Mixing in near-shore coastal environments [electronic resource]

Coral reefs are among the most biologically diverse and economically important ecosystems on the planet. While there are a number of factors that contribute to a healthy coral reef, turbulent mixing generated over corals has been shown to be important. Mixing over corals controls many biologically important processes such as grazing rates by benthic organisms, mass transfer of dissolved constituents, larval dispersal and waste removal. While elevated levels of turbulence are often found right above coral beds, corals are often located in environments with extreme heating throughout the day resulting in high levels of stratification which can limit vertical exchange. Motivated by the importance of the dynamically evolving turbulent structure found over coral reefs, I aimed to quantify the level of mixing found over changing coral reef conditions and compare it to mixing found in surface ocean environments. Three field sites were used for this analysis; a deep water site approximately 1 km off the coast of Eilat, a fringing coral reef (Eilat, Israel) and a back reef site (Palau). High resolution microstructure profiling data in the top 40 m of a deep ocean environment showed the changing dynamics of a surface mixed later and the layer below during heating, cooling, and windy conditions (Eilat, Israel). While this provided a baseline from which to compare coral mixing rates, it also allowed us to compare the varying parameterizations of mixing efficiency and vertical diffusivity. The single value of mixing efficiency (usually 0.17-0.20) was found to over estimate the mixing efficiency in most of the water column regardless of the mixing efficiency parameterization used. We outlined the difficulties with using the different parameterizations (mixing efficiency and vertical diffusivity) under changing conditions and when caution should be taken. Filtering that decreased amplified Thorpe scales in weakly stratified conditions were applied. Additionally, a new averaging method that groups turbulence parameters with similar Thorpe length scales was applied to all data presented. This allows bulk estimates of turbulent Froude and Reynolds numbers over a given mixing region. For this specific data set we found that the Shih et al. [2005] parameterization for mixing efficiency and the Osborn [1980] parameterization for vertical diffusivity were able to calculate the largest number of mixing efficiency estimates while reflecting the changing dynamics of the water column. A six meter tower supporting 6 ADVs over a fringing coral reef in Eilat, Israel provided turbulence data for the second field study. Twenty thermistors spaced along the tower provided temperature and overturning length scales. This field work was unique in that the ADVs were tethered to shore so that data could be viewed in real time and there were no data storage or battery limitations. In addition, fast conductivity and temperature sensors were located on two of the ADVs allowing direct measurement of buoyancy frequency as well as mixing efficiency. Concentrations of phytoplankton at four corners of a defined control volume were also measured during this study allowing the coupling of phytoplankton grazing rates and turbulence quantities over the reef. Unfortunately, noise associated with the fast conductivity sensor limited the applicability of the direct measurements of buoyancy flux. However, preliminary data suggests that the Shih et al. [2005] mixing efficiency parameterization needs to be adjusted at high values of turbulent activity numbers. This site showed that flows over a coral reef are highly turbulent and that surface stratification events reach down to the corals. Comparison of the production of turbulent kinetic energy calculated with Reynolds stress and as the sum of the buoyancy flux and dissipation were in agreement only 40 % of the time. This indicates that advection and transport played a key role in production estimates at this site. In regards to grazing rate, using a more detailed sliced control volume methodology allowed us to put a vertical cap on our flux estimates based on measurements of vertical diffusivity. These biological measurements show that enhanced turbulence near the bed enables high rates of exchange which decrease in the upper part of the water column. The field site in Palau provided a good coral comparison site to the Eilat coral site. Due to its back reef location, velocities at this site were much smaller however, coral coverage was much higher (approximately 70 % vs. approximately 14 % in Eilat) and the corals were much taller (approximately 1 m vs approximately 0.1 m in Eilat). Given the very different field site conditions, dissipation (a key factor in calculating mixing efficiency and vertical diffusivity rates) remained high at this site indicating that coral roughness plays a big part in mixing over corals even when other forcing parameters are decreased. Measurements of turbulence at this site were coupled with measurements of DIC, ALK and pH. The experimental setup at this site is unique in that sixteen tubes were fixed from four corners of the control volume and were extended to a stationary boat. Through the use of continuous pumping, chemical samples were taken continuously throughout the study (approximately 6 days). While turbulence characterization of coral reefs remains the main focus of this work, preliminary results seem to indicate a correlation between DIC and pH measurements with vertical diffusivity. The coupling of biological measurements with turbulence data show mixing is a key mechanism for the health and sustainability of coral reef ecosystems.

Advisor: Koseff Jeffrey Russell primary advisor. Thesis advisor
Dunbar Robert advisor. Thesis advisor
Fong Derek advisor. Thesis advisor
Monismith Stephen Gene advisor. Thesis advisor