A fourth branch of life?

The Tree of Life has three great branches: the eukaryotes, including all plants, animals, fungi, and single-celled creatures like malaria parasites and amoebae. There are the prokaryotes, or bacteria. And there are the Archaea, a group of single-celled organisms divergent from both the other groups.

Life on this planet is overwhelmingly single-celled. A cup of sea water or soil teems with thousands of species, many yet to be discovered. But for the most part, microbiologists only know about those organisms that they can grow in the lab.

Now Jonathan Eisen at the UC Davis Genome Center and colleagues may have discovered signs of a fourth, novel branch of life — or they may have found a lot of weird viruses. Eisen says that he really doesn’t know the answer, but he’s putting the data out there (a paper appeared last week in the journal Public Library of Science (PLoS) One).

On his blog, Eisen tells the story behind this research, which began some years ago when he was working at The Institute for Genome Research with J. Craig Venter on analyzing seawater samples from the Sargasso Sea.

Eisen and colleagues had pioneered a new approach to finding microbes, by simply extracting DNA from environmental samples, sequencing short pieces of it, then reassembling it to find new species. Eisen calls this “Environmental Shotgun Sequencing.”

When they did the original Sargasso Sea sequencing, Eisen and colleagues came up with some sequences that did not fit properly. Now, after going back and looking at new sequences, they were able to fit them into a robust phylogenetic tree, with some new branches.

From Eisen’s blog:

We then propose and discuss four potential mechanisms that could lead to the existence of such evolutionarily novel sequences.  The two we consider most likely are the following

(1) The sequences could be from novel viruses

(2) The sequences could be from a fourth major branch on the tree of life

Unfortunately, we do not actually know what is the source of these sequences.  So we cannot determine which of the theories is correct.  Obviously if there is a novel lineages of cellular organisms out there, well, that would be cool.  But we have no evidence right now if that is what is going on.  Personally, I think it is most likely that these novel sequences are from weird viruses.  But as far as we can tell, they truly could be from a fourth major branch of cellular organisms and thus even though we did not have the story completely pinned down, we decided to finally write up the paper to get other people to think about this issue.

Over at the Loom, Carl Zimmer does an excellent job of explaining the background to this, including the existence of “giant viruses” which might be candidates for this new branch of life.

More coverage: from New Scientist, “Biology’s Dark Matter.”

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