Boundary layer turbulence and flow structure over a fringing coral reef

Measurements of velocity and rates of turbulence were made across a fringing coral reef in the Gulf of Aqaba, Red Sea, to determine the effect that the rough topography has on boundary layer mixing and flow dynamics. Observations were made at two fore-reef sites and a nearby sandy slope. The friction velocity, u*, and drag coefficient, CD, were determined directly from turbulent Reynolds stresses measured using acoustic Doppler velocimeters. Values of CD for the coral substrates ranged from 0.009 to 0.015, three to five times greater than over the sandy bottom site. The turbulence dissipation rate, e, was determined by fitting spectra of vertical velocity to the theoretical ‘‘5/3’’ law expected for the inertial subrange of turbulence. There was a local balance between production and dissipation of turbulent kinetic energy, signifying that we could estimate u* from either the mean velocity profile, turbulence, or dissipation rate of turbulent kinetic energy. Estimates from all three measures agreed well with mean u*/Uo ranging from 0.10 6 0.03 to 0.12 6 0.03, indicating that existing turbulent boundary layer flow theory can be applied to flows over the rough topography of coral reefs. The bottom topography, by enhancing both reef scale and local drag and mixing levels, allows reef biota to more effectively exchange dissolved and particulate matter with oceanic waters. Many coral-reef organisms have limited or no mobility and thus depend on water motion for their basic functions, including food delivery (Kiflawi and Genin 1997; Sebens et al. 1997), production (Koehl and Alberte 1988; Denisson and Barnes 1988), respiration (Goldshmid et al. 2004), uptake of nutrients (Patterson et al. 1991; Atkinson et al. 2001), and larval dispersal (Harii and Kayanne 2003; Sponaugle et al. 2005). The relevant hydrodynamics range from large-scale circulation patterns that determine rates of dispersal across the reef (Hamner and Wolanksi 1988) through microscale turbulence, e.g., motions with length scales near the Kolmogorov scale (Tennekes and Lumley 1972), that influence particle capture and mass flux on the scale of an individual coral polyp (Sebens 1997; Helmuth et al. 1997). The link between these scales is the bottom friction, i.e., shear stresses that develop because of flow over the reef. At intermediate scales of water motion over centimeters to meters, dispersal processes and food acquisition depend on how near-bed flow dynamics exchange mass between the reef and the surrounding ocean. For example, the boundary layer within a few meters of the reef is sometimes severely depleted of planktonic food (Yahel et al. 1998, 2005) because of grazing by the reef community. Replenishment of these food sources depends upon turbulent mixing near the reef (Genin et al. 2002). Although local, instantaneous turbulent events are important to benthic communities (Abelson and Denny 1997; Crimaldi et al. 2002), the temporally and spatially integrated structure of the boundary layer often best describes relations between flow and transport processes. For instance, it has been shown that the uptake of nutrients by reefs is proportional to the friction velocity, u* (Baird and Atkinson 1997; Falter et al. 2004). In the same way, it is known that turbulent mixing, represented by the nearbed eddy diffusivity, plays a key role in determining the strength of concentration boundary layers that develop because of benthic grazing (O’Riordan et al. 1993). The average bed stress also plays a critical role in controlling exchange between the reef and the open ocean (Hearn 1999; Monismith et al. 2006). Therefore, an understanding of the structure and dynamics of boundary layer flows and how it relates to smallerand larger-scale flow phenomena offers valuable insight into the functioning of coral reefs. 1 Present address: Department of Integrative Biology, University of California, Berkeley, California 94720. 2 Corresponding author. 3 Present address: Department of Biology, University of Victoria, P.O. Box 3020 Stn CSC, Victoria, British Columbia, V8W 3N5 Canada. Acknowledgments We thank Moty Ohevia, Shiri Eckstein, Ruty Motro, Inbal Ayalon, Eaton Dunkelberger, Roi Holtzman, and Susanne Neilsen for their technical support to the field program and Derek Fong for his assistance in bathymetry mapping. This work was funded by the National Science Foundation grant OCE 0117859, US-Israel Binational Science Foundation grant 1997450, and the Stanford Bio-X Interdisciplinary Initiatives program. M. Reidenbach was also supported by a Stanford Graduate Fellowship. Limnol. Oceanogr., 51(5), 2006, 1956–1968 E 2006, by the American Society of Limnology and Oceanography, Inc.