UC Berkeley scientists classify hundreds of bacteria, define new branch on tree of life

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A research team led by UC Berkeley scientists has defined a new branch on the tree of life after sequencing about 800 largely unknown bacteria genomes.

The researchers classified these very small symbiotic bacteria as biologically distinct from most other bacteria types, saying they compose 35 new phyla classifications, one of the classifications of organisms similar to a species or a kingdom. All vertebrates represent just one phylum. The research, published online Monday in the journal Nature, may allow for a better understanding of how ecosystems work.

“Most of what we know about bacteria comes from organisms that can be grown in the lab,” said Jill Banfield, the lead author of the paper and a UC Berkeley professor of earth and planetary science. The groups of bacteria studied cannot be grown in a lab culture, so researchers used different methods to sequence their genomes, she said.

The team collected samples of groundwater from a site in Rifle, Colorado. They then used a process called shotgun metagenomics to sequence the genes. The process involves chopping up DNA from many organisms into smaller pieces, sequencing the pieces and assembling them into complete genomes.

The researchers fully sequenced only eight of the genomes, but most of the sequences are nearly complete. They reveal that the bacteria are very different from most other known types.

They grow without oxygen and produce energy through fermentation — a process much simpler than respiration, which more complex organisms use — according to Christopher Brown, a co-author of the study and a graduate student in the campus plant and microbial biology department. The bacteria are not able to synthesize DNA or the amino acids used to build proteins but instead scavenge for these materials.

The bacteria in the new test phyla grow in diverse places, including the insides of the human mouth. Brown said future research would likely concentrate on the biological context of the bacteria.

“We want to know what the relationships they have with other organisms look like,” Brown said.

About half the genes from the bacteria were previously unidentified and could give researchers insight into many biological processes. Applications will crop up everywhere, Banfield said.

Microorganisms play key roles in almost all environments, so this research could lead to a greater understanding of a variety of ecosystems, Brown said. In particular, these bacteria play a role in the human body, and they live in many places without oxygen.

“This is really groundbreaking work,” said Philip Long, a geological project scientist at Lawrence Berkeley National Laboratory, about the genome sequencing. “This is a huge step forward in our ability to predict what these organisms will do under various conditions, such as climate change.”

Contact Mira Chaplin at [email protected].