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The vivid colors in the spring are the result of pigmented bacteria in the microbial mats that grow around the edges of the mineral-rich water. The bacteria produce colors ranging from green to red; the amount of color in the microbial mats depends on the ratio of chlorophyll to carotenoids and on the temperature of the water which favors one bacterium over another. In the summer, the mats tend to be orange and red, whereas in the winter the mats are usually dark green.[8] The center of the pool is sterile due to extreme heat.

The deep blue color of the water in the center of the pool results from the intrinsic blue color of water, itself the result of water's selective absorption of red wavelengths of visible light. Though this effect is responsible for making all large bodies of water blue, it is particularly intense in Grand Prismatic Spring because of the high purity and depth of the water in the middle of the spring.

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