In an experiment by Brown et al. the power of next-generation sequencing was focused to take a molecular census of an aquifer adjacent to the Colorado River near the town of Rifle, Colorado. In the process of the experiment, they did something clever. They used a unusually small filter to trap the bacteria for harvest instead of the typical 0.45 µm filter often used in these types of experiments. This trapped very small bacteria, that are often lost. In addition, they sequenced all the DNA, not just the ribosomal genes, thus obtaining much more information about the microbes genetic makeup.
Eight complete draft genomes and 789 partial genomes were constructed. There were some big surprises. More than 15% of the microbes found were part of a new radiation of phyla, in fact these candidate phyla radiation (CPR) bacteria are so far removed from other life forms, Bacteria, Archaea, and Eukarya, that they probably need to be placed into their own domain. CPR bacteria have a limited metabolic ability and probably depend upon other organisms to obtain the nutrients they need, explaining the inability to culture them. In addition, their ribosomal RNA genes are split by introns, meaning they would not be picked up in previous molecular surveys. In other words, we didn't know they were there because we didn't know how to look for them! In the coming years the CPR bacteria will redefine exactly what life is on this planet.