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Microcystis is a type of blue-green algae, also known as cyanobacteria, found in fresh water. An algae bloom is growth of large quantities of Microcystis in nutrient rich water. According to the World Health Organization toxic hazards may occur if concentrations of algae exceed 100,000 cells per milliliter.

An algae bloom was reported by the Boston Globe in the lower reaches of the Charles River in Boston in the summer of 2006. It was considered possibly poisonous to humans and animals. It was believed to be due to heavy runoff from spring rains which washed nutrients into the river. The Charles, a nutrient rich river, has had minor infestations of algae previously, but not of this magnitude. The problem was first reported by the Charles River Watershed Association and confirmed by testing done by the United States Environmental Protection Agency and the Massachusetts Department of Environmental Protection which showed over million cells per milliliter at one location. Toxicity has not been confirmed.

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