Microbial explorations. Many environments, including this lake, are full of mysterious microbes (inset) that can now be characterized by single-cell genomics.

Alyse Hawley and Steven Hallam/U.British Columbia; (inset) Xiangzhen Li and Wen-Tso Liu/U. Illinois at Urbana-champaign

ScienceShot: Shining Light on the 'Dark Matter of Life'

It lives around the world, yet nobody has ever seen it. Meet TM6, a newly revealed group of bacteria that are part of the "dark matter of life," organisms that are all around us but are hard to study because they can't be grown in the lab. Since 1996, the only clue that the TM6 bacteria existed were their trademark 16S genes, which all bacteria have and which are used like an ID card in surveys of the microbes living in a certain place. (16S sequencing is the basis of the Human Microbiome Project, for instance.) Similar 16S genes were occasionally turning up around the world in water pipes, peat bogs, and caves, leading microbiologists to name the group and classify it as a phylum, a classification several levels higher than species. (The upper right of this image shows a family tree of all phyla of bacteria; TM6 is a thin branch near the top.) Researchers found a few cells of the elusive microbes in a hospital restroom sink drain. Using new computational techniques, they were able to reconstruct a TM6 genome, even though it was mixed with that from other microbes. With the resulting sequence (shown as the large circular image above), they were able to sketch out some of TM6's characteristics. As they report online today in the Proceedings of the National Academy of Sciences, members of this phylum can probably live with or without oxygen and may even have a niche as parasites inside larger cells like amoebas. The techniques used could pave the way to discovering more of the elusive, impossible-to-grow microbes that make up the dark matter of life.

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