Research into the extremeophiles living in Yellowstone bacterial mats is ongoing.

Image: Creative Commons, Closeup of a bacterial mat – Colony of thermophilic bacteria at Mickey Hot Springs, Oregon

Extremeophiles are organisms which live in conditions which would be toxic to most living species. Thermophiles are extremeophiles who live in very hot conditions which would seriously burn most animals.

Image: West Thumb thermal bacterial mat, Yellowstone National Park

Bacterial mats occur where hot springs spill over warm earth.

It takes some digging to discover the source of the colors in the bacterial mats. Here is a forum post where source material is provided:

Yellowstone thermophilic Bacillus thermocatenulatus and other Bacillus thermophiles with yellow pigmentation have carotenoids.
http://books.google.com/books?id=X703AVm…
The orange strains of Thermus aquaticus have phytoene and carotene while the red strains have pigments like neurosporoxanthin and retrodehydro gamma carotene
http://books.google.com/books?id=X703AVm…

Source: Yahoo Answers.

A green hue may be caused by heat-loving bacteria that produce their nutrients via photosynthesis. A brownish hue may be rust, if the heat-loving bacteria has ingested iron-rich soil for nutrients.

Source: Geyser Basin colors.