The tree of life, which depicts how life has evolved and diversified on the planet, is getting a lot more complicated.
Researchers at the University of California, Berkeley, who have discovered more than 1,000 new types of bacteria and Archaea over the past 15 years lurking in Earth’s nooks and crannies, have dramatically rejiggered the tree to account for these microscopic new life forms.
“The tree of life is one of the most important organizing principles in biology,” said Jill Banfield, a UC Berkeley professor of earth and planetary science and environmental science, policy and management. “The new depiction will be of use not only to biologists who study microbial ecology, but also biochemists searching for novel genes and researchers studying evolution and earth history.”
Much of this microbial diversity remained hidden until the genome revolution allowed researchers like Banfield to search directly for their genomes in the environment, rather than trying to culture them in a lab dish. Many of the microbes cannot be isolated and cultured because they cannot live on their own: they must beg, borrow or steal stuff from other animals or microbes, either as parasites, symbiotic organisms or scavengers.
The new tree, to be published online April 11 in the new journal Nature Microbiology, reinforces once again that the life we see around us – plants, animals, humans and other so-called eukaryotes – represent a tiny percentage of the world’s biodiversity.
“Bacteria and Archaea from major lineages completely lacking isolated representatives comprise the majority of life’s diversity,” said Banfield, who also has an appointment at Lawrence Berkeley National Laboratory. “This is the first three-domain genome-based tree to incorporate these uncultivable organisms, and it reveals the vast scope of as yet little-known lineages.”
According to first author Laura Hug, a former UC Berkeley postdoctoral fellow who is now on the biology faculty at the University of Waterloo in Ontario, Canada, the more than 1,000 newly reported organisms appearing on the revised tree are from a range of environments, including a hot spring in Yellowstone National Park, a salt flat in Chile’s Atacama desert, terrestrial and wetland sediments, a sparkling water geyser, meadow soil and the inside of a dolphin’s mouth. All of these newly recognized organisms are known only from their genomes.
“What became really apparent on the tree is that so much of the diversity is coming from lineages for which we really only have genome sequences,” she said. “We don’t have laboratory access to them, we have only their blueprints and their metabolic potential from their genome sequences. This is telling, in terms of how we think about the diversity of life on Earth, and what we think we know about microbiology.”…
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