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The Great Barrier Reef is the world's largest coral reef system, composed of roughly 3,000 individual reefs and 900 islands that stretch for 2,600 kilometres (1,616 mi) and cover an area of approximately 344,400 km². The reef is located in the Coral Sea, off the coast of Queensland in northeast Australia. A large part of the reef is protected by the Great Barrier Reef Marine Park.
The Great Barrier Reef's environmental pressures include lowered water quality from runoff including suspended sediment, excess nutrients, pesticides, and fluctuations in salinity. The effects of climate change, including increased temperatures, storms and coral bleaching. Cyclic outbreaks of the crown-of-thorns starfish, overfishing which disrupts food chains, and shipping routes which can result in oil spills or improper ballast discharge also cause damage to the reef.
Water quality was first identified as a threat to the Great Barrier Reef in 1989. Thirty "major rivers" and hundreds of small streams comprise the Great Barrier Reef catchment area, which covers 423,000 square kilometres (163,000 sq mi) of land. Queensland has several major urban centres on the coast including Cairns, Townsville, Mackay, Rockhampton and the industrial city of Gladstone. Dredging in the Port of Gladstone is raising concern after dead and diseased fish where found in the harbour. Cairns and Townsville are the largest of the coastal cities, with populations of approximately 150,000 each.
There are many major water quality variables affecting coral reef health including water temperature, salinity, nutrients, suspended sediment concentrations, and pesticides. The species in the Great Barrier Reef area are adapted to tolerable variations in water quality however when critical thresholds are exceeded they may be adversely impacted. River discharges are the single biggest source of nutrients, providing significant pollution of the Reef during tropical flood events with over 90% of this pollution being sourced from farms.
Due to the range of human uses made of the water catchment area adjacent to the Great Barrier Reef, some 700 of the 3000 reefs are within a risk zone where water quality has declined owing to the naturally acidic sediment and chemical runoff from farming, and to coastal development and the loss of coastal wetlands which are a natural filter. Industries in the water catchment area are cotton growing, comprising approximately 262 km²; 340 dairy farms with an average area of 2 km² each, 158 km² cattle grazing, 288 km² horticulture including banana growing, sugarcane farming, and cropping of approximately 8,000 km² wheat, 1,200 km² barley, and 6,000 to 7000 km² sorghum and maize. Fertiliser use in the cotton, dairy, beef, horticulture and sugar industries is essential to ensure productivity and profitability. However, fertiliser and byproducts from sugar cane harvesting methods form a component of surface runoff into the Great Barrier Reef lagoon. Principal agricultural activity is sugar cane farming in the wet tropics and cattle grazing in the dry tropics regions. Both are considered significant factors affecting water quality. Copper, a common industrial pollutant in the waters of the Great Barrier Reef, has been shown to interfere with the development of coral polyps. Flood plumes are flooding events associated with higher levels of nitrogen and phosphorus. In February 2007, due to a monsoonal climate system, plumes of sediment runoff have been observed reaching to the outmost regions of the reef.
Runoff is especially concerning in the region south of Cairns, as it receives over 3000 mm of rain per year and the reefs are less than 30 kilometres (19 mi) away from the coastline. Farm run off is polluted as a result of overgrazing and excessive fertiliser and pesticide use. Mud pollution has increased by 800% and inorganic nitrogen pollution by 3,000% since the introduction of European farming practices on the Australian landscape. This pollution has been linked to a range of very significant risks to the reef system, including intensified outbreaks of the coral-eating Crown of Thorns Starfish which contributed to a loss of 66% of live coral cover on sampled reefs in 2000.
It is thought that the mechanism behind excess nutrients affecting the reefs is due to increased light and oxygen competition from algae, but unless herbivory is unusually low, this will not create a phase shift from the Great Barrier Reef being primarily made up of coral to being primarily made up of algae.
It has been suggested that poor water quality due to excess nutrients encourages the spread of infectious diseases among corals. In general, the Great Barrier Reef is considered to have low incidences of coral diseases. Skeletal Eroding Band, a disease of bony corals caused by the protozoan Halofolliculina corallasia, affects 31 species of corals from six families on the reef. The long-term monitoring program has found an increase in incidences of coral disease in the period 1999-2002, although they dispute the claim that on the Great Barrier Reef, coral diseases are caused by anthropogenic pollution.
Elevated nutrient concentrations result in a range of impacts on coral communities and under extreme conditions can result in a collapse. It also affects coral by promoting phytoplankton growth which increases the number of filter feeding organisms that compete for space. Excessive inputs of sediment from land to coral can lead to reef destruction through burial, disruption of recruitment success or deleterious community shifts. Sediments affect coral by smothering them when particles settle out, reducing light availability and potentially reducing photosynthesis and growth. Coral reefs exist in seawater salinities from 25 to 42%. Salinity impacts to corals are increased by other flood-related stresses.
The Australian and Queensland Governments have committed to act to protect the reef, and water quality monitoring programmes are in place. However, the World Wildlife Fund has criticised that progress against these commitments has been slow, saying that as many as 700 reefs are at risk from sediment runoff.
Most people believe that the most significant threat to the status of the Great Barrier Reef and of the planet's other tropical reef ecosystems is climate change, consisting chiefly of global warming and the El Niño effect. and turn colourless, revealing their white calcium carbonate skeletons, under the stress of waters that remain too warm for too long. At this stage the coral is still alive, and if the water cools, the coral can regain its zooxanthellae. If the water does not cool within about a month, the coral will die of starvation. Australia experienced its warmest year on record in 2005. Abnormally high sea temperatures during the summer of 2005-2006 have caused massive coral bleaching in the Keppel Island group.
Most scientists studying the issue believe that climate change poses a massive threat to the future of the Great Barrier Reef. A draft report by the UN Intergovernmental Panel on Climate Change, the world's preeminent gathering of climate scientists, states that the Great Barrier Reef is at grave risk and will be "functionally extinct" by 2030, warning that coral bleaching will likely become an annual occurrence.
However, a few scientists hold that coral bleaching may in some cases be less of a problem than the mainstream believes. Professor Ridd, from James Cook University in Townsville was quoted in The Australian (a conservative newspaper) as saying; "They are saying bleaching is the end of the world, but when you look into it, that is a highly dubious proposition". Research by scientist Ray Berkelmans "... has documented astonishing levels of recovery on the Keppel outcrops devastated by bleaching in 2006."  A related article in The Australian newspaper goes on to explain that; "Those that expel their zooxanthellae have a narrow opening to recolonise with new, temperature-resistant algae before succumbing. In the Keppels in 2006, Berkelmans and his team noticed that the dominant strain of zooxanthellae changed from light and heat-sensitive type C2, to more robust types D and C1." 
Nevertheless, most coral reef researchers anticipate severely negative effects from climate change already occurring, and potentially disastrous effects as climate change worsens. The future of the Reef may well depend on how much the planet's climate changes, and thus, on how high atmospheric greenhouse gas concentration levels are allowed to rise. On 2 September 2009, a report by the Australian Great Barrier Reef Marine Park Authority revealed that if carbon dioxide levels reached 450 parts per million corals and reef habitats will be highly vulnerable. If carbon dioxide levels are managed at or below 380 parts per million they will be only moderately vulnerable and the reefs will remain coral-dominated.
Global warming may have triggered the collapse of reef ecosystems throughout the tropics. Increased global temperatures are thought by some to bring more violent tropical storms, but reef systems are naturally resilient and recover from storm battering. Most people agree that an upward trend in temperature will cause much more coral bleaching; others suggest that while reefs may die in certain areas, other areas will become habitable for corals, and new reefs will form. However, the rate at which the mass bleaching events occur is estimated to be much faster than reefs can recover from, or adjust to.
However, Kleypas et al. in their 2006 report suggest that the trend towards ocean acidification indicates that as the sea's pH decreases, corals will become less able to secrete calcium carbonate. In 2009, a study showed that Porites corals, the most robust on the Great Barrier Reef, have slowed down their growth by 14.2% since 1990. It suggested that the cause was heat stress and a lower availability of dissolved calcium to the corals.
Climate change and global warming are one of the greatest threats to the reef. A temperature rise of between two and three degrees Celsius would result in 97% of the Great Barrier Reef being bleached every year. Reef scientist Terry Done has predicted that a one-degree rise in global temperature would result in 82% of the reef bleached, two degrees resulting in 97% and three degrees resulting in "total devastation". A predictive model based on the 1998 and 2002 bleaching events has concurred that a temperature rise of three degrees would result in total coral mortality.
Climate change has implications for other forms of life on the Great Barrier Reef as well - some fish's preferred temperature range lead them to seek new areas to live, thus causing chick mortality in seabirds that prey on the fish. Also, in sea turtles, higher temperatures mean that the sex ratio of their populations will change, as the sex of sea turtles is determined by temperature. The habitat of sea turtles will also shrink.
The Crown-of-Thorns Starfish is a coral reef predator which preys on coral polyps by climbing onto them, extruding its stomach over them, and releasing digestive enzymes to absorb the liquified tissue. An individual adult of this species can eat up to six square metres of living reef in a single year. Geological evidence suggests that the Crown-of-Thorns Starfish has been part of the Great Barrier Reef's ecology for "at least several thousand years", but there is no geological evidence for Crown-of-Thorns outbreaks. Large outbreaks of these starfish can devastate reefs. In 2000, an outbreak contributed to a loss of 66% of live coral cover on sampled reefs in a study by the CRC Reefs Research Centre. Although large outbreaks of these starfish are believed to occur in natural cycles, human activity in and around the Great Barrier Reef can worsen the effects. Reduction of water quality associated with agriculture can cause the crown-of-thorns starfish larvae to thrive. Overfishing of its natural predators, such as the Giant Triton, is also considered to contribute to an increase in the number of crown-of-thorns starfish. The CRC Reef Research Centre defines an outbreak as when there are more than 30 adult starfish in an area of one hectare.
The unsustainable overfishing of keystone species, such as the Giant Triton and sharks, can cause disruption to food chains vital to life on the reef. Fishing also impacts the reef through increased pollution from boats, by-catch of unwanted species (such as dolphins and turtles) and reef habitat destruction from trawling, anchors and nets. Overfishing of herbivore populations can cause algal growths on reefs. The Batfish Platax pinnatus has been observed to significantly reduce algal growths in studies simulating overfishing. Sharks are fished for their meat, and when they are part of bycatch, it is common to kill the shark and throw it overboard, as there is a belief that they interfere with fishing. As of 1 July 2004, approximately one-third of the Great Barrier Reef Marine Park is protected from species removal of any kind, including fishing, without written permission. However, illegal poaching is not unknown in these no-take zones.
Shipping accidents continue to be perceived as a threat, as several commercial shipping routes pass through the Great Barrier Reef. The GBRMPA estimates that about 6000 vessels greater than 50 metres (164 ft) in length use the Great Barrier Reef as a route. From 1985 to 2001, 11 collisions and 20 groundings occurred along the Great Barrier Reef shipping route, with human error identified as the leading cause of shipping accidents.
Reef pilots have stated that they consider the reef route safer than outside the reef in the event of mechanical failure, since a ship can sit safely while being repaired. The inner route is used by 75% of all ships that travel over the Great Barrier Reef. As of 2007, over 1,600 known shipwrecks have occurred in the Great Barrier Reef region.
Waste and foreign species discharged from ships in ballast water (when purging procedures are not followed) are a biological hazard to the Great Barrier Reef. Tributyltin (TBT) compounds found in some antifouling paint on ship hulls leaches into seawater and is toxic to marine organisms and humans; as of 2002, efforts are underway to restrict its use.
In April 2010, the bulk coal carrier Shen Neng 1 ran aground on the Great Barrier Reef, causing the largest grounding scar to date. The spill caused damage to a 400,000sqm section of the Great Barrier Reef and the use of oil dispersant resulted in oil spreading to reef islands 25 km away.
It was suspected that the Great Barrier Reef is the cap to an oil trap, after a 1923 paper suggested that it had the right rock formation to support "oilfields of great magnitude". After the Commonwealth Petroleum Search Subsidies Act of 1957, exploration activities increased in Queensland, including a well drilled at Wreck Island in the southern Great Barrier Reef in 1959. In the 1960s, drilling for oil and gas was investigated throughout the Great Barrier Reef, by seismic and magnetic methods in the Torres Strait, along "the eastern seaboard of Cape York to Princess Charlotte Bay" and along the coast from Cooktown to Fraser Island. In the late 1960s, more exploratory wells were drilled near Wreck Island in the Capricorn Channel, and near Darnley Island in the Torres Strait, but "all results were dry".
In 1970, responding to concern about oil spills such as the Torrey Canyon, two Royal Commissions were ordered "into exploratory and production drilling for petroleum in the area of the Great Barrier Reef". After the Royal Commissions, the federal and state governments ceased allowing petroleum drilling on the Great Barrier Reef. A study in 1990 concluded that the reef is too young to contain oil reserves. Oil drilling remains prohibited on the Great Barrier Reef, yet oil spills due to shipping routes are still a threat to the reef system, with a total of 282 oil spills between 1987-2002.
Tropical cyclones are a cause of ecological disturbance to the Great Barrier Reef. The types of damage caused by tropical cyclones to the Great Barrier Reef is varied, including fragmentation, sediment plumes, and decreasing salinity following heavy rains (Tropical Cyclone Joy). The patterns of reef damage are similarly 'patchy'. From 1910–1999, 170 cyclones' paths came near or through the Great Barrier Reef. Most cyclones pass through the Great Barrier Reef within a day. In general, compact corals such as Porites fare better than branching corals under cyclone conditions. The major damage caused by Tropical Cyclone Larry was to underlying reef structures, and breakage and displacement of corals, which is overall consistent with previous tropical cyclone events. Severe tropical cyclones hit the Queensland coast every 200 to 300 years; however, during the period 1969–1999 most cyclones in the region were very weak – category one or two on the Australian Bureau of Meteorology scale.
On 2 February 2011, Severe Tropical Cyclone Yasi struck northern Queensland and caused severe damage to a stretch of hundreds of kilometres within the Great Barrier Reef. The corals could take a decade to recover fully. Cyclone Yasi had wind speeds of 290 kilometers per hour.
On the second day of the 2013 round of the biennial training exercise 'Talisman Saber', in which 28,000 US and Australian military personnel conduct joint activities over a three-week period,four unarmed bombs were dropped into the Great Barrier Reef by two US AV-8B Harrier jets that were unable to land with the weight of the weapons. To minimize potential harm to the reef, the four bombs, weighing a total 1.8 metric tons (4,000 pounds), were dropped into more than 50 meters (164 ft) of water away from the reef's coral structures. The bomb drop was originally planned to occur at the Townshend Island bombing range, but after controllers reported that the area was not clear of hazards, the emergency jettison occurred. Australian senator Larissa Waters responded to the news by asking, "Have we gone completely mad? Is this how we look after our World Heritage area now? Letting a foreign power drop bombs on it?"