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Biology's 'dark matter' hints at fourth domain of life

Step far enough back from the tree of life and it begins to look quite simple. At its heart are just three stout branches, representing the three domains of life: bacteria, archaea and eukaryotes. But that's too simple, according to a band of biologists who believe we may be on the verge of discovering the fourth domain of life.
The bold statement is the result of an analysis of water samples collected from the world's seas. Jonathan Eisen at the University of California, Davis, Genome Center has identified gene sequences hidden within these samples that are so unusual they seem to have come from organisms that are only distantly related to cellular life as we know it. So distantly related, in fact, that they may belong to an organism that sits in an entirely new domain.
Most species on the planet look like tiny single cells, and to work out where they fit on the tree of life biologists need to be able to grow them in the lab. Colonies like this give them enough DNA to run their genetic analyses. The problem is, the vast majority of these species – 99 per cent of them is a reasonable bet – refuse to be cultured in this way. "They really are the dark matter of the biological universe," says Eisen.

Life's dark matter

To probe life's dark matter, Eisen, Craig Venter of the J. Craig Venter Institute in Rockville, Maryland, and their colleagues have resorted to a relatively new technique called metagenomics. This can "sequence the crap out of any DNA samples", whether they are collected from the environment or come from lab cultures, says Eisen.
When Eisen and Venter used the technique on samples collected from theGlobal Ocean Sampling Expedition, they found that some sequences belonging to two superfamilies of genes – recA and rpoB – were unlike any seen before.
"The question is, what are they from?" says Eisen. Because the team has no idea what organism the genes belong to, the question remains unanswered. There are two possibilities, he says. "They could represent an unusual virus, which is interesting enough. More interestingly still, they could represent a totally new branch in the tree of life."
The exciting but controversial idea has met with mixed reactions. "It's a very good piece of careful work," says Eugene Koonin at the National Center for Biotechnology Information in Bethesda, Maryland.

Younger than they look?

But Koonin and others think any talk of a fourth domain of cellular life is premature. Radhey Gupta at McMaster University in Hamilton, Ontario, Canada, calls the finding "very exciting", but cautions that there are other explanations.
For instance, the sequences could be from cellular organisms living in unique habitats that caused their genes to undergo rapid evolution. That would give the false impression that the "new" life forms diverged from all others a very long time ago.
"There is still debate [over] how to clearly distinguish the three proposed domains of life, and how they are interrelated," Gupta says. "The suggestion [of] a fourth domain will only add to the confusion."
Eric Bapteste at Pierre and Marie Curie University in Paris, France, is far more receptive. "The facts are that there is lots of genetic diversity, and unquestionably most of it is unknown to us," he says. "It's legitimate to consider that there's genuinely new stuff out there."
Further analysis of the samples could determine whether the two gene families studied have evolved unusually rapidly or are from a cellular organism with a universally bizarre genome, he says.

Parent organism

Looking at the actual samples could also help pin down exactly which organism the strange genetic sequences belong to, says Eisen.
If Eisen's gene sequences did turn out to belong to a new domain of life, it wouldn't be the first time the tree of life has had to be redrawn. Until the 1990s, it had just two branches: one for eukaryotes – animals, plants, fungi and some other strange forms, including the slime moulds – and one for everything else. Then, gene analysis revealed that the "everything else" branch could be divided into two domains: bacteria and archaea.
Not only that, some believe that mimivirus, the largest known virus, may also represent a new domain of life: despite being recognised as a virus, it contains many genes found only in cellular organisms. "People have suggested they might be a fourth branch themselves," says Eisen. "If you think of those mimiviruses as a fourth branch, maybe our sequences represent a fifth branch – we just don't know yet."

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