Arsenic is present in small quantities in the Earth's crust. The element arsenic is 53^rd in terms of abundance. Elemental arsenic has several allotropic forms - gray, yellow, and black arsenic- but only gray arsenic is ordinarily stable. Arsenic occurs naturally in soils, rocks, water, air, plants, and animals. Minerals that contain arsenic include arsenopyrite (FeAsS), realgar (AsS), orpiment (As₂S₃), and arsenolite (As₂O₃). The quantity of arsenic associated with lead and copper ores may range from 2-3%, whereas gold ores may contain up to 11% arsenic.

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Millions of years ago, as it drifted northwards, the Indian subcontinent collided with Asia. The resulting upward pressure created the Tibetan Plateau and the Himalayan mountain range. The region is drained by two rivers, the Ganges and the Brahmaputra, which subsequently join together to form a large, low-lying delta and alluvial plain. About half of the territory of Bangladesh is situated in this river delta. One third of the delta lies in India, more specifically in West Bengal. It is estimated that something like 2.5 gigatonnes of sediment are carried downstream each year. The sediments contain a mixture of fine sand and clay. Their composition reflects that of the parent rock: large amounts of oxygen, silicon, iron and sulfur, but also trace elements such as gold and arsenic. The sediment carried down from the mountains, however, contains thousands of ppm of arsenic, which can bind to minerals in the soil or dissolve in water. This phenomenon is not restricted to Bangladesh. It also occurs in some areas of Argentina, Chile, India, Mexico, Taiwan, Thailand and the USA.

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Since 1998, a huge arsenic poisoning problem has been known to exist in Bangladesh. In the Bangladeshi soil arsenic is chemically bound to sand, clay or other soil particles. Arsenic is also absorbed on fine iron and manganese oxyhydroxides, which decompose slowly and release arsenic. The type of chemical binding and its solubility are determined by various factors, such as the oxidation number, humidity, acidity, the amount of available oxygen, etc. Has arsenic over the years been released by the falling water table (due to the operation of numerous handpumps) and the penetration of oxygen or oxygen-rich water into the subsoil? Did certain soil bacteria play a role? The geochemical cause of the arsenic problem is still not fully understood, but pyrite oxidation appears to play a major role. Pumping lowers the water table so that oxygen-rich water can enter the soil which was previously saturated. The oxygen causes decomposition of pyrite and the included trace elements are released.

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Arsenic in the atmosphere comes from various sources. Volcanoes release about 3,000 tonnes per year and micro-organisms release volatile methylarsines to the extent of 20,000 tonnes per year, but human activity is responsible for much more than these natural sources. About 80,000 tonnes of arsenic per year are released from the burning of fossil fuels. Each year, as much as 100,000 tons of arsenic is produced worldwide, with most of it obtained as a by-product of the smelting of copper, lead, cobalt, and gold ores. Most rivers and streams contain arsenic concentrations less than 1 ppb. However, geothermal springs in Yellowstone National Park often have arsenic concentrations that exceed 1000 ppb. Oxygen-rich ground water can leach arsenic from arsenopyrite or other minerals and in this way the element can contamine aquifers.