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Dead zones are hypoxic (low-oxygen) areas in the world's oceans and large lakes, caused by "excessive nutrient pollution from human activities coupled with other factors that deplete the oxygen required to support most marine life in bottom and near-bottom water. (NOAA)." In the 1970s oceanographers began noting increased instances of dead zones. These occur near inhabited coastlines, where aquatic life is most concentrated. (The vast middle portions of the oceans, which naturally have little life, are not considered "dead zones".)
In March 2004, when the recently established UN Environment Programme published its first Global Environment Outlook Year Book (GEO Year Book 2003), it reported 146 dead zones in the world's oceans where marine life could not be supported due to depleted oxygen levels. Some of these were as small as a square kilometre (0.4 mi²), but the largest dead zone covered 70,000 square kilometres (27,000 mi²). A 2008 study counted 405 dead zones worldwide.
Aquatic and marine dead zones can be caused by an increase in chemical nutrients (particularly nitrogen and phosphorus) in the water, known as eutrophication. These chemicals are the fundamental building blocks of single-celled, plant-like organisms that live in the water column, and whose growth is limited in part by the availability of these materials. Eutrophication can lead to rapid increases in the density of certain types of these phytoplankton, a phenomenon known as an algal bloom.
Internationally celebrated limnologist Dr. David Schindler, notable for research at the Experimental Lakes Area which led to the banning of harmful phosphates in detergents, warned about algal blooms and dead zones,
"The fish-killing blooms that devastated the Great Lakes in the 1960s and 1970s haven't gone away; they've moved west into an arid world in which people, industry, and agriculture are increasingly taxing the quality of what little freshwater there is to be had here....This isn't just a prairie problem. Global expansion of dead zones caused by algal blooms is rising rapidly...(Schindler and Vallentyne 2008) "
The major groups of algae are Cyanobacteria, Green Algae, Dinoflagellates, Coccolithophores and Diatom Algae. Increase in input of nitrogen and phosphorus generally causes Cyanobacteria to bloom and this causes Dead Zones. Cyanobacteria are not good food for zooplankton and fish and hence accumulate in water, die, and then decompose. Other algae are consumed and hence do not accumulate to the same extent as Cyanobacteria. Dead zones can be caused by natural and by anthropogenic factors. Use of chemical fertilizers is considered the major human-related cause of dead zones around the world. Natural causes include coastal upwelling and changes in wind and water circulation patterns. Runoff from sewage, urban land use, and fertilizers can also contribute to eutrophication.
Notable dead zones in the United States include the northern Gulf of Mexico region, surrounding the outfall of the Mississippi River, and the coastal regions of the Pacific Northwest, and the Elizabeth River in Virginia Beach, all of which have been shown to be recurring events over the last several years.
Additionally, natural oceanographic phenomena can cause deoxygenation of parts of the water column. For example, enclosed bodies of water, such as fjords or the Black Sea, have shallow sills at their entrances, causing water to be stagnant there for a long time. The eastern tropical Pacific Ocean and northern Indian Ocean have lowered oxygen concentrations which are thought to be in regions where there is minimal circulation to replace the oxygen that is consumed (e.g. Pickard & Emery 1982, p 47). These areas are also known as oxygen minimum zones (OMZ). In many cases, OMZs are permanent or semipermanent areas.
Remains of organisms found within sediment layers near the mouth of the Mississippi River indicate four hypoxic events before the advent of artificial fertilizer. In these sediment layers, anoxia-tolerant species are the most prevalent remains found. The periods indicated by the sediment record correspond to historic records of high river flow recorded by instruments at Vicksburg, Mississippi.
Changes in ocean circulation triggered by ongoing climate change could also add or magnify other causes of oxygen reductions in the ocean 
In a study of the Gulf killifish by the Southeastern Louisiana University done in three bays along the Gulf Coast, fish living in bays where the oxygen levels in the water dropped to 1 to 2 parts per million (ppm) for three or more hours per day were found to have smaller reproductive organs. The male gonads were 34% to 50% as large as males of similar size in bays where the oxygen levels were normal (6 to 8 ppm). Females were found to have ovaries that were half as large as those in normal oxygen levels. The number of eggs in females living in hypoxic waters were only one-seventh the number of eggs in fish living in normal oxygen levels. (Landry, et al., 2004)
Fish raised in laboratory-created hypoxic conditions showed extremely low sex hormone concentrations and increased elevation of activity in two genes triggered by the hypoxia-inductile factor (HIF) protein. Under hypoxic conditions, HIF pairs with another protein, ARNT. The two then bind to DNA in cells, activating genes in those plant cells.
Under normal oxygen conditions, ARNT combines with estrogen to activate genes. Hypoxic cells in vitro did not react to estrogen placed in the tube. HIF appears to render ARNT unavailable to interact with estrogen, providing a mechanism by which hypoxic conditions alter reproduction in fish. (Johanning, et al., 2004)
It might be expected that fish would flee this potential suffocation, but they are often quickly rendered unconscious and doomed. Slow moving bottom-dwelling creatures like clams, lobsters and oysters are unable to escape. All colonial animals are extinguished. The normal re-mineralization and recycling that occurs among benthic life-forms is stifled.
Mora et al. 2013 showed that future changes in oxygen could affect most marine ecosystems and have socio-economic ramifications due to human dependency on marine goods and services.
In the 1970s, marine dead zones were first noted in areas where intensive economic use stimulated "first-world" scientific scrutiny: in the U.S. East Coast's Chesapeake Bay, in Scandinavia's strait called the Kattegat, which is the mouth of the Baltic Sea and in other important Baltic Sea fishing grounds, in the Black Sea, (which may have been anoxic in its deepest levels for millennia, however) and in the northern Adriatic.
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A dead zone exists in the central part of Lake Erie from east of Point Pelee to Long Point and stretches to shores in Canada and the United States. The zone has been noticed since the 1950s to 1960s, but efforts since the 1970s have been made by Canada and the US to reduce runoff pollution into the lake as means to reverse the dead zone growth. Overall the lake's oxygen level is poor with only a small area to the east of Long Point that has better levels. The biggest impact of the poor oxygen levels is to marine life and fisheries industry.
A dead zone exists in the Lower St. Lawrence River area from east the Saguenay River to east of Baie Comeau, greatest at depths over 275 metres (902 ft) and noticed since the 1930s. The main concerns for Canadian scientists is the impact of fish found in the area.
Off the coast of Cape Perpetua, Oregon, there is also a dead zone with a 2006 reported size of 300 square miles (780 km²). This dead zone only exists during the summer, perhaps due to wind patterns.
Currently, the Gulf of Mexico's dead zone, off the coast of Louisiana and Texas, is the largest hypoxic zone in the United States. The Mississippi River, which is the drainage area for 41% of the continental United States, dumps high-nutrient runoff such as nitrogen and phosphorus into the Gulf of Mexico. According to a 2009 fact sheet created by NOAA, "seventy percent of nutrient loads that cause hypoxia are a result of this vast drainage basin." which includes the heart of U.S. agribusiness, the Midwest. The discharge of treated sewage from urban areas (pop. c 12 million in 2009) combined with agricultural runoff deliver c. 1.7 million tons of potassium and nitrogen into the Gulf of Mexico every year.
The frequency of occurrence of hypoxia in the Gulf of Mexico hypoxic zone was mapped annually every summer from 1985 through 1999. The size varies annually from a record high in 2002 when it encompassed more than 21,756 sq kilometers (8,400 square miles) to a record low in 1988 of 39 sq kilometers (15 square miles). In 2010 it was the size of New Jersey. Nancy Rabalais of the Louisiana Universities Marine Consortium in Cocodrie predict the dead zone or hypoxic zone in 2012 will cover an area of 17,353 sq kilometers (6,700 square miles) which is larger than Connecticut. In 2011 it was about 17,521 sq kilometers (6,765 square miles). In 2014, the Gulf of Mexico was 5,052 square miles, a shrinking from previous years, but nowhere near the trim that scientists had hoped for. 
In late summer 1988 the dead zone disappeared as the great drought caused the flow of Mississippi to fall to its lowest level since 1933. During times of heavy flooding in the Mississippi River Basin, as in 1993, "the "dead zone" dramatically increased in size, approximately 5,000 km (3,107 mi) larger than the previous year."
On average the dead zone doubled in size since the late 1980s. "Hypoxia in bottom waters covered an average of 8,000–9,000 km2 in 1985–92 but increased to 16,000–20,000 km2 in 1993–99."  In March 1998, the National Science and Technology Council's Committee on Environment and Natural Resources and The Mississippi River/Gulf of Mexico (MR/GM) Watershed Nutrient Task Force developed and approved an assessment plan calling for six teams of experts from inside and outside of government to perform in-depth studies examining the issue of hypoxia and the watershed–Gulf system including oceanographic, hydrologic, agricultural and economic factors.
There is some concern that the Deepwater Horizon oil spill from April to July 2010 may have significantly affected the dead zone. However, Terry Hazen, a microbial ecologist with the Lawrence Berkeley National Laboratory, has suggested that the oil released from the spill did not travel far enough west in appreciable quantities to affect the current size of the dead zone.
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The dead zone threatens lucrative commercial and recreational fisheries in the Gulf of Mexico. "In 2009, the dockside value of commercial fisheries in the Gulf was $629 million. Nearly three million recreational fishers further contributed about $10 billion to the Gulf economy, taking 22 million fishing trips."  Scientists are not in universal agreement that nutrient loading has a negative impact on fisheries. Grimes makes a case that nutrient loading enhances the fisheries in the Gulf of Mexico. Courtney et al. assert that nutrient loading has made significant contributions to the increases in red snapper production in the northern and western Gulf of Mexico.
Shrimp trawlers first reported a 'dead zone' in the Gulf of Mexico in 1950 but it wasn't until 1970 when the size of the hypoxic zone had increased that scientists began to investigate.
The conversion of forests and wetlands for agricultural and urban developments accelerated after 1950. "Missouri River Basin has had hundreds of thousands of acres of forests and wetlands (66 000 000acres) replaced with agriculture activity [. . .] In the Lower Mississippi one third of the valley's forests were converted to agriculture between 1950 and 1976." 
The Energy Independence and Security Act of 2007 calls for the production of 36 billion US gallons (140,000,000 m3) of renewable fuels by 2022, including 15 billion US gallons (57,000,000 m3) of corn-based ethanol, a tripling of current production that would require a similar increase in corn production. Unfortunately, the plan poses a new problem; the increase in demand for corn production results in a proportional increase in nitrogen runoff. Although nitrogen, which makes up 78% of the Earth's atmosphere, is an inert gas, it has more reactive forms, one of which is used to make fertilizer.
According to Fred Below, a professor of crop physiology at the University of Illinois at Urbana-Champaign, corn requires more nitrogen-based fertilizer because it produces a higher grain per unit area than other crops and, unlike other crops, corn is completely dependent on available nitrogen in soil. The results, reported 18 March 2008 in Proceedings of the National Academy of Sciences, showed that scaling up corn production to meet the 15-billion-US-gallon (57,000,000 m3) goal would increase nitrogen loading in the Dead Zone by 10–18%. This would boost nitrogen levels to twice the level recommended by the Mississippi Basin/Gulf of Mexico Water Nutrient Task Force (Mississippi River Watershed Conservation Programs), a coalition of federal, state, and tribal agencies that has monitored the dead zone since 1997. The task force says a 30% reduction of nitrogen runoff is needed if the dead zone is to shrink.
Dead zones are reversible, though numerous extinct organisms that are lost due to its appearance are not. The Black Sea dead zone, previously the largest in the world, largely disappeared between 1991 and 2001 after fertilizers became too costly to use following the collapse of the Soviet Union and the demise of centrally planned economies in Eastern and Central Europe. Fishing has again become a major economic activity in the region.
While the Black Sea "cleanup" was largely unintentional and involved a drop in hard-to-control fertilizer usage, the U.N. has advocated other cleanups by reducing large industrial emissions. From 1985 to 2000, the North Sea dead zone had nitrogen reduced by 37% when policy efforts by countries on the Rhine River reduced sewage and industrial emissions of nitrogen into the water. Other cleanups have taken place along the Hudson River and San Francisco Bay.