Illuminating Biology’s Dark Matter


In cosmology, dark matter is said to account for the majority of mass in the universe. Its presence, however, is inferred by indirect effects rather than detected through telescopes. The biological equivalent is “microbial dark matter,” a largely unexplored realm of microbial life on Earth that can profoundly influence key environmental processes such as plant growth, nutrient cycles, the global carbon cycle, and climate processes. An international collaboration, led by the U.S. Department of Energy’s Joint Genome Institute (DOE JGI) where the sequencing of genomes isolated from single cells was carried out, targeted uncultivated microbial cells from nine diverse habitats, derived from 28 major, but previously uncharted branches of the tree of life. The results fall into three main areas: 1) metabolic features previously only seen in bacteria are also found in Archaea, such as an enzyme used by bacteria to “thin out” their protective cell wall so that the cell can expand during cell division; 2) the ability to correctly assign data from 340 million DNA fragments from other habitats to the proper lineage, linking these fragments to organisms and particular ecosystems, as well as providing insights into possible functional roles; and 3) the ability to more accurately resolve microbial taxonomical relationships within and between microbial phyla, which is critical to predict ecological niches and capabilities. The new results will enable scientists to better predict metabolic properties and other useful traits of different microbial groups. The Nature publication builds upon a DOE JGI pilot project, the Genomic Encyclopedia of Bacteria and Archaea (GEBA).

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Rinke, C., P. Schwientek, A. Sczyrba, N. N. Ivanova, I. J. Anderson, J.-F. Cheng, A. Darling, S. Malfatti, B. K. Swan, E. A. Gies, J. A. Dodsworth, B. P. Hedlund, G. Tsiamis, S. M. Sievert, W.-T. Liu, J. A. Eisen, S. Hallam, N. C. Kyrpides, R. Stepanauskas, E. M. Rubin, P. Hugenholtz, and T. Woyke. 2013. “Insights into the Phylogeny and Coding Potential of Microbial Dark Matter,” Nature 499 , 431–37. DOI: 10.1038/nature12352.