Algal blooms are the result of a nutrient, like nitrogen or phosphorus from fertilizer runoff, entering the aquatic system and causing excessive growth of algae. An algal bloom affects the whole ecosystem. Consequences range from the benign feeding of higher trophic levels, to more harmful effects like blocking sunlight from reaching other organisms, causing a depletion of oxygen levels in the water, and, depending on the organism, secreting toxins into the water. The process of the oversupply of nutrients leading to algae growth and oxygen depletion is called eutrophication. Blooms that can injure animals or the ecology are called "harmful algal blooms" (HAB), and can lead to fish die-offs, cities cutting off water to residents, or states having to close fisheries. Blooms are the result of a nutrient that the particular algae need being introduced to the local aquatic system. This growth-limiting nutrient is typically nitrogen or phosphorus, but can also be iron, vitamins, or amino acids. There are several mechanisms for the addition of these nutrients in water. In the open ocean and along coastlines, upwelling from both winds and topographical ocean floor features can draw nutrients to the photic, or sunlit zone of the ocean. Along coastal regions and in freshwater systems, agricultural, city, and sewage runoff can cause algal blooms.

Algal blooms, especially large algal bloom events, can reduce the transparency of the water and can discolor the water. The photosynthetic pigments in the algal cells, like chlorophyll and photoprotective pigments, determine the color of the algal bloom. Depending on the organism, its pigments, and the depth in the water column, algal blooms can be green, red, brown, golden, and purple. Bright green blooms in freshwater systems are frequently a result of cyanobacteria (colloquially known as "blue-green algae") such as Microcystis. Blooms may also consist of macroalgal (non-phytoplanktonic) species. These blooms are recognizable by large blades of algae that may wash up onto the shoreline.

Once the nutrient is present in the water, the algae begin to grow at a much faster rate than usual. In a mini bloom, this fast growth benefits the whole ecosystem by providing food and nutrients for other organisms. Of particular note are the rare harmful algal blooms (HABs), which are algal bloom events involving toxic or otherwise harmful phytoplankton. There are many species that can cause harmful algal blooms. For example, Gymnodinium nagasakiense can cause harmful red tides, dinoflagellates Gonyaulax polygramma can cause oxygen depletion and result in large fish kills, cyanobacteria Microcystis aeruginosa can make poisonous toxins, and diatom Chaetoceros convolutus can damage fish gills.

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