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.

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 the Global 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." ...

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." ...

via Biology's 'dark matter' hints at fourth domain of life - life - 18 March 2011 - New Scientist.