29 new branches on the tree of life

The current rage in physics drives researchers to learn about dark matter, the missing mass in the universe that must exist according to theories of the universe. On biological frontiers, a similar challenge lurks: the vast majority of species exist in a sort of 'dark matter' biomass. But new tools are shedding light on the microscopic organisms that, although invisible to our eyes, constitute the "most diverse and abundant" life forms on earth.

Much of the tree of life remains undefined because these microorganisms fail to grow in a petri dish in a lab environment. Advances in genetic sequencing enable identification of the genome from a single microbe, eliminating the need to multiply the sample by culturing before genetic analysis can succeed.

Excerpt of image showing environmental sample processing leading to genome sequencing© Courtesy of C Rinke et al. Nature 000, 1-7 (2013) doi:10.1038/nature12352
A report in Nature details the use of this technology to map 201 genomes. It is a small but decisive step towards understanding the millions of undescribed species around us. Tanja Woyke, senior author on the article, notes:

To try to capture 50 percent of just the currently known phylogenetic diversity, we would have to sequence 20,000 more genomes, and these would have to be selected based on being members of underrepresented branches on the tree. And, to be sure, these are only what are known to exist.

But the first couple hundred microbes have already drawn 29 more branches onto the tree of life. Although the existence of these species was known from previous RNA surveys, their place in the family of lifeforms was not fully charted until these genomes were available. After aligning the genomes to the branches of known phyla, the research team recommends 29 additional phyla be created to describe the new diversity.

Keep in mind that phyla represent early splits of the branches. To put it in perspective: there are only about 35 known phyla in the animal kingdom and 12 in the plant kingdom. So 29 new phyla represents a huge leap forward in our knowledge about the diversity of the microbial domains of Bacteria, Archaea, and Eucarya.

The geographic location of all 475 metagenome sample sites© Courtesy of C Rinke et al. Nature 000, 1-7 (2013) doi:10.1038/nature12352
Perhaps this study will do even more than add branches to the tree, though. One shocking result of the new genomic data, as described by corresponding author Philip Hugenholtz:

For me the most surprising findings were the numerous instances of genes moving between domains (Bacteria, Archaea, Eucarya) that encode functions that were previously thought to be highly conserved within a domain.

This suggests that life cannot so easily be understood merely by a tree structure, with shared characteristics dropping away as life evolves in distinct directions. Instead, we see life re-using solutions that work for one lifeform in another context.

Tags: Algae | Bacteria | Biodiversity | Biomass | Evolution


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