Bacteria in Tree of Life Expand by 50% Thanks to Water Filters and Algorithms

An invisible metropolis of microscopic bacteria has been brought into the limelight for the first time, thanks to a tremendous advance in scientific technology.

In the past, biologists used substances called primers to extract 16S rRNA genes from potential new species. These genes contain a unique genetic code for each organism—but sometimes 16S rRNA genes don’t respond well to primers, so these bacteria are left in the dark, practically non-existent by human standards.

But a new strategy zooms in closer, forgoing the help of primers.

Here’s Kevin Harnett, reporting for Quanta Magazine:

DNA sequencing is at the heart of this current study, though the researchers’ success also owes a debt to more basic technology. The team gathered water samples from a research site on the Colorado River near the town of Rifle, Colo. Before doing any sequencing, they passed the water through a pair of increasingly fine filters—with pores 0.2 and 0.1 microns wide—and then analyzed the cells captured by the filters. At this point they already had undiscovered life on their hands, for the simple reason that scientists had not thought to look on such a tiny scale before. […]

The researchers extracted the DNA from the cellular material and sent it to the Joint Genome Institute for sequencing. What they got back was a mess. Imagine being handed a box of pieces from thousands of different jigsaw puzzles and having to assemble them without knowing what any of the final images look like. That’s the challenge researchers face when performing metagenomic analysis—sequencing scrambled genetic material from many organisms at once.

Extremely fine water filters helped scientists discover smaller-than-ever bacterial species.

To assemble the puzzle pieces for each species, the scientists used two algorithms—the first part of a process called genome binning, which arranges individual bits of DNA into slightly longer sections, called contigs. The second algorithm, devised by the study’s co-author Itai Sharon, combines contigs to reconstruct the genome sequence. Once the entire process was complete, the researchers had final copies of eight full bacterial genomes and 789 drafts of others. These organisms have relatively short genomes, limited metabolic function, use fermentation to create energy, and probably rely on other species for survival. The team’s results were published in Nature on July 9.

Organisms that had at least 75% of their 16S rRNA gene code in common were lumped into the same phylum; in the end, the scientists counted 35 phyla (types) of bacteria, 28 of which were new. This addition brings the total number of known phyla up to 90 (a nearly 50% increase). Biologists suspect that someday soon we’ll have identified at least 1,300. That’s a far cry from what Carl Woese could have envisioned even just 40 years ago—and it implies that the tree of life will continue to surprise us with new and diverse outgrowths.

Play the Evolution Lab to explore how the tree of life is shaped by a remarkable force.