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Living in the Canopy of the Animal Forest: Physical and Biogeochemical Aspects

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Book cover Marine Animal Forests

Abstract

Long-lived hard and soft coral species that are able to develop dense patches with a complex, three-dimensional structure form an animal forest canopy, similar to trees in terrestrial systems. Aside from the shelter provided by this canopy to other organisms, the animal forest can significantly modify the local physical and biogeochemical environment.

In the first part of this chapter, the modification of benthic boundary layer hydrodynamics in and above canopies is described, with a focus on the impacts of canopy density and flexibility. In the second part of this chapter, the structure of diffusive and advective mass transfer in canopies will be presented and discussed in relation to the biogeochemical transformations observed in animal forest canopies. Ongoing challenges in the conceptualization of physical and biogeochemical processes in animal forest canopies are also exposed. In the third part of this chapter, we review the factors that form the basis of a mechanistic explanation of the development of micro-niches, which explain the large diversity hosted in animal forest canopies.

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References

  • Ackerman JD, Okubo A. Reduced mixing in a marine macrophyte canopy. Funct Ecol. 1993;7:305–9.

    Article  Google Scholar 

  • Bartholomew A. New dimensionless indices of structural habitat complexity: predicted and actual effects on a predators foraging success. Mar Ecol Prog Ser. 2000;206:45–58.

    Article  Google Scholar 

  • Benedetti-Cecchi L, Pannacciulli F, Bulleri F, Moschella PS, Airoldi L, Relini G, Cinelli F. Predicting the consequences of anthropogenic disturbance: large-scale effects of loss of canopy algae on rocky shores. Mar Ecol Prog Ser. 2001;214:137–50.

    Article  Google Scholar 

  • Bentham T, Britter R. Spatially averaged flow within obstacle arrays. Atmos Environ. 2003;37:2037–43.

    Article  CAS  Google Scholar 

  • Berg P, Roy H, Janssen F, Meyer V, Jorgensen BB, Huettel M, De Beer D. Oxygen uptake by aquatic sediments measured by a novel non-invasive eddy correlation technique. Mar Ecol Prog Ser. 2003;261:75–83.

    Article  Google Scholar 

  • Beukers JS, Jones GP. Habitat complexity modifies the impact of piscivores on a coral reef fish population. Oecologia. 1997;114(1):50–9.

    Article  Google Scholar 

  • Bilger RW, Atkinson MJ. Anomalous mass transfer of phosphate on coral reef flats. Limnol Oceanogr. 1992;37(2):261–72.

    Article  CAS  Google Scholar 

  • Bruno JF. Whole-community facilitation through substrate stabilization by the intertidal grass Spartina alterniflora. Ecology. 2000;81:1179–92.

    Article  Google Scholar 

  • Bruno JF, Bertness MD. Habitat modification and facilitation in benthic marine communities. In: Bertness MD, Hay ME, Gaines SD, editors. Marine community ecology. Sunderland: Sinauer; 2001. p. 201–18.

    Google Scholar 

  • Cau A, Bramanti L, Angiolillo M, Bo M, Canese S, Cuccu D, Cannas R, Follesa MC, Guizien K. Habitat constraints and self-thinning shape Mediterranean red coral deep population structure: implications for conservation practice. Sci Report. 2016;6:23322.-1-10

    Article  CAS  Google Scholar 

  • Cerrano C, Danovaro R, Gambi C, Pusceddu A, Riva A, Schiaparelli S. Gold coral (Savalia savaglia) and gorgonian forests enhance benthic biodiversity and ecosystem functioning in the mesophotic zone. Biodivers Conserv. 2010;19(1):153–67.

    Article  Google Scholar 

  • Cheng H, Castro IP. Near wall flow over urban-like roughness. Bound-Layer Meteorol. 2002;104(2):229–59.

    Article  Google Scholar 

  • Cordes EE, McGinley MP, Podowski EL, Becker EL, Lessard-Pilon S, Viada ST, Fisher CR. Coral communities of the deep Gulf of Mexico. Deep-Sea Res I Oceanogr Res Pap. 2008;55(6):777–87.

    Article  Google Scholar 

  • Cornelisen CD, Thomas FIM. Prediction and validation of flow-dependent uptake of ammonium over a seagrass-hardbottom community in Florida Bay. Mar Ecol Prog Ser. 2009;386:71–81.

    Article  CAS  Google Scholar 

  • Dahl LA. Surface area in ecological analysis: quantification of benthic coral-reef algae. Mar Biol. 1973;23:239–49.

    Article  Google Scholar 

  • Dennison WC, Barnes DJ. Effect of water motion on coral photosynthesis and calcification. J Exp Mar Biol Ecol. 1988;115:67–77.

    Article  Google Scholar 

  • Du Z, Li Y, Chen J, Guo JJ, Zheng RE. Feasibility investigation on deep ocean compact autonomous Raman spectrometer developed for in-situ detection of acid radical ions. Chin J Oceanol Limnol. 2015;33(2):545–50.

    Article  CAS  Google Scholar 

  • Duarte CM. Marine biodiversity and ecosystem services: an exlusive link. J Exp Mar Biol Ecol. 2000;250(1-2):117–31.

    Article  CAS  PubMed  Google Scholar 

  • Eckman JE. Flow disruption by an animal- tube mimic affects sediment bacterial colonization. J Mar Res. 1985;43:419–35.

    Article  Google Scholar 

  • Eckman JE, Duggins OD. Sewel AT ecology of understory kelp environments. Effects of kelps on flow and particle transport near the bottom. J Exp Mar Biol Ecol. 1989;129:173–87.

    Article  Google Scholar 

  • Emslie MJ, Alistair JC, Johns KA. Retention of habitat complexity minimizes disassembly of reef fish communities following disturbances: a large-scale natural experiment. PLoS One. 2014;9(8):e105384.-1-9

    Article  PubMed  PubMed Central  Google Scholar 

  • Fabricius KE, Metzner J. Scleractinian walls of mouths: predation on coral larvae by corals. Coral Reefs. 2004;23:245–8.

    Article  Google Scholar 

  • Falter JL, Atkinson MJ, Merrifield MA. Mass-transfer limitation of nutrient uptake by a wave-dominated reef flat community. Limnol Oceanogr. 2004;49(5):1820–31.

    Article  CAS  Google Scholar 

  • Finelli CM, Clarke RD, Robinson HE, Buskey EJ. Water flow controls distribution and feeding behavior of two co-occuring coral reef fishes: I. Field Meas Coral Reefs. 2009;28:461–73.

    Article  Google Scholar 

  • Fredsoe J, Deigaard R. Mechanics of coastal sediment transport. Advanced series on ocean engineering. 3rd ed. Singapore: World Scientific Publishing Co. Pte. Ltd; 1992.

    Google Scholar 

  • Freiwald A, Roberts JM. Cold water corals and ecosystems. Berlin: Springer publishing; 2005.

    Book  Google Scholar 

  • Ghisalberti M. Obstructed shear flows: similarities across systems and scales. J Fluid Mech. 2009;641:51–61.

    Article  Google Scholar 

  • Ghisalberti M, Nepf H. Mixing Layers and coherent structures in vegetated aquatic flows. J Geophys Res Oceans. 2002;107(C2):3011-1-11.

    Article  Google Scholar 

  • Ghisalberti M, Nepf H. The limited growth of vegetated shear layers. Water Resour Res. 2004;40(7):W07502.-1–12.

    Article  Google Scholar 

  • Ghisalberti M, Nepf H. Mass transport in vegetated shear flows. Environ Fluid Mech. 2005;5(6):527–51.

    Google Scholar 

  • Ghisalberti M, Nepf H. The structure of the shear layer in flows over a rigid and flexible canopies. Environ Fluid Mech. 2006;6:277–301.

    Article  Google Scholar 

  • Ghisalberti M, Nepf H. Shallow flows over a permeable medium: the hydrodynamics of submerged aquatic canopies, Transp Porous Md. 2009;78(3):385–402. doi:10.1007/s10652-006-0002-4.

    Google Scholar 

  • Ghisalberti M, Schlosser T. Vortex generation in oscillatory canopy flow. J Geophys Res Oceans. 2013;118:1534–42. doi:10.1002/jgrc.20073.

    Article  Google Scholar 

  • Ghisalberti M, Gold DA, Laflamme M, Clapham ME, Narbonne GM, Summons RE, Johnston DT, Jacobs DK. Canopy flow analysis reveals the advantage of size in the oldest communitiesof multi-cellular Eukaryotes. Curr Biol. 2014;24:305–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grant WD, Madsen OS. Combined wave and current interaction with a rough bottom. J Geophys Res. 1979;84(C4):1797–808.

    Article  Google Scholar 

  • Gutt J, Cummings V, Dayton P, Isla E, Jentsch A, Sciaparelli S. Antartic marine animal forests: three-dimensionnal communities in Southern ocean ecosystems. In: Rossi S, editor. Marine animal forests. Switzerland: Springer International Publishing; 2015. doi:10.1007/978-3-319-170001-5_8-1.

    Google Scholar 

  • Guizien K, Dohmen-Janssen M, Vittori G. 1DV bottom boundary layer modeling under combined wave and current: turbulent separation and phase lag effects. J Geophys Res. 2003;108(C1):16 : 1–15.

    Article  Google Scholar 

  • Goreau TJ. Control of atmospheric carbon-dioxide. Glob Environ Chang Hum Policy Dimens. 1992;2(1):5–11.

    Article  Google Scholar 

  • Hauri C, Fabricius KE, Schaffelke B, Humphrey C. Chemical and physical environmental conditions underneath mat- and canopy-forming macroalgae, and their effects on understorey corals. PLoS One. 2010;5(9):e12685.1-9

    Article  PubMed  PubMed Central  Google Scholar 

  • Hench JL, Rosman JH. Observations of spatial flow patterns at the coral colony scale on a shallow reef flat. J Geophys Res. 2013;118:1142–56. doi:10.1002/jgrc.20105.

    Article  Google Scholar 

  • Holling CS. Cross-scale morphology, geometry and dynamics of ecosystems. Ecol Monogr. 1992;62:447–502.

    Article  Google Scholar 

  • Holling CS. Resilience and stability of ecological systems. Annu Rev Ecol Syst. 1973;4:1–23.

    Article  Google Scholar 

  • Hutchinson GE. Concluding remarks. Cold Spring Harb Symp Quant Biol. 1957;22(2):415–27.

    Article  Google Scholar 

  • Jenssen BL, Sumer BM, Fredsoe J. Turbulent oscillatory boundary layers at high Reynolds numbers. J Fluid Mech. 1989;206:265–97.

    Article  Google Scholar 

  • Jones CG, Lawton JH, Shachak M. Organisms as ecosystem engineers. Oikos. 1994;69(3):373–86.

    Article  Google Scholar 

  • Jonsson IG. Wave boundary layers and friction factors. Proc 10th Conf Coastal Eng. 1966;1:127–48.

    Google Scholar 

  • Koehl MAR, Reidenbach MA. Swimming by microscopic organisms in ambient water flow. Exp Fluids. 2007;43:755–68.

    Article  Google Scholar 

  • Koehl MAR, Strother JA, Reidenbach MA, Koseff JR, Hadfield MG. Individual-based model of larval transport to coral reefs in turbulent, wave-driven flow: behavioral responses to dissolved settlement inducer. Mar Prog Ecol Series. 2007;335:1–18.

    Article  Google Scholar 

  • Kregting LT, Stevens CL, Cornelisen CD, Pilditch CA, Hurd CL. Effects of a small-bladed macroalgal canopy on benthic boundary layer dynamics: implications for nutrient transport. Aquat Biol. 2011;14(1):41–56.

    Article  Google Scholar 

  • Lawton JH. What do species do in ecosystems ? Oikos. 1994;71(3):367–74.

    Article  Google Scholar 

  • Long MH, Berg P, de Beer D, Zieman JC. In situ coral reef oxygen metabolism: an eddy correlation study. PLoS One. 2013;8(3):e58581.1–11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lewis JB. Feeding behaviour and feeding ecology of the octocorallia (coelenterata: Anthozoa). J Zool. 1982;196(3):371–84.

    Article  Google Scholar 

  • Lowe RJ, Koseff JR, Monismith SG. Oscillatory flow through submerged canopies. Part 1. Velocity structure. J Geophys Res. 2005;110:C10016. doi:10.1029/2004JC002788.

    Article  Google Scholar 

  • Lowe RJ, Shavit U, Falter JL, Koseff JR, Monismith SG. Modelling flow in coral committes with and without waves: a synthesis of porous media and canopy flow approaches. Limnol Oceanogr. 2008;53(6):2668–80.

    Google Scholar 

  • Luckenbach MW. Sediment stability around animal tubes: the roles of hydrodynamic processes and biotic activity. Limnol Oceanogr. 1986;31:779–87.

    Article  Google Scholar 

  • MacArthur R, MacArthur JW. On bird species-diversity. Ecology. 1961;42(3):594–8.

    Article  Google Scholar 

  • MacDonald RW. Modelling the mean velocity profile in the urban canopy layer. Bound-Layer Meteorol. 2000;97:25–45.

    Article  Google Scholar 

  • MacDonald CB, Koseff JR, Monismith SG. Effects of the depth to coral height ratio on drag coefficients for unidirectional flow over coral. Limnol Oceanogr. 2006;51:1294–301.

    Article  Google Scholar 

  • Maldonado M, Aguilar R, Bannister RJ, Bell JJ, Conway KW, Dayton PK, Diaz C, Gutt J, Kelly M, Kenchington ELR, Leys SP, Pomponi SA, Rapp HS, Rützler K, Tendal OS, Vacelet J, Young CM. Sponge grounds as key marine habitats: a synthetic review of types, structure, functional roles, and conservation concerns. In: Rossi S, editor. Marine animal forests. Switzerland: Springer International Publishing; 2015. doi:10.1007/978-3-319-170001-5_24-1.

    Google Scholar 

  • Monismith SG. Hydrodynamics of coral reefs. Annu Rev Fluid Mech. 2007;39:37–55.

    Article  Google Scholar 

  • Moulin FY, Guizien K, Thouzeau G, Chapalain G, Mülleners K, Bourg C. Impact of an invasive species Crepidula fornicata on the hydrodynamics and transport properties of the benthic layer. Aquat Living Resour. 2007;20(1):15–31.

    Article  Google Scholar 

  • Nielsen P. Coastal bottom boundary layers and sediment transport, Advanced series on ocean engineering. 4River Edge: World Scientific Publishing Co. Pte. Ltd; 1992.

    Google Scholar 

  • Nikuradse J. Stromungsgesetze in glatten und rauhen rohren. Berlin: VDI-Forschungsh 361; 1933.

    Google Scholar 

  • Raupach MR, Thom AS, Edwards I. A wind-tunnel study of turbulent flow close to regularly arrayed rough surfaces. Bound-Layer Meteorol. 1980;18:373–97.

    Article  Google Scholar 

  • Reidenbach MA, Monismith SG, Koseff JR, Yahel G, Genin A. Boundary layer turbulence and flow structure over a fringing coral reef. Limnol Oceanogr. 2006;51(5):1956–68. doi:10.4319/lo.2006.51.5.1956.

    Article  Google Scholar 

  • Riisgard HU, Larsen PS. Filter-feeding zoobenthos and hydrodynamics. In: Rossi S, editor. Marine animal forests. Switzerland: Springer International Publishing; 2015.doi:10.1007/978-3-319-170001-5_19-1.

    Google Scholar 

  • Rosman JH, Hench JL. A framework for understanding drag parameterizations for coral reefs. J Geophys Res. 2011;116:C08025. doi:10.1029/2010JC006892.

    Article  Google Scholar 

  • Ross S, Quattrini A. The fish fauna associated with deep coral banks off the southeastern United States. Deep Sea Res I. 2007;54:975–1007.

    Article  Google Scholar 

  • Scinto A, Bertolino M, Calcinai B, Huete-Stauffer C, Previati M, Romagnoli T, Cerrano C. Role of Paramuricea clavata forest in modifying the coralligenous assemblages. In: Proceedings of the First Mediterranean Symposium on the Conservation of the Coralligenous and Other Calcareous Bio-concretions. Tabarka; 2009. 15–16 Jan 2009.

    Google Scholar 

  • Shapiro OH, Fernandez VI, Garren M, Guasto JS, Debaillon-Vesque FP, Kramarsky-Winter E, Vardi A, Stocker R. Vortical ciliary flows actively enhance mass transport in reef corals. Proc Natl Acad Sci U S A. 2014;111(37):13391–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shashar N, Kinane S, Patterson PLJ, Patterson MR. Hydromechanical boundary layers over a coral reef. J Exp Mar BioI Ecol. 1996;199:17–28.

    Article  Google Scholar 

  • Singh R, Bandi MM, Mahadevan A, Mandre S. Linear stability analysis for monami in submerged seagrass bed. J Fluid Mech. 2016;786:R1. doi:10.1017/jfm.2015.642.

    Article  Google Scholar 

  • Sleath JFA. Sea bed mechanics (ocean engineering). New York: Wiley-Interscience; 1984 .335 p

    Google Scholar 

  • Sleath JFA. Turbulent oscillatory flows over rough beds. J Fluid Mech. 1987;182:369–409.

    Article  Google Scholar 

  • Smith F, Witman JD. Species diversity in subtidal landscapes: maintenance by physical processes and larval recruitment. Ecology. 1999;80:51–69.

    Article  Google Scholar 

  • Stephens TA, Hepburn CD. Mass-transfer gradients across kelp beds influence Macrocystis pyrifera growth over small spatial scales. Mar Ecol Prog Ser. 2014;515:97–109.

    Article  Google Scholar 

  • Thistle D, Eckman JE. The effect of a biologically produced structure on the benthic copepods of a deep-sea site. Deep-Sea Res. 1990;37:541–54.

    Article  Google Scholar 

  • Trebilco R, Dulvy NK, Steward H, Salomon AK. The rôle of habitat complexity in the size structure of a temperate reef fish community. Mar Ecol Prog Ser. 2015;532:197–211.

    Article  Google Scholar 

  • Vogel S. Life in moving fluids. 2nd ed. Princeton University Press: Princeton; 1994.

    Google Scholar 

  • Wilcox DC. Turbulence modelling for CFD. 2nd ed. La Cañada Flintridge: DCW Industries; 2000.

    Google Scholar 

  • Wooding RA, Bradley EF, Marshall JK. Drag due to regular arrays of roughness elements of varying geometry. Bound.-Lay. Meteorol. 1973;5:285–308.

    Article  Google Scholar 

  • Yonge CM. Studies on the physiology of corals. I. Feeding mechanisms and food. In: Great barrier reef expedition 1928–29, scientific report. London: British Museum (Natural History); 1930. p. 13–57.

    Chapter  Google Scholar 

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Guizien, K., Ghisalberti, M. (2017). Living in the Canopy of the Animal Forest: Physical and Biogeochemical Aspects. In: Rossi, S., Bramanti, L., Gori, A., Orejas , C. (eds) Marine Animal Forests. Springer, Cham. https://doi.org/10.1007/978-3-319-21012-4_14

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