No abstract

Scott Reef is a remote yet biodiverse coral reef atoll, rising from depths > 1000 m on the edge of the continental shelf of northwestern Australia. An intensive 2‐week field study was conducted to assess how physical oceanographic processes influence reef communities in South Scott's deep (~ 50 m) and expansive (~ 300 km2) semi‐enclosed lagoon. The study covered a spring–neap tidal cycle, during which moored instruments measured temperature and velocities at a lagoon entrance and ship‐based vertical profilers measured water quality parameters. Tidally driven internal bores advected cooler and deeper offshore waters (up to 4.5°C, mean 2.4°C) into the lagoon, which were also richer in nutrients and chlorophyll a than lagoon waters. This offshore water originated from approximately 75 m depth. We used the strong observed relationship between in situ measurements of nitrate and temperature to estimate nitrate concentrations from high temporally and spatially resolved temperature measurements at the lagoon entrance, and then estimated the horizontal nitrate fluxes into the lagoon using the velocity measurements. The depth‐integrated, time‐averaged nitrate flux during spring tides (1.46 kg m−1 d−1) was over three times larger than during neap tides (0.46 kg m−1 d−1), despite a passing tropical storm that temporarily deepened the offshore thermocline and reduced the magnitude of the fluxes. Our observations indicate that colder, deeper, and nutrient‐rich water associated with internal tidal bores during spring tide is likely to be the primary mechanism through which allochtonous nutrients are delivered to benthic and pelagic communities within the lagoon of this isolated atoll.

Interactions between oceanic and atmospheric processes within coral reefs can significantly 2 alter local scale (< kilometers) water temperatures, and consequently drive variations in heat stress and bleaching severity. The Scott Reef atoll system was one of many reefs affected by the 2015-2016 mass coral bleaching event across tropical Australia, and specifically experienced sea surface temperature anomalies of 2°C that caused severe mass bleaching (61-90%) over most of this system; however, the bleaching patterns were not uniform. Little is known about the processes governing thermodynamic variability within atolls, particularly those that are dominated by large amplitude tides. Here we identify three mechanisms at Scott Reef that alleviated heat stress during the marine heatwave in 2016:1) the cool wake of a tropical cyclone that induced temperature drops of 1.3°C over a period of 10 days; 2) air-sea heat fluxes that interacted with the reef morphology during neap tides at one of the atolls to reduce water temperatures by up to 2.9°C; 3) internal tidal processes that forced deeper and cooler water (up to 2.7°C) into some sections of the shallow reefs.The latter two processes created localized areas of reduced temperatures that led to lower incidences of coral bleaching for parts of the reef. We predict these processes are likely to occur in other similar tide-dominated reef environments worldwide. Identifying locations where physical processes reduce heat stress will likely be critical for coral reefs in the future, by maintaining communities that can help facilitate local recovery of reefs following bleaching events that are expected to increase in frequency and severity in the coming decades.

The hydrodynamics of a tidally forced semi-enclosed coral reef atoll (North Scott) at the edge of the continental shelf of northwestern Australia were investigated by combining field observations and numerical modeling. The observations revealed that the spring tidal range outside the atoll reaches 4 m, and as the water level drops below mean sea level, the reef rim surrounding the shallow (~10-15 m) lagoon becomes exposed. During this time, the lagoon can only exchange with the open ocean through two narrow channels, resulting in highly asymmetric water levels and velocities that were most pronounced during spring tide. On average, the ebb tide duration was~2 hr longer than the flood, with rapid flood velocities in the channel reaching 2 m/s. We applied an unstructured grid model Delft3D-Flexible Mesh to simulate the atoll hydrodynamics and were able to replicate the asymmetric water levels and complex velocities in the lagoon. The results revealed that at higher tidal stages, a dominant momentum balance exists between the pressure gradient (established by the propagation of the tide on the shelf) and the local flow acceleration of water throughout the interior of the atoll. At lower tidal stages, which coincided with a reversal of the offshore tidal pressure gradient, the lagoon became isolated from offshore dynamics and all momentum terms were negligible. This resulted in a tidally averaged residual westward flow within the lagoon that drove an asymmetric flushing pattern within the atoll, which we propose would be a common flushing mechanism within other tide-dominated atolls worldwide.Key Points:• The hydrodynamics of a tide-dominated atoll reef system were assessed with field observations and numerical modeling • The semi-enclosed atoll morphology and large tidal range resulted in highly asymmetric water levels, velocities, and residual flows • A residual east-west flow, caused by interactions between the phasing of the ocean tide and lagoon water levels, dominated flushingSupporting Information:• Supporting Information S1

Wave breaking on reefs, many of which have steep slopes, results in elevated mean water levels (or wave setup) across the reef, which can drive mean flows over the reef and inside adjacent lagoons (if present) (e.g., Lowe & Falter, 2015;Monismith, 2007). The mean flows and setup dynamics in such environments have been found to greatly depend on the reef properties at both large scales (reef geometry and bathymetry Abstract Two-dimensional mean wave-driven flow and setup dynamics were investigated at a reef-lagoon system at Ningaloo Reef, Western Australia, using the numerical wave-flow model, SWASH. Phase-resolved numerical simulations of the wave and flow fields, validated with highly detailed field observations (including >10 sensors through the energetic surf zone), were used to quantify the main mechanisms that govern the mean momentum balances and resulting mean current and setup patterns, with particular attention to the role of nonlinear wave shapes. Momentum balances from the phaseresolved model indicated that onshore flows near the reef crest were primarily driven by the wave force (dominated by radiation stress gradients) due to intense breaking, whereas the flow over the reef flat and inside the lagoon and channels was primarily driven by a pressure gradient. Wave setup inside the lagoon was primarily controlled by the wave force and bottom stress. The bottom stress reduced the setup on the reef flat and inside the lagoon. Excluding the bottom stress contribution in the setup balance resulted in an over prediction of the wave-setup inside the lagoon by up to 200-370%. The bottom stress was found to be caused by the combined presence of onshore directed wave-driven currents and (nonlinear) waves. Exclusion of the bottom stress contribution from nonlinear wave shapes led to an over prediction of the setup inside the lagoon by approximately 20-40%. The inclusion of the nonlinear wave shape contribution to the bottom stress term was found to be particularly relevant in reef regions that experience a net onshore mass flux over the reef crest.Plain Language Summary Coral reefs that are located in close proximity to a coastline are typically characterized by a steep slope and reef crest that is connected to the coast or front a shallow lagoon. At the reef crest, waves break and drive onshore-directed currents and elevate the mean (timeaveraged) water level in the lagoon. In this study, we combined measurements of waves, currents and water levels with simulations from an advanced computer model to understand the physical mechanisms that determine the current patterns and water level variations at a coral reef-lagoon system in Western Australia. Friction generated by the water moving over the rough reef structures was found to reduce the mean water levels inside the lagoon. This friction was explained by the combined presence of both waves and mean currents. Furthermore, near the reef crest, the waves peak and pitch forward before they break, and this nonlinear wave shape was found to enhance the friction from ...

This study uses numerical modeling to study hydrodynamic drivers of fine-scale connectivity within a coral reef atoll off the North West Shelf of Australia.

Waves and tides are often the two primary forcing mechanisms responsible for driving hydrodynamic processes within coral reefs worldwide. Although wave‐ and tide‐driven flows are individually well understood, there remain considerable gaps in our understanding of how their interactions control the reef circulation, and consequently how they shape a range of ecological processes. During 11 months of hydrodynamic measurements across Mermaid Reef, a coral reef atoll off northwestern Australia, the atoll was regularly exposed to a range of wave and tidal conditions. Using a validated wave‐flow numerical model, we showed that wave‐ and tidally driven processes interacted to drive the reef's circulation through several mechanisms including wave‐current interactions and tidal water level modulation of wave‐driven flows. The atoll morphology, particularly the higher elevation of the western reef flat, was found to be a key factor controlling the relative importance of waves and tides. Wave‐driven processes dominated for tidal ranges smaller than required to expose the shallower western reef flat. In contrast, tidal processes dominated for larger tidal ranges, when the western reef flat temporarily acted as a physical barrier to incoming and outgoing flows. The residual (tidally averaged) circulation was consistently directed eastward across the atoll. Over time scales of several months to years, Mermaid Reef can be classified as a tide‐dominated reef. However, due to the incident wave energy and spring‐neap tidal range variability, the relative importance of the dominant hydrodynamic drivers can vary on time scales of hours to days allowing wave processes to episodically dominate the reef circulation.

Coral reefs have evolved over millennia to survive disturbances. Yet, in just a few decades chronic local pressures and the climate catastrophe have accelerated so quickly that most coral reefs are now threatened. Rising ocean temperatures and recurrent bleaching pose the biggest threat, affecting even remote and well-managed reefs on global scales. We illustrate how coral bleaching is altering reefs by contrasting the dynamics of adjacent reef systems over more than two decades. Both reef systems sit near the edge of northwest Australia's continental shelf, have escaped chronic local pressures and are regularly affected by tropical storms and cyclones. The Scott reef system has experienced multiple bleaching events, including mass bleaching in 1998 and 2016, from which it is unlikely to fully recover. The Rowley Shoals has maintained a high cover and diversity of corals and has not yet been impacted by mass bleaching. We show how the dynamics of both reef systems were driven by a combination of local environment, exposure to disturbances and coral life history traits, and consider future shifts in community structure with ongoing climate change. We then demonstrate how applying knowledge of community dynamics at local scales can aid management strategies to slow the degradation of coral reefs until carbon emissions and other human impacts are properly managed.