A tale of two reefs : hydrodynamics of a fringing reef & a reef atoll

Coral reefs are some of the most biodiverse ecosystems on the planet and serve as natural breakwaters that protect our coasts from storm impacts. Due to their sessile nature, corals' ability to thrive is at the mercy of their physical environment; flow rates, temperature, and flushing of the water that surround them determine their health. In the past 6 thousand years with relatively stable sea level, coral have adapted to the changing ocean, but anthropogenic influence has led to oceanic changes at accelerated rates, which raises the question `how will reefs fair with the changing climate?' To answer this question, we first need to understand the physics that drive flow in reef systems. We can then apply this fundamental understanding to models that can forecast their future state. This dissertation reports field experiments that were conducted at two different reefs, in both cases with the goal of understanding their fundamental flow dynamics. These were: (1) a fringing reef in Ofu, American Samoa that is notable for being more hydrodynamically rough than are most fringing reefs that have been previously studied and are home to heat resilient corals; and (2) Scott Reef, a reef atoll off the coast of Australia, where previous work has observed corals with remarkable ability to recover from severe bleaching. Ultimately, the Ofu project sought to understand how the high hydrodynamic roughness affected the flow dynamics in a fringing reef lagoon system. The work included: (1) lagoon-scale circulation dynamics; (2) wave-driven flow dynamics on the reef flat; and (3) wave transformations across shore. We observed lagoon-wide wave setup that led to: rip-currents and undertow across the reef flat; along-reef flow on the reef flat; and, a momentum balance on the reef flat that differed from what is commonly observed on reef flats in reef-lagoon systems. The momentum balance on the flat was between an offshore pressure gradient force, an onshore radiation stress gradient, and a depth varying shear stress that led to development of an undertow. Additional observations included: baroclinic flow in the channel generated by heating of the shallow lagoon that led to a cross-shore temperature gradient; a transfer of wave energy from high to low frequencies; examination of the mechanisms leading to energy dissipation of short waves at cross-shore stations; and, identification of a divergent circulation pattern that creates `pools' in the lagoon. These pools were initially observed by biologists to be regions in the lagoon that contain genetically distinct coral ecosystems. The project at South Scott reef was designed to understand the thermodynamics on the atoll rim. Additionally, and unexpectedly, flows across the rim were found to be due to amplification in the lagoon of the local tide. On the shallow rim of the atoll, we found the heat budget to be a balance of advective heating, surface atmospheric heating, and local heating (unsteadiness). The momentum balance was between bottom friction and a pressure gradient force that was set by the difference in free-surface elevation due to tidal amplification in the lagoon. Pulses of cold water were also observed to travel down the forereef slope (oceanside), with a generation mechanism linked to the shallow rim water cooling at night and being pushed off by tidal flow. Lastly, the lagoon amplification generated higher high tides and lower low tides in the lagoon that led to a reversed tidal flow on the rim, where the tide flooded outward (toward ocean) and ebbed inward (toward lagoon). The amplification was associated with the wide deep sill opening at the north end of South Scott reef that allowed tidal flow to enter without attenuation, which is often observed in reef atolls. The amplification in the free-surface was associated with the deceleration of tidal flow as it approached the atoll rim.

Advisor: Monismith Stephen Gene 
Koseff Jeffrey Russell 
Lowe Ryan