Tropical Marine Ecology. Daniel M. Alongi

FIGURE 4.7 Schematic of an idealised coral reef showing various reef zones from the reef front to the back reef. Zones are not to scale.

      The geological development of coral reefs is controlled by temperature, nutrient availability, hydrology, and changes in sea‐level and ocean chemistry. Most research has focused on sea‐level changes in relation to ancient reef development and evolution (Montaggioni and Braitwaite 2009). Changes in sea‐level are related to the availability of habitats suitable for coral reef development and such changes, when large enough, have triggered mass extinctions (Chapter 5).

      Biotic controls play a role in reef development (Montaggioni and Braitwaite 2009). The evolutionary history of coral reefs shows an increase in biological disturbance such that there was an increase during the Cretaceous and Cenozoic in predators specialised for corals, including bioeroders and herbivores. These specialised organisms influenced the community structure of coral reef ecosystems. Such organisms limit the distribution and abundance of sessile organisms, such as corals, which require a stable substrate and quiescent sedimentological conditions.

      Coastal lagoons can be most simply defined as natural enclosed or semi‐enclosed water bodies parallel to the shoreline. Lagoons are sometimes confused with other coastal ecosystems, such as estuaries and coral reef lagoons. Thus, coastal lagoons can be most precisely defined as ‘shallow aquatic ecosystems that develop at the interface between coastal terrestrial and marine ecosystems and can be permanently open or intermittently closed off from the adjacent sea by depositional barriers’ (Esteves et al. 2008). The waters of coastal lagoons can span the range of salinities from fresh to hypersaline depending on the balance of hydrological drivers, including local precipitation, river inflow, evaporation, groundwater discharge, and seawater intrusion through or directly via the depositional barrier.

The geophysical characteristics that contribute to the formation and maintenance of a coastal lagoon are important and help in identifying different types of lagoons (Eisma 1997). The first characteristic is whether the coastal lagoon has a connection to the sea. Some lagoons are lentic non‐tidal, that is, without permanent connection to the sea or lentic micro‐tidal, permanently connected to the sea. The second characteristic of a coastal lagoon is its origins. Most lagoons have originated from the flooding of lowland coastal areas due to the global rise in sea‐level during the Late Quaternary marine transgression (Esteves et al. 2008). Lagoons originating in this way generally have large surface areas and are located parallel to the coastline which increases the probability for marine intrusions through or over the depositional barrier. Other lagoons have originated by the build‐up of sediments at the mouths of rivers due to the working of waves and tides to form a barrier. Such lagoons have a branched configuration and a high perimeter to area ratio and are formed by the flooding of river valleys. Due to their geomorphology, high levels of dissolved and particulate materials from land enter such coastal lagoons.

      Perhaps no other coastal environments are as complex as coastal lagoons. The heterogeneity of geomorphologies observed among coastal lagoons has created a vast array of physicochemical and ecological gradients and microhabitats crucial in supporting fisheries and humans. Coastal lagoon complexes exist in many dry tropical regions, originating as wave‐cut terraces when sea‐levels were lower during the Pleistocene glaciations (Eisma 1997). In the Arabian Gulf, for instance, marine terraces or ‘sabkhas’ surround these high salinity lagoons. Aeolian dunes migrate across the terraces under the influence of NW or ‘shamal’ winds. Other high salinity lagoonal pools are equally ancient, formed by similar sea‐level changes isolating areas behind raised coral reefs receiving a subterranean supply of seawater seeping through coral stone.

      Not all coastal lagoons are hypersaline. Large stretches of the Pacific coast of Mexico consist of lagoons frequently lying between rivers and connected by ‘esteros’, narrow and winding sea channels which permit ocean water to enter as a typical salt wedge and having all the characteristics of stratified estuaries. Salinities vary in relation to the dry and wet seasons. Lagoons in the wet tropics are frequently oligohaline for long periods of time. The lagoons along the north coast of the Gulf of Guinea (Ivory Coast) are situated in an equatorial climate where the annual rainfall is about 2000 mm. In Ebrié Lagoon, the largest of three main gulf systems, temperature varies little, but salinity varies with season and in different parts of the lagoon, ranging from euryhaline to oligohaline (Albaret and Laé 2003). The lagoon, like most lagoons worldwide, is frequently deoxygenated by pollution and by lack of circulation in the deeper areas. Coastal lagoons experience forcing from river inputs, wind stress, tides, the balance of precipitation to evaporation, different salinity regimes, and many human‐induced changes, all of which make each lagoon unique. This is probably why no universal classification scheme for coastal lagoons has ever been developed.

Abiotic factors are central to understanding the myriad properties of coastal lagoons. Flushing of a lagoon maintains water quality and physicochemical conditions and provides a mechanism for the import and export of nutrients, plankton, and fish. The overall characteristics of a lagoon are determined by salt and heat fluxes controlling warming and cooling. Geomorphological factors that play important roles in coastal lagoons include inlet and outlet configuration, lagoon size and orientation with respect to wind direction, bottom topography, and water depth. The size of the inlet/outlet controls the exchange of water and associated dissolved and suspended material and biota. The effects of sand bar openings can have a significant effect on physicochemical variables but can also have effects on the biota. For instance, the spatial variation in pH, dissolved oxygen, and nutrients in a hypertrophic coastal lagoon in Brazil (the Grussai lagoon) was linked to anoxic and nutrient‐rich groundwater discharge, the development of aquatic macrophytes, the biological activities of the phytoplankton community, and marine inputs (Suzuki et al. 1998). Whenever the sand bar closes, and the lagoon is cut off from the sea, the lagoon water becomes supersaturated with dissolved oxygen, exhibiting high pH and chlorophyll a, and low levels of dissolved nutrients. When the passage re‐opens, there is an enrichment of dissolved inorganic nutrients and a decrease in pH and in dissolved oxygen. Within a few days, marine conditions return suggesting that biological mechanisms in the lagoon are highly efficient. Groundwater can play an equally important role in forcing physiochemical conditions in some lagoons. For example, there are two different types of groundwater in the Celestun Lagoon, Mexico: one derived from springs within the lagoon and a second characterised by moderate salinities compared to the low‐salinity groundwater, mixed lagoon water, and seawater (Young et al. 2008). Groundwater discharge occurs through small and large springs scattered throughout the lagoon and the relative proportions of low versus moderate salinity groundwater vary over the tidal cycle. Substantial groundwater discharges can occur during both the dry and rainy seasons and can have a huge impact on nutrient concentrations and salinity in the lagoon.

The main boundaries of the coastal ocean (Figure 4.8) encompass the upper limit at the tidal freshwater zone (1) down to the river, estuary, and adjacent inner shelf waters, (2) with the seaward limit at the coastal boundary layer, (3) which is often delineated by a tidal front. These areas comprise the coastal zone where the seaward limit is dynamic, oscillating over time and space, especially in the wet season when it is displaced further seawards and the actual boundary layer breaks down. Boundary layers are formed when turbid coastal waters are mixed and trapped along the coast during calm conditions. These boundary layers break down not only during periods of high river discharge but also during periods of sustained strong winds. The coastal zone varies greatly in length and breadth depending on the strength and characteristics of local coastal circulation, river discharge, shelf width, climate, and latitude. On a semi‐arid or arid continental shelf, the coastal zone may not be located close to shore as such shelves are often macro‐tidal,