Calcification is highest in the warm, sunlit waters of the tropics and subtropics where the concentrations of calcium and carbonate ions are highest. As discussed in Chapter 2, these three factors are considered to be the major determinants for where coral reefs grow, with waters becoming the too cold, dim and low in the abundance of these crucial ions as one goes poleward. This association of calcification with low latitude environments appears to have held for many hundreds of millions of years, resulting in huge deposits of calcium carbonate within the Earth's geological structure.

The organisms that calcify on coral reefs are diverse and include a large number of phyla including cnidar-ians, molluscs, crustaceans and foraminifera as well as green and red algae. Many of the organisms that calcify at high rates are also symbiotic with dinoflagellates such as Symbiodinium (see Chapter 7). This association with organisms having high photosynthetic capabilities is considered to be indicative of the high energy requirements of the calcification process. These organisms take up calcium and carbonate ion from the super-saturated concentrations typical of tropical and subtropical waters, depositing either calcite or aragonite (two forms of calcium carbonate crystals). The form of calcium carbonate deposited depends mostly on the organism involved. Corals, for example, deposit aragonite while red coralline algae deposit Mg-calcite.

Organisms use calcium carbonate to create skeletons that either provide rigid support structures and/ or protective shells or cases. These functions are likely to be crucial in the highly dynamic coral reef ecosystem, where competition and predation can be high.

The mechanism by which organisms produce calcium carbonate skeletons has yet to be conclusively determined. Within the water column of tropical and subtropical oceans that is saturated with respect to both calcium and carbonate ions, there appears to be three possible ways in which a high rate of precipitation can be fostered. The first depends on bulk metabolic energy to concentrate calcium and carbonate ions within confined spaces and subsequently to cause a rapid precipitation of aragonite or calcite. The second is that the symbionts assist by removing so-called 'crystal poisons' such as phosphate that otherwise retard the formation of crystals. The third is the production of specialised proteins that are often referred to as 'skeletal matrix proteins'. These particular proteins tend to be highly anionic (covered in negative charges) and contain regions that are associated with enzymes such as carbonic anhydrase (that catalyses the rapid conversion of carbon dioxide to bicarbonate and protons, a reaction that occurs rather slowly in the absence of a catalyst). Although there is some debate over which is more important, there is good evidence that all of these processes may play roles of differing importance within the variety of organisms that calcify within coral reef environments.

There are a number of ways calcium carbonate deposition is measured. These are outlined in Box 8.1. The rates of calcification on coral reefs can be extremely high in equatorial or low latitude areas of the planet. On a more regional scale, the deposition of calcium carbonate varies with the presence or absence of rivers, where high nutrients and sedimentation may slow the deposition of calcium carbonate. In this respect, inshore coral reefs on the GBR do not deposit calcium carbonate as fast as those reefs that are in more offshore positions. Again, this is a consequence of changes in factors such as light, temperature and nutrients. At the scale of a reef, calcium carbonate deposition can be quite dynamic and will vary between the slope, crest and back-reef areas as discussed already in Chapter 7. Coral reefs are also dynamic in geological time frames, with the shape of deposited calcium carbonate varying over time in response to prevailing winds and currents. These aspects of reef construction are discussed in Chapter 2.

The skeletons of calcifying organisms build up and construct the accumulated calcium carbonate debris that constitutes the solid component of the framework of coral reefs. Calcifiers on coral reefs can have different roles, for example the massive and branching structures provided by corals require the activities of encrusting red algae to essentially glue them into a consolidated framework (Fig. 8.1A). The rate of calcification normally greatly exceeds the rate of erosion on carbonate coral reefs. Estimates of calcification suggest that rates vary from 1-2 m per century while rates of reef growth are about 1-2 m per millennium. Based on these rough figures, this would suggest that rates of calcification are between 3-10 times higher than the rate at which calcium carbonate is removed by physical and biological erosion. As we will see later in this chapter, the balance between the two forces (calcification versus erosion) is critical to understanding the impacts of global change, such as ocean acidification.

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