Despite the multitudes of microbes that reside on earth, our knowledge of them is quite limited. Of the estimated nonillion (1030) that exist, scientists have or are in the process of decoding 2,000 microbial genomes,  which means there is a vast unknown realm awaiting those researchers intent on exploring microorganisms that inhabit this planet.

In hopes of exploring that realm and expanding our understanding of microbes, a team from the the Department of Energy's Joint Genome Institute (DOE JGI) have released the first volume of the Genomic Encyclopedia of Bacteria and Archaea (GEBA), an analysis of the first 56 genomes representing two of the three domains of the tree of life. The encyclopedia is detailed in the December 24 issue of Nature.

The researchers point out that 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,” said senior author Jonathan Eisen, DOE JGI Phylogenomics Program Head and University of California, Davis Professor. “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.”

Eisen says that there are many benefits to be gained from this phylogeny-driven approach. 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.

Already, 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—enzymes capable of breaking down plant material into sugars that can be rendered into transportation fuel—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,” said Eisen, reinforcing the magnitude of the project beyond the pilot phase.  “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.”  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.

Citation: Wu, D. et al., 'A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea', Nature 2009, 462, 1056-1060; doi:10.1038/nature08656