Environmental Microbiology

Environmental Microbiology: The earth’s family tree just got bigger

Contributed by paustian on Aug 13, 2016 - 04:28 PM

Professor Jillian Banfield’s group has been research the diversity of various communities for many years. As the power of DNA sequencing has moved from a being able to generate a 500 bp in 2 weeks in the 1980, to thousands of basepairs a day in the 1990’s, to hundreds of thousands in 2000, and now with illumina technology, billions of base pairs a day, so has our understanding of what makes up the environment. Up until a few years ago, a molecular census of of a microbial community would involve isolating the genes that code for the ribosome and sequencing them. That is, until now…

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.