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Boldly illuminating biology's 'dark matter'
Date:7/14/2013

ific Rise; the Homestake Mine in South Dakota; and the Great Boiling Spring in Nevada. From these samples, the team laser-sorted 9,000 cells, from which they were able to reassemble and identify 201 distinct genomes, which then could be aligned to 28 major previously uncharted branches of the tree of life.

"Microbes are the most abundant and diverse forms of life on Earth," said Tanja Woyke, DOE JGI Microbial Program Head and senior author on the Nature publication. "They occupy every conceivable environmental niche from the extreme depths of the oceans to the driest of deserts. However, our knowledge about their habits and potential benefits has been hindered by the fact that the vast majority of these have not yet been cultivated in the laboratory. So we have only recently become aware of their roles in various ecosystems through cultivation-independent methods, such as metagenomics and single-cell genomics. What we are now discovering are unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the domains of life."

To get around the difficulty of growing most microbes in the lab, recent efforts have focused on conducting surveys based on sequencing marker or 16S ribosomal RNA genes that are conserved across microbial lineages because of their essential role as "housekeeping" genescritical for the organism's survival. Genome sequencing of the rest of the genomes of most of these lineages is however proceeding much more slowly. "Microbial genome representation in the databases is quite skewed," said Chris Rinke, DOE JGI postdoctoral fellow and first author of the study. "More than three-quarters of all sequenced genomes fall into three taxonomic groups or phyla but there are over 60 phyla we know of." For the majority of them, however, there are no cultivated members available.

"Based on 16S surveys we know they're out there, but we don't know much about themthat's why we
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Contact: David Gilbert
degilbert@lbl.gov
DOE/Joint Genome Institute
Source:Eurekalert

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