Tropical Marine Ecology. Daniel M. Alongi

baroclinic circulation but also as the result of tidal pumping and mixing, especially in the turbidity maximum zone. A turbidity maximum zone is formed within an estuary where the residual inward bottom flow meets the outflow river flow. This zone is usually at the most landward point reached by the saline water flow. The water is generally shallowest at this point because this is a convergence point where sediment accumulates, the bulk of which creeps along the bottom. Some suspended matter settles here as the net current velocities in the zone are low; the zone is not stationary but moves with tidal ebb and flood.

      In relation to the turbidity maximum, flocculation of particles begins at salinities often <1; the largest flocs remain near the river bottom. The small flocs and unflocculated particles move further downstream with the currents where they aggregate with local particles (Gratiot and Anthony 2016). As floc size increases, they move towards the riverbed where they are entrained upstream by the baroclinic circulation. Due to tidal pumping, these flocs are carried further upstream at flood tide rather than downstream at ebb tide. The flocs are a loose matrix of clay and silt particles, typically a few micrometres in diameter, with their small size controlled somewhat by the strength of the tidal currents. Disaggregation starts when tidal velocities exceed 1 m s⁻¹. During spring tides, flocs are typically between 15 and 40 μm in diameter and are larger during neap tides. These flocs are colonised by bacteria, protists, and fungi and their extracellular mucus and threads, which help to cement the flocs and to maintain size when subjected to turbulence. Within the forest, flocs can remain in suspension owing to turbulence generated by flow around the trees. The settling of flocs occurs for a short period when the tides turn from rising to falling and the waters are quiescent. Settling is facilitated by the sticking of microbial mucus and by formation of invertebrate faecal pellets.

      It is thus correct to state that mangroves actively help to settle fine particles and are not just passive importers. The size, shape, and distribution patterns of mangrove trees have a profound impact on sedimentation. Tree species with large above‐ground root systems, such as Rhizophora, facilitate the deposition of particles to a much greater degree than tree species without extensive roots. The flocculation of particles results in faster settling velocities; most flocs settle within 30 minutes just before high slack tide. Until slack water, turbulent wakes created by tree trunks, roots, and pneumatophores maintain particles in suspension. Once in the forest, however, conditions are unfavourable for them to be resuspended as the high vegetation density inhibits water motion.

3.5 Coral Reef Hydrodynamics

The circulation of water in and around an individual coral reef is similarly complex and is central to understanding the high biodiversity and grandeur of these beautiful structures and their food webs. From individual coral colonies to entire coral reefs, hydrodynamics regulate their structure and function. Unlike mangroves, coral reefs thrive in highly physical conditions where water rapidly circulates and where residence times are short (Monismith 2007).

      At the scale of an individual branching coral, denser branching tends to divert more water flow to the exterior, whereas coral geometries with less dense branching allow more flow through the interior (Reidenbach et al. 2006). At a finer scale, branches create wakes that lead to blocking of interior flows. In the presence of waves, the flow through a coral colony is different, with the velocities inside the colony like those outside the colony. As colonies are living structures, flow variations inside the colony may induce localized calcification and a specific growth form or may lead to branch orientation that optimises functions such as the capture of prey or the uptake of nutrients. With higher flow velocities, the coral skeleton invariably becomes uniformly thicker, reducing the spaces between branches. This phenomenon suggests the possible importance of internal translocation of nutrients, etc., in the tissue layer that connects the polyps of a colony. Coral skeletal growth is often positively related to mean current velocity and to velocity fluctuations (Lenihan et al. 2015). Corals thus benefit directly from increased currents, probably through enhanced autotrophy (i.e. photosynthesis of coral symbionts) and/or heterotrophy (feeding on particles and living organisms) and indirectly by reduced feeding on corals by corallivorous fish.

      At the scale of 1–10 m, bottom drag is critical in water circulation. The bottom drag coefficient, C_D, for coral reefs is roughly 10 times greater than for a sandy unconsolidated seabed (Rosman and Hench 2011). Because of this roughness and because of the complex nature of corals, reefs have much higher transfer rates of water flow than predicted by simple engineering models. Waves are the dominant water feature of corals at this scale. Indeed, nutrient uptake is linked directly to the wave regime of the reef. However, as roughness increases, mass transfer is reduced, that is, water movement decreases. Lower parts of the rough coral surface are sheltered from wave action, that is, velocities of water movement are higher near the tops of coral colonies than in the troughs between colonies. As greater roughness leads to greater water motion, this has the practical result of making grazing by corals more efficient. Turbulence produced by the coral reef also affects the uptake and kinetics of the rate that particulates suspended in the water column can be grazed by the reef community. As a reef grows and becomes rougher, it can support denser benthic assemblages, such as sponges, which in turn leads to a richer reef community.

      At the scale of 100–1000 m, waves dominate coral reefs. The basic pattern is that incident waves break over the offshore face of the reef front and pushes water over the reef flat and then into the lagoon (if there is one). There are two regimes of flow behaviour when water flows over the front and the reef flat: (i) reef‐top control, when the reef flat flow is in a friction–pressure gradient balance when the mean water level is sufficiently above the reef flat and (ii) reef‐rim control, when the lagoon end of the reef flat determines the depth of the overall flow when the mean water level is at or below the reef flat (Gourlay 1996a,b). In the latter situation, wave breaking occurs on the reef front and wave‐driven flow is due to swash running up and onto the reef flat.

When the depth over the reef is shallow, flows will be weak due to the friction of the reef flat, whereas if water is deep over the reef, flows will be weak because of limited wave breaking (Hearn 2011). There will thus be a water depth at which the wave‐driven flow is maximum. Tidal variations also induce variations in mean flows over a reef as tides will vary the water depth over the reef front and reef flat thereby affecting water flow. For instance, in the Puerto Morelos fringing reef lagoon off Mexico where tides are small, surface wave‐induced flow is the predominant flux with some influence from the Yucatán Current (YC) and trade winds (Coronado et al. 2007). The wave flow regime is modulated by the presence of the YC offshore. Similarly, cool, clear water flow up onto the flat of the fringing coral reef off the south coast of Molokai, Hawaii, during flood tide (Storlazzi et al. 2004). At high tide, sediment resuspension increases due to greater wave energy being available to propagate onto the reef flat. Trade‐wind driven surface currents and wave breaking at the reef front cause increasing water depth on the reef flat, enhancing the development of depth‐limited waves and sediment resuspension. As the tide ebbs, water and suspended sediment flow off the reef flat and is advected offshore and to the west by trade winds and tidally driven currents. Thus, the muddy, shallow reef flat is linked to suspended sediments on the deeper reef front where coral growth is maximal.

      Each coral reef is unique, but water flow on all reefs conforms roughly to the same general pattern of water flow impinging on the reef front and flowing over the reef flat and attenuating into a lagoon or back reef. Water circulation in reef lagoons is rapid compared to adjacent oceanic waters, but reef lagoons are quiescent and usually deep enough to accumulate unconsolidated carbonate mud and sand deposits.

      Water circulation in and around coral reefs thus depends greatly on reef type and geomorphology. Reefs fringing a shoreline such as the fringing reefs of Pago Bay, Guam, have a simpler hydrology than an individual oceanic reef; water flow on the Pago Bay reefs is driven mainly by wave height in the reef flat and channel (Comfort et al. 2019). Wind and wave directions that are directly across‐shore contribute to faster flow speeds throughout the bay. On the fore reef, wave height is the strongest predictor of current speed, but wind direction has a strong influence on current direction. Flow in the channel and on the reef flat is more tightly tied to environmental factors of wind and waves than flow on the fore reef. Cold