The fundamental tree of life might have to be redrawn. Researchers looking into the branch that contains all bacteria have discovered that it is far more complex than previously thought. By sequencing hundreds of bacterial genomes, they’ve found a staggering 35 new phyla.
“This is a new view of the tree of life,” explained Professor Jill Banfield, lead author of the study. “These new major features on the tree of life mean that it probably won't be the simple three-domain view we have now.”
Currently, the second highest level of classification is called the “domain,” which is split into three divisions. The domain “eukaryotes” contains all animals, plants and fungi; “archaea” represent some of the oldest known forms of life; and “bacteria” is comprised of life that lacks a nuclear membrane. After analyzing groundwater samples taken in California, researchers from UC Berkeley found that many of the organisms present belonged to a massive radiation, or rapid diversification, within the bacterial group, and that they were totally different to any previously known.
“We were really surprised to find how diverse these groups are within the bacterial domain, and just how consistently different the organisms within this radiation are from the rest of bacteria,” said Christopher Brown, who co-authored the paper published in Nature. “No one had been able to put all the pieces together before.”
It was already suspected that many of these new phyla existed as a lot of the newly described bacteria had been seen before, just never sequenced. This is mainly due to the minuscule size of the organisms in question, some of which are the smallest known forms of life on Earth. It simply has not been possible to culture them in the lab, as the researchers suspect that because they are so small, they lack the ability to make the key building blocks of life, such as amino acids. They probably rely on other organisms to make them first and then scavenge them.
But by passing the groundwater through 0.2 micron filters, the team was able to catch bacteria normally missed due to their tiny size. They then carried out a technique called “shotgun sequencing,” which is where DNA is broken up into lots of small fragments, sequenced separately, and then joined back together to form the original strand. By doing this, the researchers were able to reassemble eight complete bacterial genomes, and 789 draft bacterial genomes that were 90% complete. From this, they identified the 35 new phyla.
Of the genes identified so far in these phyla, about half are unlike any other known genes. In fact, some of the genes identified are so distinct it makes the bacteria invisible to normal genomic testing. “I think what this is telling us is that a large part of bacteria and bacterial lifestyles are very different from what we thought before. There is a lot of biology that we haven't been able to understand from our current methods,” said Brown.
It’s predicted that there are around 100 phyla of bacteria, though previously only 29 were known for sure. Compare this to just 35 animal phyla, and 12 for plants, and it’s clear that the diversity of the organisms we see around us is swamped by that of bacteria.