag partition on rough surfaces. Bound. Layer Meteorol. 60:375–95
    [Google Scholar]
  126. Raupach MR, Antonia RA, Rajagopalan S 1991. Rough-wall turbulent boundary layers. Appl. Mech. Rev. 44:1–25
    [Google Scholar]
  127. Raupach MR, Finnigan JJ, Brunet Y 1996. Coherent eddies and turbulence in vegetation canopies: the mixing-layer analogy. Boundary-Layer Meteorology: 25th Anniversary Volume, 1970–1995 JR Garratt, PA Taylor 351–82 Dordrecht, Neth: Springer
    [Google Scholar]
  128. Raupach MR, Shaw R. 1982. Averaging procedures for flow within vegetation canopies. Bound. Layer Meteorol. 22:79–90
    [Google Scholar]
  129. Raupach MR, Thom AS. 1981. Turbulence in and above plant canopies. Annu. Rev. Fluid Mech. 13:97–129
    [Google Scholar]
  130. Reid EC, DeCarlo TM, Cohen AL, Wong GT, Lentz SJ et al. 2019. Internal waves influence the thermal and nutrient environment on a shallow coral reef. Limnol. Oceanogr. 64:1949–65
    [Google Scholar]
  131. Reidenbach MA, Koseff JR, Koehl MAR 2009. Hydrodynamic forces on larvae affect their settlement on coral reefs in turbulent, wave-driven flow. Limnol. Oceanogr 54:318–30
    [Google Scholar]
  132. Reidenbach MA, Koseff JR, Monismith SG 2007. Laboratory experiments of fine-scale mixing and mass transport within a coral canopy. Phys. Fluids 19:075107
    [Google Scholar]
  133. Reidenbach MA, Monismith SG, Koseff JR, Yahel G, Genin A 2006. Boundary layer turbulence and flow structure over a fringing coral reef. Limnol. Oceanogr. 51:1956–68
    [Google Scholar]
  134. Ribes M, Atkinson MJ. 2007. Effects of water velocity on picoplankton uptake by coral reef communities. Coral Reefs 26:413–21
    [Google Scholar]
  135. Risk MJ. 1972. Fish diversity on a coral reef in the Virgin Islands. Atoll Res. Bull. 153:1–4
    [Google Scholar]
  136. Rogers JS, Maticka SA, Chirayath V, Woodson CB, Alonso JJ, Monismith SG 2018. Connecting flow over complex terrain to hydrodynamic roughness on a coral reef. J. Phys. Oceanogr. 48:1567–87
    [Google Scholar]
  137. Rogers JS, Monismith SG, Dunbar RB, Koweek D 2015. Field observations of wave-driven circulation over spur and groove formations on a coral reef. J. Geophys. Res. Oceans 120:145–60
    [Google Scholar]
  138. Rominger JT, Nepf HM. 2011. Flow adjustment and interior flow associated with a rectangular porous obstruction. J. Fluid Mech. 680:636–59
    [Google Scholar]
  139. Rosman JH, Hench JL. 2011. A framework for understanding drag parameterizations for coral reefs. J. Geophys. Res. Oceans 116:C08025
    [Google Scholar]
  140. Sanford TB, Lien RC. 1999. Turbulent properties in a homogeneous tidal bottom boundary layer. J. Geophys. Res. Oceans 104:1245–57
    [Google Scholar]
  141. Sanitjai S, Goldstein RJ. 2004. Heat transfer from a circular cylinder to mixtures of water and ethylene glycol. Int. J. Heat Mass Transf. 47:4785–94
    [Google Scholar]
  142. Sarpkaya T. 1975. Forces on cylinders and spheres in a sinusoidally oscillating fluid. J. Appl. Mech. Mar. 42:32–37
    [Google Scholar]
  143. Schlichting H. 1937. Experimental investigation of the problem of surface roughness Tech. Memo. 823, Natl. Advis. Comm. Aeronaut Washington, DC:
  144. Schultz MP, Flack KA. 2009. Turbulent boundary layers on a systematically-varied rough wall. Phys. Fluids 21:015104
    [Google Scholar]
  145. Sebens KP, Grace SP, Helmuth B, Maney EJ, Miles JS 1998. Water flow and prey capture by three scleractinian corals, Madracis mirabilis, Montastrea cavernosa and Porites porites, in a field enclosure. Mar. Biol 131:347–60
    [Google Scholar]
  146. Sebens KP, Helmuth B, Carrington E, Agius B 2003. Effects of water flow on growth and energetics of the scleractinian coral Agaricia tenuifolia in Belize. Coral Reefs 22:35–47
    [Google Scholar]
  147. Sebens KP, Witting J, Helmuth BST 1997. Effects of water flow and branch spacing on particle capture by the reef coral Madracis mirabilis (Duchassaing and Michelotti). J. Exp. Mar. Biol. Ecol. 211:1–28
    [Google Scholar]
  148. Shapiro OH, Fernandez VI, Garren M, Guasto JS, Debaillon-Vesque FP et al. 2014. Vortical ciliary flows actively enhance mass transport in reef corals. PNAS 111:13391–96
    [Google Scholar]
  149. Shih LH, Koseff JR, Ivey GN, Ferziger JH 2005. Parameterization of turbulent fluxes and scales using homogeneous sheared stably stratified turbulence simulations. J. Fluid Mech. 525:193–214
    [Google Scholar]
  150. Sigal A, Danberg JE. 1990. New correlation of roughness density effect on the turbulent boundary layer. AIAA J 28:554–56
    [Google Scholar]
  151. Sleath JFA. 1987. Turbulent oscillatory flow over rough beds. J. Fluid Mech. 182:369–409
    [Google Scholar]
  152. Stacey MT, Monismith SG, Burau JR 1999. Measurements of Reynolds stress profiles in unstratified tidal flow. J. Geophys. Res. Oceans 104:10933–49
    [Google Scholar]
  153. Stocking JB, Laforsch C, Sigl R, Reidenbach MA 2018. The role of turbulent hydrodynamics and surface morphology on heat and mass transfer in corals. J. R. Soc. Interface 15:20180448
    [Google Scholar]
  154. Stocking JB, Rippe JP, Reidenbach MA 2016. Structure and dynamics of turbulent boundary layer flow over healthy and algae-covered corals. Coral Reefs 35:1047–59
    [Google Scholar]
  155. Storlazzi C, Logan J, Field M 2003. Quantitative morphology of a fringing reef tract from high-resolution laser bathymetry: southern Molokai, Hawaii. Geol. Soc. Am. Bull. 115:1344–55
    [Google Scholar]
  156. Swart D. 1974. Offshore sediment transport and equilibrium beach profiles Tech. Rep. 131, Delft Hydraul. Lab Delft, Neth:.
  157. Taebi S, Lowe RJ, Pattiaratchi CB, Ivey GN, Symonds G, Brinkman R 2011. Nearshore circulation in a tropical fringing reef system. J. Geophys. Res. Oceans 116:C02016
    [Google Scholar]
  158. Takeshita Y, McGillis W, Briggs EM, Carter AL, Donham EM et al. 2016. Assessment of net community production and calcification of a coral reef using a boundary layer approach. J. Geophys. Res. Oceans 121:5655–71
    [Google Scholar]
  159. Talke SA, Horner-Devine AR, Chickadel CC, Jessup AT 2013. Turbulent kinetic energy and coherent structures in a tidal river. J. Geophys. Res. Oceans 118:6965–81
    [Google Scholar]
  160. Tanino Y, Nepf HM. 2008. Laboratory investigation of mean drag in a random array of rigid, emergent cylinders. J. Hydraul. Eng. 134:34–41
    [Google Scholar]
  161. Taylor PA. 1987. Comments and further analysis on effective roughness lengths for use in numerical three-dimensional models. Bound. Layer Meteorol. 39:403–18
    [Google Scholar]
  162. Teixeira MAC, Belcher SE. 2002. On the distribution of turbulence by a progressive surface wave. J. Fluid Mech. 458:229–67
    [Google Scholar]
  163. Teneva L, Dunbar RB, Mucciarone DA, Dunckley JF, Koseff JR 2013. High-resolution carbon budgets on a Palau back-reef modulated by interactions between hydrodynamics and reef metabolism. Limnol. Oceanogr. 58:1851–70
    [Google Scholar]
  164. Terray EA, Donelan MA, Agrawal YC, Drennan WM, Kahma KK et al. 1996. Estimates of kinetic energy dissipation under breaking waves. J. Phys. Oceanogr. 26:792–807
    [Google Scholar]
  165. Thomas FIM, Atkinson MJ. 1997. Ammonium uptake by coral reefs: effects of water velocity and surface roughness on mass transfer. Limnol. Oceanogr. 42:81–88
    [Google Scholar]
  166. Trowbridge JH, Lentz SJ. 2018. The bottom boundary layer. Annu. Rev. Mar. Sci. 10:397–420
    [Google Scholar]
  167. Turner JS. 1973. Buoyancy Effects in Fluids Cambridge, UK: Cambridge Univ. Press
  168. van Rij JA, Belnap BJ, Ligrani PM 2002. Analysis and experiments on three-dimensional, irregular surface roughness. J. Fluids Eng. 124:671–77
    [Google Scholar]
  169. van Woesik R, Irikawa A, Anzai R, Nakamura T 2012. Effects of coral colony morphologies on mass transfer and susceptibility to thermal stress. Coral Reefs 31:633–39
    [Google Scholar]
  170. Veron JEN. 1995. Corals in Space and Time: The Biogeography and Evolution of the Scleractinia Ithaca, NY: Cornell Univ. Press
  171. Walter RK, Nidzieko NJ, Monismith SG 2011. Similarity scaling of turbulence spectra and cospectra in a shallow tidal flow. J. Geophys. Res. Oceans 116:C10019
    [Google Scholar]
  172. Warner SJ, MacCready P. 2009. Dissecting the pressure field in tidal flow past a headland: When is form drag “real”. ? J. Phys. Oceanogr. 39:2971–84
    [Google Scholar]
  173. Wolanski E, Delesalle B. 1995. Upwelling by internal waves, Tahiti, French Polynesia. Cont. Shelf Res. 15:357–68
    [Google Scholar]
  174. Wooding RA, Bradley EF, Marshall JK 1973. Drag due to regular arrays of roughness elements of varying geometry. Bound. Layer Meteorol. 5:285–308
    [Google Scholar]
  175. Wright DG, Thompson KR. 1983. Time-averaged forms of the nonlinear stress law. J. Phys. Oceanogr. 13:341–45
    [Google Scholar]
  176. Wyatt AS, Falter JL, Lowe RJ, Humphries S, Waite AM 2012. Oceanographic forcing of nutrient uptake and release over a fringing coral reef. Limnol. Oceanogr. 57:401–19
    [Google Scholar]
  177. Yaglom AM, Kader BA. 1974. Heat and mass transfer between a rough wall and turbulent fluid flow at high Reynolds and Péclet numbers. J. Fluid Mech. 62:601–23
    [Google Scholar]
  178. Yates KK, Zawada DG, Smiley NA, Tiling-Range G 2017. Divergence of seafloor elevation and sea level rise in coral reef ecosystems. Biogeosciences 14:1739
    [Google Scholar]
  179. Yu X, Rosman JH, Hench JL 2018. Interaction of waves with idealized high-relief bottom roughness. J. Geophys. Res. Oceans 123:3038–59
    [Google Scholar]
  180. Zawada DG, Brock JC. 2009. A multiscale analysis of coral reef topographic complexity using lidar-derived bathymetry. J. Coast. Res. 25:SP536–15
    [Google Scholar]
/content/journals/10.1146/annurev-marine-042120-071823
Loading
/content/journals/10.1146/annurev-marine-042120-071823
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error