We present findings from two sets of measurements that quantified currents around and over the full extent of a giant kelp (Macrocystis pyrifera) forest located at Mohawk Reef, Santa Barbara, California. Velocities were damped inside this 200-m 3 300-m forest, but not to the extent reported for larger (kilometer-scale) kelp beds, suggesting that alongshore currents may play a greater role in exchange than has often been assumed. Secondary flow features that bear on the performance of forest organisms were observed, including a region along the forest's outer boundary where velocities exceeded incident speeds by up to 200%. An offshore current on the order of 1 cm s 21 developed within the kelp bed, likely due to pressure gradients established across the forest coupled with topography. Wake recirculations that might have facilitated leeward retention of waterborne subsidies were not apparent. Calculations suggest that kelp beds can interact with (and thus potentially filter) substantial 1 Corresponding author (bpgaylord@ucdavis.edu;

[1] In a hydrodynamic sense, a coral reef is a complex array of obstacles that exerts a net drag force on water moving over the reef. This drag is typically parameterized in ocean circulation models using drag coefficients (C D ) or roughness length scales (z 0 ); however, published C D for coral reefs span two orders of magnitude, posing a challenge to predictive modeling. Here we examine the reasons for the large range in reported C D and assess the limitations of using C D and z 0 to parameterize drag on reefs. Using a formal framework based on the 3-D spatially averaged momentum equations, we show that C D and z 0 are functions of canopy geometry and velocity profile shape. Using an idealized two-layer model, we illustrate that C D can vary by more than an order of magnitude for the same geometry and flow depending on the reference velocity selected and that differences in definition account for much of the range in reported C D values. Roughness length scales z 0 are typically used in 3-D circulation models to adjust C D for reference height, but this relies on spatially averaged near-bottom velocity profiles being logarithmic. Measurements from a shallow backreef indicate that z 0 determined from fits to point measurements of velocity profiles can be very different from z 0 required to parameterize spatially averaged drag. More sophisticated parameterizations for drag and shear stresses are required to simulate 3-D velocity fields over shallow reefs; in the meantime, we urge caution when using published C D and z 0 values for coral reefs.Citation: Rosman, J. H., and J. L. Hench (2011), A framework for understanding drag parameterizations for coral reefs,

[1] Macrocystis pyrifera (Giant Kelp) forests form important habitats in temperate coastal regions. Hydrodynamics control the transport of nutrients, food particles, larvae and spores at scales ranging from boundary layers around individual blades to entire kelp forests. Our measurements include vertical profiles of current and temperature, and concurrent wave measurements, at a number of different locations in and around a kelp forest at Santa Cruz, California. We find that flow at the site is dominated by variations at diurnal and semidiurnal frequencies. A vertically sheared across-shore flow, consistent with flow driven by an across-shore density gradient, is thought to be important for exchange between the kelp forest and the surrounding coastal ocean. Within the kelp forest, currents are reduced by a factor that correlates with surface canopy coverage, higher frequency internal waves are damped, and onshore transport due to waves (Stokes drift) is estimated to be similar in magnitude to that due to currents. Richardson numbers within the kelp forest are higher than those outside the kelp forest and indicate that the water column within the kelp forest is usually stable to turbulence generation by mean velocity shear.

We describe a laboratory investigation into the effect of turbulent hydrodynamic stresses on clam larvae in the settlement phase of the recruitment process. A two-component laser-Doppler anemometer (LDA) was used to measure time histories of the instantaneous turbulence structure at potential recruitment sites within reconstructed beds of the adult Asian clam, Potamocorbula amurensis. Measurements were made for two flow speeds over beds with three different clam densities and two different clam heights. We analyze the statistical effect of the turbulence on the larval flux to the bed and on the probability of successful anchoring to the substrate. It is shown that the anchoring probability depends on the nature of the instantaneous stress events rather than on mean stresses. The instantaneous turbulence structure near the bed is altered by the flow rate and the spacing and height of adult clams living in the substrate. The ability to anchor quickly is therefore extremely important, since the time sequence of episodic turbulent stress events influences larval settlement success. The probability of successful larval settlement is predicted to decrease as the spacing between adults decreases, implying that the hydrodynamics impose negative feedback on clam bed aggregation dynamics.

[1] Although small-scale spatial flow variability can affect both larger-scale circulation patterns and biological processes on coral reefs, there are few direct measurements of spatial flow patterns across horizontal scales <100 m. Here flow patterns on a shallow reef flat were measured at scales from a single colony to several adjacent colonies using an array of acoustic Doppler velocimeters on a diver-operated traverse. We observed recirculation zones immediately behind colonies, reduced currents and elevated dissipation rates in turbulent wakes up to 2 colony diameters downstream and enhanced Reynolds stresses in shear layers around wake peripheries. Flow acceleration zones were observed above and between colonies. Coherent flow structures varied with incident flow speeds; recirculation zones were stronger and wakes were more turbulent in faster flows. Low-frequency (<0.03 Hz) flow variations, for which water excursions were large compared with the colony diameters (Keulegan-Carpenter number, KC >1), had similar spatial patterns to wakes, while higher-frequency variations (0.05-0.1 Hz, KC < 1) had no observable spatial structure. On the reef flat, both drag and inertial forces exerted by coral colonies could have significant effects on flow, but within different frequency ranges; drag dominates for low-frequency flow variations and inertial forces dominate for higherfrequency variations, including the wave band. Our scaling analyses suggest that spatial flow patterns at colony and patch scales could have important implications for both physical and biological processes at larger reef scales through their effects on forces exerted on the flow, turbulent mixing, and dispersion.

Surface waves introduce velocity correlations that bias and often dominate Reynolds stress estimates made using the traditional variance method for acoustic Doppler current profilers (ADCPs). This analysis shows that the wave bias is the sum of a real wave stress and an error due to instrument tilt, both of which have a large uncertainty. Three alternative extensions to the variance method for calculating Reynolds stress profiles from ADCP measurements in wavy conditions are analyzed. The previously proposed variance fitting method (Variance Fit) is evaluated and two more general methods that use along- and between-beam velocity differencing with adaptive filtering (Vertical AF and Horizontal AF) are derived. The three methods are tested on datasets containing long-period monochromatic swell (Moorea, French Polynesia) and shorter-period mixed swell (Santa Barbara, California). The Variance Fit method leaves a residual wave bias in beam velocity variances, especially for intermediate waves, but gives physically reasonable Reynolds stress estimates because most of the residual wave bias cancels when the variance method is applied. The new Vertical AF method does not produce inherent wave bias in beam velocity variances, but yields comparable Reynolds stresses to the Variance Fit method. The Horizontal AF method performs poorly for all but monochromatic waves. Error remaining after one of the above methods is applied can be attributed to residual wave error, correlation of turbulence between points chosen for differencing, or correlation between waves and turbulence. A simple procedure is provided for determining the minimum bin separation that can be used.

The effects of a Macrocystis pyrifera forest on currents and turbulence were investigated in a controlled laboratory setting using a dynamically matched 1/25-scale model. Two kelp configurations with surface canopies and one without a surface canopy were considered. Profiles of mean velocities and turbulence statistics were measured using acoustic Doppler velocimeters. Since flow within the model kelp forest was very heterogeneous, spatially averaged forms of the governing equations were used for the analysis. Stress gradients were small compared with pressure gradient, drag, and acceleration terms of the momentum budget. A good model for kelp drag is therefore required for simulating flow through a kelp forest, while the model for Reynolds and dispersive stresses is less critical. The bulk drag coefficient is highest at the up-current end of a kelp forest and decays with down-current distance as the velocity profile adjusts to the drag profile. Modeling a kelp forest as an array of vertical cylinders underestimates the net drag by a factor of 1.5 to 3 if a substantial surface canopy is present. Turbulence is generated predominantly by small-scale shear in kelp wakes. Vertical mixing of scalars is expected to be significantly smaller than in the surrounding coastal ocean because of the combination of smaller turbulent eddies and reduced currents. The decrease in horizontal transport and vertical mixing within kelp forests may have important implications for nutrient availability to kelp forest organisms and may affect the dispersal or retention of their larvae and spores.Macrocystis pyrifera (Linneaus) Agardh (commonly Giant Kelp) forests are important components of temperate coastal ecosystems, providing food and shelter for a diverse array of organisms. Many kelp forest organisms, including M. pyrifera itself, extract nutrients, plankton, or particulates from the water column. The availability of these quantities is determined by mean water motion primarily due to currents and by vertical and lateral mixing due to turbulence and spatial variations in the flow. Most kelp forest organisms release larvae or spores into the water column, and the paths and eventual destinations of these particles are also determined to a large extent by water motion. A good understanding of kelp forest hydrodynamics is therefore required to estimate nutrient availability to different parts of a kelp forest or to predict dispersal distances of reproductive propagules released within a kelp forest.M. pyrifera forests exert much greater drag on the flow than do kelp-free areas, and, thus, they significantly alter the local flow environment. Field observations indicate that depth-averaged currents within M. pyrifera forests can be reduced by a factor of 1.5 to 5 relative to nearby kelp-free areas (Jackson 1998;Gaylord et al. 2007;Rosman et al. 2007). For a given current direction, the upstream edge of the kelp forest experiences stronger currents, while the downstream edge sees smaller currents. However, as current direction ty...

Abstract. Extracting benthic oxygen fluxes from eddy covariance time series measured in the presence of surface gravity waves requires careful consideration of the temporal alignment of the vertical velocity and the oxygen concentration. Using a model based on linear wave theory and measured eddy covariance data, we show that a substantial error in flux can arise if these two variables are not aligned correctly in time. We refer to this error in flux as the time lag bias. In one example, produced with the wave model, we found that an offset of 0.25 s between the oxygen and the velocity data produced a 2-fold overestimation of the flux. In another example, relying on nighttime data measured over a seagrass meadow, a similar offset reversed the flux from an uptake of −50 mmol m −2 d −1 to a release of 40 mmol m −2 d −1 . The bias is most acute for data measured at shallow-water sites with short-period waves and low current velocities. At moderate or higher current velocities (> 5-10 cm s −1 ), the bias is usually insignificant. The widely used traditional time shift correction for data measured in unidirectional flows, where the maximum numerical flux is sought, should not be applied in the presence of waves because it tends to maximize the time lag bias or give unrealistic flux estimates. Based on wave model predictions and measured data, we propose a new time lag correction that minimizes the time lag bias. The correction requires that the time series of both vertical velocity and oxygen concentration contain a clear periodic wave signal. Because wave motions are often evident in eddy covariance data measured at shallow-water sites, we encourage more work on identifying new time lag corrections.