Microbes mediate almost every conceivable biological process on the planet and genome sequencing has revolutionized our understanding of the diverse roles that they play. The information from this first set of organisms has provided a rich source of novel enzymes and detailed biochemical pathways that can help scientists optimize processes of critical importance to areas of the DOE mission, such as biofuels production, bioremediation, and how carbon is captured and cycled in the environment.

—DOE JGI Director Eddy Rubin

Most studies in microbiology have exploited a narrow subset of the evolutionary diversity of bacteria and archaea known to exist, and were selected more for convenience (and because they cause diseases) rather than the opportunity to advance discovery science. From the tree of microbial diversity the genomes from only a few branches have been sequenced. The DOE JGI is now exploring Earth’s microbial “dark matter” with a project to sequence little-studied microbial species that will inform other microbes and complex microbial communities.

The main driver behind the GEBA project is that while the currently available sequenced genomes cover a wide range of biological and functional diversity, they have not covered a wide enough range of phylogenetic diversity. What distinguishes GEBA is that it is less about the individual genomes and more about building a more balanced catalog of the diversity of genomes present on the planet which in turn should facilitate searches for novel functions and our understanding of the complex processes of the biosphere.

—senior author Jonathan Eisen, DOE JGI Phylogenomics Program Head and Professor at UC Davis

Beyond filling in what he refers to as the “phylogenetic dark matter of the biological universe,” Eisen said that the information flowing from the project will shed light on the diversity of gene families and improve the understanding of how microbes acquire new functions. In addition, the newly sequenced organisms will provide urgently needed anchors for the improved annotation (assessment of biological function) of data emerging from the many ongoing projects that have expanded upon the idea of studying individual microbes by studying entire communities, deciphering specific microbial capabilities from complex environmental samples. A key outcome will be new gene products and enzymes previously unknown to biologists.

Several of the characterized microbes from the first GEBA “volume” are paying dividends. DOE JGI researchers Natalia Ivanova and Athanasios Lykidis discovered a novel set of cellulases in a variety of GEBA organisms. In partnership with the DOE Joint BioEnergy Institute, researchers synthesized these genes and have begun to characterize them. These enzymes are of particular interest because they should be active in highly acidic environments, which could make them valuable for the liquid pretreatment of biomass feedstocks for biofuels.

This is only the start. The known phylogenetic diversity of bacteria and archaea is immense with hundreds of major lineages and probably millions if not hundreds of millions of species. This encyclopedia project is starting at the top—with the major phylogenetic groups—100 genomes from across the tree. But we have barely scratched the surface of characterizing the diversity on the planet.

—Jonathan Eisen

Eisen and his colleagues hope to extend GEBA beyond the pilot phase to sequence hundreds, and perhaps even thousands, of genomes from additional unknown microbes.

Detailed descriptions for all of the individual sequenced GEBA organisms are being published in the recently launched Journal Standards in Genomic Sciences (SIGS) the official open access online publication of the Genomic Standards Consortium (GSC).

Resources

• List of the GEBA pilot project targets

• Dongying Wu et al. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462, 1056-1060 doi: 10.1038/nature08656

• The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet (NAS 2007)