Structure and dynamics of turbulent boundary layer flow over healthy and algae-covered corals

Stocking, Jonathan B.; Rippe, John P.; Reidenbach, Matthew A.

doi:10.1007/s00338-016-1446-8

Cited by 38 publications

(33 citation statements)

References 35 publications

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“…Changes in epigenetic marks based on the detection of environmental cues provides an avenue to effect phenotypic plasticity (Shea et al, 2011). Detailed data on systematic variation in temperature, flow and light regimes depending on polyp location within a colony and colony morphology are accumulating (Edmunds & Burgess, 2018;Ong, King, Kaandorp, Mullins, & Caley, 2017;Stocking, Rippe, & Reidenbach, 2016). Remarkably, there was some correspondence between genes previously shown to be differentially expressed, and those that were differentially methylated, indicating that methylation differences may translate into gene expression differences.…”

Section: Discussionmentioning

confidence: 99%

What drives phenotypic divergence among coral clonemates of Acropora palmata?

et al. 2019

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Evolutionary rescue of populations depends on their ability to produce phenotypic variation that is heritable and adaptive. DNA mutations are the best understood mechanisms to create phenotypic variation, but other, less well‐studied mechanisms exist. Marine benthic foundation species provide opportunities to study these mechanisms because many are dominated by isogenic stands produced through asexual reproduction. For example, Caribbean acroporid corals are long lived and reproduce asexually via breakage of branches. Fragmentation is often the dominant mode of local population maintenance. Thus, large genets with many ramets (colonies) are common. Here, we observed phenotypic variation in stress responses within genets following the coral bleaching events in 2014 and 2015 caused by high water temperatures. This was not due to genetic variation in their symbiotic dinoflagellates (Symbiodinium “fitti”) because each genet of this coral species typically harbours a single strain of S. “fitti”. Characterization of the microbiome via 16S tag sequencing correlated the abundance of only two microbiome members (Tepidiphilus, Endozoicomonas) with a bleaching response. Epigenetic changes were significantly correlated with the host's genetic background, the location of the sampled polyps within the colonies (e.g., branch vs. base of colony), and differences in the colonies’ condition during the bleaching event. We conclude that long‐term microenvironmental differences led to changes in the way the ramets methylated their genomes, contributing to the differential bleaching response. However, most of the variation in differential bleaching response among clonemates of Acropora palmata remains unexplained. This research provides novel data and hypotheses to help understand intragenet variability in stress phenotypes of sessile marine species.

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Section: Discussionmentioning

confidence: 99%

What drives phenotypic divergence among coral clonemates of Acropora palmata?

et al. 2019

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“…If we continue to move vertically up the coral structures, the two velocity profiles 415 collapsed at approximately 27 mm above the coral surface. In an experimental analysis, 416 Reidenbach and Stocking et al [41,47] turbulent stress takes place within 20 mm above the top of the coral. In the current 500 analysis, the locations of maximum stress for all of the components are found within 20 501 mm above the coral surface, and the magnitude of the stress components are within the 502 same order of magnitude as those found in the experiment.…”

Section: Resultsmentioning

confidence: 99%

“…Though this analysis is useful in describing a boundary profile for a large 45 coral reef, it does not make clear the impacts of the individual coral colony on the flow 46 structure. Recently, Chang et al [30] have used magnetic resonance velocimetry [31] to 47 reveal the internal flow profile of corals for two different branching patterns. Though 48 the results provided an excellent visualization of the flow field inside the coral, the study 49 did not provide sufficient information regarding the change in the velocity profile along 50 the length of the coral.…”

Section: Introductionmentioning

confidence: 99%

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Effects of coral colony morphology on turbulent flow dynamics

Hossain

Staples

2019

Preprint

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Local flow dynamics play a central role in physiological processes like respiration and nutrient uptake in coral reefs. Despite the importance of corals as hosts to a quarter of all marine life, and the pervasive threats currently facing corals, little is known about the detailed hydrodynamics of branching coral colonies. Here, in order to investigate the effects of the colony branch density and surface roughness on the local flow field, three-dimensional simulations were performed using immersed boundary, large-eddy simulations for four different colony geometries under low and high unidirectional oncoming flow conditions. The first two colonies were from the Pocillopora genus, one with a densely branched geometry, and one with a comparatively loosely branched geometry. The second pair of colony geometries were derived from a scan of a single Montipora capitata colony, one with the verrucae covering the surface intact, and one with the verrucae removed. We found that the mean velocity profiles in the densely branched colony changed substantially in the middle of the colony, becoming significantly reduced at middle heights where flow penetration was poor, while the mean velocity profiles in the loosely branched colony remained similar in character from the front to the back of the colony, with no middle-range velocity deficit appearing at the center of the colony. When comparing the turbulent flow statistics at the surface of the rough and smooth M. capitata colonies, we found higher Reynolds stress components for the smooth colony, indicating higher rates of mixing and transport compared to the rough colony, which must sacrifice mixing and transport efficiency in order to maintain its surface integrity in its natural high-flow environment. These results suggest that the densely branched, roughly patterned corals found in high flow areas may be more resistant not only to breakage, but also to flow penetration. motions transport planktonic food to the reef, while diffusion [3,4] takes place at a 6 much smaller scale at the coral surface. For the smaller scale processes, experimental 7 studies [5,6] show that growth direction, dimensions, and sparsity of branches depend 8 on the flow profile inside the coral [7][8][9]. Similarly, the velocity profile controls the 9 nutrient distribution [7,[10][11][12][13]. and physiological processes like photosynthesis and 10 respiration [14-17] near the coral surface. Flow motion also controls the thermal 11 micro-environment [18,19] at the coral surface, which is extremely important for 12 incidents like coral bleaching. Both the transfer of nutrients from the water column to 13 the coral and the transfer of byproducts from the coral to the water column depend on 14 the details of the flow through and around the coral [20, 21]. It is clear from the 15 discussion that all of these physical parameters are directly related to the flow 16 conditions in and around the coral geometry. To obtain a clear picture of this 17 interdependent relationship, the authors tried to find answers ...

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“…Stocking, Rippe, & Reidenbach (2016) [61] use the same scripts to study the structure and dynamics of turbulent boundary layer flow over healthy and algae-covered corals. Other papers using this technique include [62] [63].…”

Section: Review Of the Piv Techniquesmentioning

confidence: 99%

Experimental Investigation Into the Effect of a Stationary Dorsal Fin for Multiple Configurations - A Bio-Inspired Perspective

Saraiya

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Results of experiments aimed at determining the performance of two quasi-two-dimensional hydrofoils arranged in an in-line configuration are presented. This thesis aims at understanding the role of pitching motion of a caudal fin in the presence of a dorsal fin, decoupled from heaving motion. A simplified model has been proposed, which accounts for pitching motion, and explores the role of frequency, amplitude, and separation distance between dorsal and caudal fins. The net thrust generated and the work done by the 2-fin model while undergoing prescribed pitching motions were calculated.The pitch experiments focus on four parameters to quantify their influence on propulsive performance; (1) frequency, (2) trailing edge amplitude, (3) separation between foils, and (4) flexibility of the fins. The experiments are conducted under both accelerating and free swimming conditions. It is hypothesized that distance of separation between the static dorsal and pitching caudal fins during free swimming will affect the work done and economy across amplitudes and frequencies due to the weakening of the wake from the leading hydrofoil. It is also expected that the change in flexibility at free-swimming speeds will cause a change in economy, and that the presence of the dorsal fin will amplify this effect. Finally, the thrust is hypothesized to follow trends similar to that of a pitching hydrofoil in terms of amplitude and frequency.While the increased drag due to the additional hydrofoil reduces the speed of motion, it also reduces the required work to move the lagging hydrofoil. The reduction in speed is ~10%, ii while the required work decreases by >20% on average, leading to an increase in economy.The effects increase with increasing amplitude and frequency during acceleration. As the distance between the hydrofoils is increased the efficiency and economy of the model reduces. Finally, flexible foils are more efficient in the presence of a stationary fin only at high frequencies and amplitudes.This study is a valuable preliminary work towards the evolution of design of bio-inspired models and possibly vehicles.A secondary aim of this thesis is the development of an inexpensive PIV technique to quantify flow fields. A PIV setup has been designed and built that allows the quantification of flows at speeds below 25.4 cm/s. At greater speeds, error margins exceed 10%.iii

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Structure and dynamics of turbulent boundary layer flow over healthy and algae-covered corals

Cited by 38 publications

References 35 publications

What drives phenotypic divergence among coral clonemates of Acropora palmata?

What drives phenotypic divergence among coral clonemates of Acropora palmata?

Effects of coral colony morphology on turbulent flow dynamics

Experimental Investigation Into the Effect of a Stationary Dorsal Fin for Multiple Configurations - A Bio-Inspired Perspective

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