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Turbulent Tales from a Rough Coral Reef: Effects of Nonuniform Roughness on Waves, Turbulence, and Scalar Fluxes /

Record Type:	Electronic resources : Monograph/item
Title/Author:	Turbulent Tales from a Rough Coral Reef: Effects of Nonuniform Roughness on Waves, Turbulence, and Scalar Fluxes // Elisabeth Boles.
Author:	Boles, Elisabeth,
Description:	1 electronic resource (265 pages)
Notes:	Source: Dissertations Abstracts International, Volume: 86-08, Section: B.
Contained By:	Dissertations Abstracts International86-08B.
Subject:	Calcification. -
Online resource:	https://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=31901326
ISBN:	9798311940764

Turbulent Tales from a Rough Coral Reef: Effects of Nonuniform Roughness on Waves, Turbulence, and Scalar Fluxes /
Boles, Elisabeth,

Turbulent Tales from a Rough Coral Reef: Effects of Nonuniform Roughness on Waves, Turbulence, and Scalar Fluxes /Elisabeth Boles. - 1 electronic resource (265 pages)

Source: Dissertations Abstracts International, Volume: 86-08, Section: B.

Coral reefs are one of the most bio-diverse ecosystems on the planet and provide crucial storm protection, food supply and livelihoods to many coastal communities. However, reefs around the world are experiencing existential threats due to compounding stressors such as overfishing, pollution, thermal bleaching and ocean acidification. Hydrodynamics play a key role in regulating coral health, controlling thermal variability, facilitating nutrient supply, reducing oxygen toxicity during bleaching events, and dispersing coral larvae. Conversely, the corals that create the foundation for a reef community also have incredible influence on their hydrodynamic environment. A defining feature of coral reefs is their remarkably large and spatially variable roughness, which produces frictional effects strong enough to balance both wave and tidal forcing as well as reduce incoming wave energy.This dissertation presents results from three years of fieldwork and related modeling on two adjacent reefs in Palau, Tabkukau and Ngederrak, where we explored how coral roughness affects turbulence, mixing, wave energy dissipation and circulation dynamics at small and intermediate scales.The first half of the dissertation focuses on small-scale measurements of turbulence and scalar mixing in the boundary layer just above the coral canopy, to examine how momentum and oxygen are mixed through the water column. The results have important implications for accurately modeling reef dynamics as well as for improving capacity to monitor reef health. In Chapter 2, we compared five methods for measuring roughness, friction velocities and drag on reefs. These included large scale momentum balance closure methods, direct measurements of boundary layer turbulence, and roughness characterization from digital elevation models of the reef surface.We found that the momentum balance approach produced estimates of drag that were three times larger than those predicted by turbulence measurements. The large difference between total drag and local turbulence implies that mass transfer and chemical exchange between corals and the overlying water-column may be somewhat decoupled from the spatially-averaged frictional effects of the reef. Topographical heterogeneity, which induces mean velocity fluxes, dispersive stresses and form drag, likely explains the difference; these effects are expected be more significant as the ratio of canopy height to water depth increases.In Chapters 3 and 4, we build on these results to first examine the vertical structure of turbulence and scalar variance, and assess how well they conform to standard log-layer scalings for turbulent bottom boundary layers over uniform roughness. We then compare two in-situ, non-invasive techniques for measuring Net Community Production (NCP) and Calcification (NCC) in aquatic environments: the eddy covariance (EC) and gradient flux (BEAMS) methods. These techniques are increasingly being used to monitor reef health, but until now their applicability in shallow, wave-dominated environments has been uncertain. We discuss challenges and provide recommendations for deployments in shallow coastal environments with waves and non-uniform, "canopy"-like roughness features. We show that spectral methods can be used to remove wave bias from EC fluxes and produce reliable estimates of NCP. BEAMS and EC flux estimates were very well correlated, but BEAMS measurements were consistently at least a factor of two larger. This result highlights the difficulty of identifying the correct mixing length-scale for the BEAMS method in environments with extremely heterogeneous roughness features. We suggest caution when comparing rates between sites and experiments, especially when different measurement techniques are employed.In the second half of the dissertation, we focus on how larger-scale, biogenic roughness features known as "spurs and grooves" (SAGs) modify surface gravity waves, wave energy dissipation and circulations dynamics. While SAGs are common features on reefs all over the world, research on how they modify hydrodynamics has been limited. Phase-resolved simulations of wave propagation over idealized SAGs (Chapter 5) are compared to observations from a detailed deployment within real SAGs on Ngederrak reef (Chapter 6). We find that the properties of a wave may become decoupled from the local depth as it propagates over nonuniform topography such as SAGs. The extent of this decoupling depends on the length of the wave relative to the spacing of the spurs; longer waves "feel" the effects of the along-shore average topography while shorter waves "feel" the local bathymetry. Over SAGs, short waves can also undergo significant refraction, drawing energy away from grooves and concentrating it atop spurs. In both simulations and in-situ measurements, this produced radiation stress gradients that were oriented in opposite directions over spurs (on-shore) and grooves (off-shore) and significantly enhanced the strength of mean flow circulation.Field measurements showed that the energy content of short period waves (T < 7 seconds) increased from off-shore over spurs and decreased over grooves. This resulted in greater apparent wave energy dissipation over grooves than spurs. Our measurements indicated that the Ngederrak SAGs had a high wave friction factor (2.4) and were capable of dissipating 30-50% of incoming wave energy through bottom friction over just 50 m. Additionally, density currents moving through the grooves contributed to large tidal asymmetries in mean velocity shear and bottom stresses. These are expected to generate net off-shore transport of sediment and coral debris, which may assist in seaward accretion of SAGs and facilitate reef recovery after damage from tropical storms.

English

ISBN: 9798311940764Subjects--Topical Terms:

3297808
Calcification.

Turbulent Tales from a Rough Coral Reef: Effects of Nonuniform Roughness on Waves, Turbulence, and Scalar Fluxes /
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520 $a Coral reefs are one of the most bio-diverse ecosystems on the planet and provide crucial storm protection, food supply and livelihoods to many coastal communities. However, reefs around the world are experiencing existential threats due to compounding stressors such as overfishing, pollution, thermal bleaching and ocean acidification. Hydrodynamics play a key role in regulating coral health, controlling thermal variability, facilitating nutrient supply, reducing oxygen toxicity during bleaching events, and dispersing coral larvae. Conversely, the corals that create the foundation for a reef community also have incredible influence on their hydrodynamic environment. A defining feature of coral reefs is their remarkably large and spatially variable roughness, which produces frictional effects strong enough to balance both wave and tidal forcing as well as reduce incoming wave energy.This dissertation presents results from three years of fieldwork and related modeling on two adjacent reefs in Palau, Tabkukau and Ngederrak, where we explored how coral roughness affects turbulence, mixing, wave energy dissipation and circulation dynamics at small and intermediate scales.The first half of the dissertation focuses on small-scale measurements of turbulence and scalar mixing in the boundary layer just above the coral canopy, to examine how momentum and oxygen are mixed through the water column. The results have important implications for accurately modeling reef dynamics as well as for improving capacity to monitor reef health. In Chapter 2, we compared five methods for measuring roughness, friction velocities and drag on reefs. These included large scale momentum balance closure methods, direct measurements of boundary layer turbulence, and roughness characterization from digital elevation models of the reef surface.We found that the momentum balance approach produced estimates of drag that were three times larger than those predicted by turbulence measurements. The large difference between total drag and local turbulence implies that mass transfer and chemical exchange between corals and the overlying water-column may be somewhat decoupled from the spatially-averaged frictional effects of the reef. Topographical heterogeneity, which induces mean velocity fluxes, dispersive stresses and form drag, likely explains the difference; these effects are expected be more significant as the ratio of canopy height to water depth increases.In Chapters 3 and 4, we build on these results to first examine the vertical structure of turbulence and scalar variance, and assess how well they conform to standard log-layer scalings for turbulent bottom boundary layers over uniform roughness. We then compare two in-situ, non-invasive techniques for measuring Net Community Production (NCP) and Calcification (NCC) in aquatic environments: the eddy covariance (EC) and gradient flux (BEAMS) methods. These techniques are increasingly being used to monitor reef health, but until now their applicability in shallow, wave-dominated environments has been uncertain. We discuss challenges and provide recommendations for deployments in shallow coastal environments with waves and non-uniform, "canopy"-like roughness features. We show that spectral methods can be used to remove wave bias from EC fluxes and produce reliable estimates of NCP. BEAMS and EC flux estimates were very well correlated, but BEAMS measurements were consistently at least a factor of two larger. This result highlights the difficulty of identifying the correct mixing length-scale for the BEAMS method in environments with extremely heterogeneous roughness features. We suggest caution when comparing rates between sites and experiments, especially when different measurement techniques are employed.In the second half of the dissertation, we focus on how larger-scale, biogenic roughness features known as "spurs and grooves" (SAGs) modify surface gravity waves, wave energy dissipation and circulations dynamics. While SAGs are common features on reefs all over the world, research on how they modify hydrodynamics has been limited. Phase-resolved simulations of wave propagation over idealized SAGs (Chapter 5) are compared to observations from a detailed deployment within real SAGs on Ngederrak reef (Chapter 6). We find that the properties of a wave may become decoupled from the local depth as it propagates over nonuniform topography such as SAGs. The extent of this decoupling depends on the length of the wave relative to the spacing of the spurs; longer waves "feel" the effects of the along-shore average topography while shorter waves "feel" the local bathymetry. Over SAGs, short waves can also undergo significant refraction, drawing energy away from grooves and concentrating it atop spurs. In both simulations and in-situ measurements, this produced radiation stress gradients that were oriented in opposite directions over spurs (on-shore) and grooves (off-shore) and significantly enhanced the strength of mean flow circulation.Field measurements showed that the energy content of short period waves (T < 7 seconds) increased from off-shore over spurs and decreased over grooves. This resulted in greater apparent wave energy dissipation over grooves than spurs. Our measurements indicated that the Ngederrak SAGs had a high wave friction factor (2.4) and were capable of dissipating 30-50% of incoming wave energy through bottom friction over just 50 m. Additionally, density currents moving through the grooves contributed to large tidal asymmetries in mean velocity shear and bottom stresses. These are expected to generate net off-shore transport of sediment and coral debris, which may assist in seaward accretion of SAGs and facilitate reef recovery after damage from tropical storms.
546 $a English
590 $a School code: 0212
650 4 $a Calcification. $3 3297808
650 4 $a Environmental conditions. $3 3550086
650 4 $a Fluid dynamics. $3 545210
650 4 $a Pandemics. $3 3464080
650 4 $a Data processing. $3 680224
650 4 $a Energy dissipation. $3 619627
650 4 $a Community. $3 531337
650 4 $a Metabolism. $3 541349
650 4 $a Wave power. $3 3564471
650 4 $a Morphology. $3 591167
650 4 $a Coral reefs. $3 3564373
690 $a 0287
710 2 $a Stanford University. $e degree granting institution. $3 3765820
720 1 $a Monismith, Stephen $e degree supervisor.
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