3. The architects of a reef

Coral reefs are tropical ecosystems but show global patterns. The Caribbean has about 60 reef-building coral species, while Southeast Asia has nearly 1,000, this number broadly diminishing with distance east and west from the Southeast Asian region. Diversity of corals also diminishes broadly with distance north and south of the equator. While basic patterns exist, there are several kinds of reef in the same sense that there are different kinds of forests, sometimes forming near-monocultures, sometimes with more diverse mixtures of species. Their key to success is that they house vast numbers of captive dinoflagellates that photosynthesize in a close symbiosis, which explains how these complex ecosystems persist in the absence of substantial fields of large, visible seaweeds. All deposit limestone in its aragonite form, in a way characteristic to each species, which has been used for distinguishing between species. The basic unit of a coral, the polyp, reproduces sexually, but more importantly by asexual budding, which allows for the growth of large colonies of polyps, all clones. Numerous other organisms have crucial associations with the coral polyp: bacteria and archaea especially, the whole forming what is now termed the coral holobiont. Aside from photosynthesis, corals have nematocysts in their tentacles to capture zooplankton food. Corals compete for space using these stinging cells also, amongst other methods. On any reef, soft corals are numerous, especially in the Caribbean, though these do not deposit limestone rock. Calcareous algae are crucial reef-building components too, particularly in the shallows.

2. Ancient reefs and islands

Reefs in deep geological time have been built by a succession of different kinds of life: plant, bacterial, and animal. Stromatolites and bryozoans were major reef-builders that persist today in minor or non-reef-building forms, sponges built entire reefs and are still important reef components, while several groups of major reef-builders flourished for a while and then became extinct: archaeocyathids which were similar to sponges, and coral-like forms including rugose and tabulate corals. Today’s reef-builders, cnidarian corals, appeared well after the great Permian-Triassic extinction event. All of these groups deposited vast quantities of limestone rock on which they live, often visible today as low mountain ranges. Reefs grow to the surface but not beyond, but upon them sand and sediments may build up, forming an island that attracts plants, then birds and other terrestrial forms of life. The sediments become cemented with the aid of rainwater too, and ‘low islands’ develop. Many islands also show their old, central volcanoes, resulting in the vast array of different combinations of coral island type. Today, however, there is a coral reef crisis due to overexploitation of a reef’s rich resources, from pollution of several kinds, and climate change.

4. The resulting structure—a reef

Reef profiles are remarkably consistent in general design because they are essentially biological constructions responding to environmental factors. All have reef flats, a horizontal expanse at low tide level that develops when the reef can no longer build upwards and extends horizontally. This is commonly the largest expanse and is the only part that early naturalists could examine until the advent of scuba diving relatively recently. However, it is always relatively depauperate because of the extremes of heat, salinity, and light that affect it. To seaward is the reef crest, commonly constructed by calcareous red algae that are the only form of life that can withstand the severe waves that pound the reef. To seaward of the crest, the reef slopes downwards, and is where environmental conditions are most benign and where the greatest biodiversity is found. The rugosity or 3-D structure of a reef is a key factor in reef biodiversity because it provides a vast number of niches for the huge diversity of life. Reefs are constantly subjected to erosion from burrowing and tunnelling forms, whose activity creates sand and sediment. This is then forced into crevices or pushed up onto the island behind it, so this erosion is also the starting point for further reef and island construction. Expanses of sand are associated with all reefs, and are home to another rich assemblage of species.

1. Geology or biology?

For centuries, reefs were used and valued for their food and shelter from storms, though for mariners they were a constant danger to be avoided because of their position at shallow depths in tropical seas. Scientific understanding started with European travellers trading with the Caribbean region and then with traders going eastwards to the Indian and Pacific oceans, especially when naturalists, commonly sponsored by patrons, accompanied the traders. The main questions included how the obviously living veneer could make the vast amounts of rock, as well as what the huge variety of sea creatures were. Darwin was the most famous naturalist who became intrigued by them and, following his Beagle voyage, he formed his theory of how they developed, which was proved true a century later. The basic underlying mechanism he proposed unified how they grew and why reefs around the world had so many common characteristics, especially why they nearly all had a similar depth and profile.

8. Global scale pressures on reefs—climate change

Ocean temperatures are rising. This is critical for corals and other reef organisms because most live very close to their thermal limits already. The rise is caused by the greenhouse effect from increasing CO2 emissions. Superimposed on a general background rise caused by the general increase in heat content of the world are pulses—ocean heatwaves—caused by vagaries in ocean circulation. Globally, this is now the greatest threat to reefs. Warming pulses cause mass coral bleaching and mortality when the overstressed symbiotic algae are expelled from the corals, showing the white limestone beneath the now transparent coral tissue. All coral reef areas of the world now exhibit mass bleaching events. Recovery of a reef is possible, but only if given some decades of stable temperatures, and predictions are that warming events are occurring increasingly frequently and are of increasing severity. Coral cover on reefs in all reef areas is declining sharply. Seawater also becomes increasingly acidic, which impedes coral calcification. Added to this, there is a lag of 20–40 years for carbon dioxide in the air to equilibrate with the ocean, so even were there to be a cessation in the rise in the atmosphere today, these effects would continue to develop for a few decades more. 350 parts per million CO2 is considered to be a threshold concentration for calcification to be possible but already the atmosphere is at about 415 ppm. Sea levels are rising too as a result, and reefs are degrading and losing their ability to act as breakwaters.

7. Regional scale pressures on reefs

One consequence of the extremely high biodiversity found on reefs is the enormous number of interlocking connections between components. But connections can be destroyed by many kinds of stressors such as pollutants, as can the species themselves. Some species or processes have high redundancy—if destroyed others can fill their role on a reef—while other species or processes may be more or less irreplaceable, in which case when they are destroyed key processes maintaining a healthy reef can be destroyed too. Because so many countries and human communities are dependent on reefs, reef degradation, which is now occurring on a very worrying scale, is of increasing concern. Impacts fall into two main categories: those caused by numerous, usually localized, impacts, such as different forms of pollution and shoreline developments that create large quantities of sediment; and those caused by the more recently recognized, and probably more serious, long-term factors associated with climate change. All of these are ultimately interlinked and all are caused by human activities. Many occur concurrently, each exacerbating the harmful effects of others, and many are synergistic in their impacts. Sewage, nutrient run-off, landfill, dredging, and sedimentation are most important, as are chemicals, pesticides, and metals. Coral diseases are increasing also, commonly as a result. In many areas now too overfishing has become critical and may be the most ecosystem-distorting factor of all.

6. Reef fish and other major predators

Fish, like corals, have geographical patterns across regions and across individual reefs, being structured in the latter case by wave energy and depth. The thousands of species show a variety of feeding patterns. Detritus feeders are very abundant, feeding on the detritus on the seabed, especially in the fine, filamentous algal turf on apparently bare rock. Plankton feeders are common also, and herbivorous fishes show a large abundance, perhaps a quarter of the total species present, cropping algae that otherwise would grow unchecked and smother coral. Since turf algae also contain many micro-species and detritus, most herbivores also ingest much food other than simple plant material. Carnivores range from extreme specialists, such as polyp-picking butterflyfish, to generalists. Sharks and barracuda only consume other fish and generally are at the top of their food chains. The complicated ecological structure of the food webs can be clarified by analysing nitrogen isotope ratios in their tissues. Other important coral carnivores include the crown of thorns starfish, which can remove almost all living coral on a reef when it develops into plagues. Overfishing by humans greatly disturbs the equilibrium of a reef, and this is increasingly causing reef degradation.

9. Doing something about it

Several political instruments are in place to tackle effects of climate change and help arrest the global decline of coral reefs. Unfortunately, most are inadequate and anyway are being ignored by many important nations. Rising ocean temperatures are not linear, but act in pulses, so that reefs degrade in steps rather than smoothly. Terminally degraded reefs are now common, and those in very good condition are rare. Several potential solutions have been proposed, none being adequate alone but all being needed to arrest the decline. Arresting the rise in CO2 is a key, long-term requirement, yet levels of this gas are still increasing, as are local requirements such as effective pollution and overfishing controls. Also important is limiting resource extraction, which essentially means limiting human populations. Most scientists consider saving coral reefs now to be a political and sociological problem, not a scientific one. We have lost nearly half the world’s coral reefs and if societies cannot act in what is becoming a diminishing window of opportunity, we will lose most of the rest within another human lifetime.

5. Microbial engines of the coral reef

The symbiosis between corals and the dinoflagellates—zooxanthellae—is the key to a tight recycling of nutrients on reefs that generally thrive best in nutrient poor parts of the oceans. But several other mechanisms and species groups aid transmission of organic matter and energy along the numerous food chains of a reef. Viruses, bacteria, and archaea are key to the recycling of carbon and organic compounds, making the ‘microbial loop’, one key but invisible aspect to how the reef functions. Cyanobacteria, formerly blue-green algae, are a major part of the micro-benthos too, and are important primary producers. Protists are also hugely abundant—larger, single-celled organisms which are eukaryotes with cells with nuclei, and this group has species that exist in planktonic and benthic forms. Foraminifera are important protists, being abundant and having calcareous tests, so that they are significant sand producers in some areas. Finally, zooplankton provide food for numerous reef species, and indeed larvae from all species form part of the plankton temporarily too.