Cyanobacteria is blue-green algae that occurs in lakes worldwide, feeding on pollution from agricultural run-off and human waste. In September 2009, following a period of warm, settled sunny weather, a smelly gooey green mass of algae began to carpet the surface of Atitlán, at times affecting around thirty percent of the lake, and only fading as the temperature cooled and high winds broke it up. In 2010 and 2011 the climate was far more favourable and there were only tiny patches of algae bloom, but the threat remains for years as phosphorus- and nitrogen-rich nutrients remain in the lake.

Meanwhile, the fishing industry, once thriving on the abundance of small fish and crabs, has been crippled by the introduction of black bass which eat the smaller fish and water birds.

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