Physical oceanography in coral reef environments [electronic resource] : wave and mean flow dynamics at small and large scales, and resulting ecological implications
Keywords: Civil and Environmental Engineering.

This dissertation investigates the physical oceanography of coral reef environments, specifically focusing on waves and mean flows at small and large scales. At small scales of order ten to a hundred meters, the role of spur and groove formations and their interaction with surface waves and mean flow is examined. Spur-and-groove formations are found on the fore reefs of many coral reefs worldwide. Although these formations are primarily present in wave-dominated environments, their effect on wave-driven hydrodynamics is not well understood. A two-dimensional, depth-averaged, phase-resolving non-linear Boussinesq model (funwaveC) was used to model hydrodynamics on a simplified spur-and-groove system. The modeling results show that the spur-and-groove formations together with shoaling waves induce a nearshore Lagrangian circulation pattern of counter-rotating circulation cells. We present results from two separate field studies of SAG formations on Palmyra Atoll which show their effect on waves to be small, but reveal a persistent order 1 cm/s depth-averaged Lagrangian offshore flow over the spur and onshore flow over the grooves. This circulation was stronger for larger, directly-incident waves and low alongshore flow conditions, consistent with predictions from modeling. Vertical flow was downward over the spur and upward over the groove, likely driven by alongshore differences in bottom stress and not by vortex forcing. We suggest that the conditions for coral recruitment and growth appear to be more favorable on the spur than the groove due to (1) higher "food" supply from higher mean alongshore velocity, downward vertical velocity, and higher turbulence, and (2) lower sediment accumulation due to higher and more variable bottom shear stress. At large scales of order hundreds of meters to kilometers, the wave and mean flow dynamics of a pacific atoll are investigated. We report field measurements of waves and currents made from Sept-2011 to Jul-2014 on Palmyra Atoll in the Central Pacific that were used in conjunction with a coupled wave and three-dimensional hydrodynamic model (COAWST) to characterize the waves and hydrodynamics operant on the atoll. Bottom friction, modeled with a modified bottom roughness formulation, is the significant source of wave energy dissipation on the atoll, a result that is consistent with available observations of wave damping on Palmyra. Indeed observed and modeled dissipation rates are an order of magnitude larger than what has been observed on other, less geometrically complex reefs. At the scale of the atoll itself, strong regional flows create flow separation and a well-defined wake, similar to the classic fluid mechanics problem of flow past a cylinder. Circulation within the atoll is primarily governed by tides and waves, and secondarily by wind and regional currents. Tidally driven flow is important at all field sites, and the tidal phasing experiences significant delay with travel into the interior lagoons. Wave driven flow is significant at most of the field sites, and is a strong function of the dominant wave direction. Wind driven flow is generally weak, except on the shallow terraces. The near bed squared wave velocity, a proxy for bottom stress, shows strong spatial variability across the atoll and exerts control over geomorphic structure and high coral cover. Based on Lagrangian float tracks, the mean age was the best predictor of geomorphic structure and appears to clearly differentiate the geomorphic structures. While high mean flow appears to differentiate very productive coral regions, low water age and low temperature appear to be the most important variables for distinguishing between biological cover types at this site. The sites with high coral cover can have high diurnal temperature variability, but their average weekly temperature variability is similar to offshore waters. The mechanism for maintaining this low mean temperature is high mean advection, which occurs at timescales of a week, and is primarily governed by wave driven flows. The resulting connectivity within the atoll system shows that the general trends follow the mean flow paths; however, some connectivity exists between all regions of the atoll system.