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Original environment rehabilitation manual 3.34
Human activity may represent the greatest threat to coral reefs. In particular, coral mining, pollution (organic and non-organic/chemical), over-fishing, blast fishing and the digging of canals and access into islands and bays are serious threats to these ecosystems. Coral reef also face high dangers from pollution, diseases, destructive fishing practices and warming oceans." In order to find answers for these problems, researchers study the various factors that impact reefs. The list of factors is long, including the ocean's role as a carbon dioxide sink, atmospheric changes, ultraviolet light, ocean acidification, biological virus, impacts of dust storms carrying agents to far flung reefs, pollutants, algal blooms and others. Reefs are threatened well beyond coastal areas.
The use of cyanide has been implicated as a driver of decline. Hughes, et al., (2003), write that "with increased human population and improved storage and transport systems, the scale of human impacts on reefs has grown exponentially. For example, markets for fish and other natural resources have become global, supplying demand for reef resources."
Overfishing (and particularly selective overfishing) results in excessive growth of organisms that can damage the reef if they appear in great numbers. For example overfishing of bullet fish, Balistidae and other natural predators such as lobsters  promote the growth of sea urchins. Also, overpopulation of acanthaster planci, Drupella, Tapiro, Terpios, and Rhodactis can destroy reefs.
Although a few fish species (e.g. Pomacentridae) can reproduce in aquaria, 95% are collected on the reef. Intense harvesting, especially in South-East Asia (including Indonesia and the Philippines), severely damages the reefs. A major catalyst of cyanide fishing is poverty within fishing communities. In areas like the Philippines where cyanide is regularly used, the percentage of the population below the poverty line is 40%. In such developing countries, a fisherman might resort to such practices in order to protect his family from starvation.
Most, 80–90%, of aquarium fish from the Philippines are captured with sodium cyanide. This toxic chemical is dissolved in sea water and released into fish shelters. It narcotizes fish, which are then easily captured. However, most fish collected with cyanide die a few months later from liver damage. Moreover, non-marketable species die in the field.
Pollution from land-based sources is a primary cause of coral reef degradation throughout the world. 
Some nutrients favor species (such as algae, seaweed, ...) that disrupt the balance of reef communities.  Some algae are toxic, and both plants reduce the levels of sunlight and oxygen, killing marine organisms such as fish and coral. The addition of nutrients such as phosphates and nitrates are very damaging to reefs. High nitrate levels are toxic to corals, while phosphates slow down the growth of coral skeleton. Reefs in close proximity to human populations, however, will also be faced with local stresses, including poor water quality from land-based sources of pollution.  Poor water quality has also been shown to encourage the spread of infectious diseases among corals.
Extensive and poorly managed land development can threaten the survival of coral reefs. Runoff caused by farming and construction of roads, buildings, ports, channels, and harbors, can carry soil laden with carbon, nitrogen, phosphorus, and minerals. This nutrient-rich water can cause fleshy algae and phytoplankton to thrive in coastal areas, known as algal blooms, which have the potential to create hypoxic conditions by using all available oxygen.
In addition to local soil runoff, additional soil (sand) is blown in from other regions. Dust from the Sahara moving around the southern periphery of the subtropical ridge moves into the Caribbean and Florida during the warm season as the ridge builds and moves northward through the subtropical Atlantic. Dust can also be attributed to a global transport from the Gobi and Taklamakan deserts across Korea, Japan, and the Northern Pacific to the Hawaiian Islands. Since 1970, dust outbreaks have worsened due to periods of drought in Africa. There is a large variability in dust transport to the Caribbean and Florida from year to year; however, the flux is greater during positive phases of the North Atlantic Oscillation. The USGS links dust events to a decline in the health of coral reefs across the Caribbean and Florida, primarily since the 1970s. Studies have shown that corals can incorporate dust into their skeletons as identified from dust from the 1883 eruption of Krakatoa in Indonesia in the annular bands of the reef-building coral Montastraea annularis from the Florida reef tract. The relative abundance of chemical elements, particularly metals, has been used to distinguish soil derived from volcanic dust from mineral dust.
Another major pollutant is generated by people. Most islanders in developing countries send sewage unfiltered into the sea. While most experts now agree that composting toilet alongside an ecological sanitation approach is appropriate in small island nations, these countries for the moment prefer to keep using traditional approaches.
Inland mines of copper, gold and others form a major center of pollution. Most of the pollution is simply soil, which ends up in rivers flowing to the sea and ultimately covers the coral, but small mineral fractions may also introduce trouble. Copper, a common industrial pollutant has been shown to interfere with the life history and development of coral polyps.
Leaked oil and chemicals (e.g. from detergents, paints, ...) flowing into the sea from factory outlets are a key threat.
Chemical fertilizers (based on ammonium nitrate) are another pollutant.
Litter is another important threat, as especially in certain places (eg the Plastic Vortex), litter kills off many acquatic organisms that are directly or indirectly beneficial to coral reefs.
Radioactive waste is often dumped by the USA near its military installations (Mororua, Fangataufa, Johnston Atoll, ... Nuclear tests (eg at Kwajalein, Bikini, Enewetak) may produce harmful fallout, yet compared to the other forms of pollution noted, their impact is small.
Any rise in the sea level due to climate change would effectively ask coral to grow faster to keep up. Also, water temperature changes can be very disturbing to the coral. This was seen during the 1998 and 2004 El Niño weather phenomena, in which sea surface temperatures rose well above normal, bleaching or killing many coral reefs. High seas surface temperature (SSTs) coupled with high irradiance (light intensity), triggers the loss of zooxanthellae, a symbiotic algae, and its dinoflagellate pigmentation in corals causing coral bleaching. Zooxanthellae provides up to 90% of the energy to the coral host. Reefs can often recover from bleaching if they are healthy to begin with and water temperatures cool. However, recovery may not be possible if CO2 levels rise to 500 ppm because there may not be enough carbonate ions present. Refer to Hoegh-Guldberg 1999 for more information.
Warming may also be the basis of a new emerging problem: increasing coral diseases. Warming (thought to be the main cause of coral bleaching) weakens corals. In their weakened state, coral is much more prone to diseases including Black band disease, White band disease and Skeletal Eroding Band. In the event of a 2°C temperature increase, it is thought that coral is not able to adapt quickly enough physiologically or genetically
A related problem to climate change is ocean acidification, which can be caused by increasing CO2 emissions.
The decreasing ocean surface pH is of increasing long-term concern for coral reefs. Increased atmospheric CO2 increases the amount of CO2 dissolved in the oceans. Carbon dioxide gas dissolved in the ocean reacts with water to form carbonic acid, resulting in ocean acidification. Ocean surface pH is estimated to have decreased from approximately 8.25 to 8.14 since the beginning of the industrial era, and it is estimated that it will drop by a further 0.3 - 0.4 units by 2100 as the ocean absorbs more anthropogenic CO2. Normally, the conditions for calcium carbonate production are stable in surface waters since the carbonate ion is at supersaturating concentrations. However, as ocean pH falls, so does the concentration of this ion, and when carbonate becomes under-saturated, structures made of calcium carbonate are vulnerable to dissolution. Research has already found that corals experience reduced calcification or enhanced dissolution when exposed to elevated CO2.
Deep sea bamboo coral supports deep sea life and also may be among the first organisms to display the effects of changes in ocean acidification caused by excess carbon dioxide, since they produce growth rings similar to those of tree and can provide a view of changes in the condition in the deep sea over time. This coral is especially long-lived; coral specimens as old as 4,000-year-old were found at the Monument, giving scientists "4,000 years worth of information about what has been going on in the deep ocean interior".
Mangroves and seagrassbeds
Within the last 20 years, once prolific seagrassbeds and mangrove forests, which absorb massive amounts of nutrients and sediment have been destroyed. Both the loss of wetlands, mangrove habitats and seagrassbeds are considered to be significant factors affecting water quality on inshore reefs.
Coral mining is another threat. Both small-scale harvesting by villagers, industrial-scale mining by companies are serious threats. Mining is often done to produce construction material, and is of particular value as these rocks are up to 50% cheaper than other rocks (eg from quarries). The rocks are ground and mixed with other materials such as cement to make concrete. Ancient coral used for construction is known as "coral rag".
Other physical destruction
Dynamite fishing is an extremely destructive method for gethering fish. Sticks of dynamite, grenades, or home-made explosives are simply thrown in the water. This method of fishing kills the fish within the main blast area, along with many inedible and/or unwanted reef animals. The blast also kills the corals in the area, eliminating the very structure of the reef, destroying the habitat for fish and other animals important for the maintenance of a healthy reef.
Boats and ships require an access point into bays and islands to load/unload cargo/people. For this, often parts of the reef are chopped away to clear a path. Although this seems but minor destruction of the reef, potential negative consequences include altered water circulation and altered tidal patterns, which then cause a turnaround in the reef's supply of nutrients; sometimes destroying a great part of the reef.
Fishing boats and other large vessels occasionally run aground on a reef. Two types of damage can result. Collision damage occurs when a coral reef is crushed and split by a vessel's hull into multiple fragments. Scarring occurs when boat propellers tear off the live coral and expose the skeleton. The physical damage can be noticed as striations in the reefs.
Mooring also causes considerable damage. To reduce the (considerable) amount of devastation, boats can use mooring buoys. They are available in most major wetparks and marine sanctuaries. Most buoys are of the Halas Mooring Buoy System-type. 
Construction also takes its toll. Building directly on the reef can alter water circulation and tides (which bring the nutrients for the reef). The main reason for building on reefs (despite possible moisture problems) is simply the lack of space.