Researchers have published the first volume of ‘Genomic Encyclopedia of Bacteria and Archaea’ (GEBA) that should lead as a resource for optimizing biofuel production, efforts at bioremediation and perhaps if the climate guys can restore some credibility, maybe carbon capture.

The researchers are from the U.S. and Germany with the first volume built out of the first 56 genomes sequenced from the two of the three domains of life. The letter has appeared in the December 24th edition of the journal NatureThe press release says, “a vast unknown realm awaits scientists intent on exploring microorganisms that inhabit this “undiscovered country.” Sort of Star Trek, but a truth.

Phylogenetic Tree of the Bacterial Domain. Click image for more info.

The planet Earth is estimated to have about a nonillion (1030) microbes in, on, around, and under it, comprising an unknown but very large number of distinct species.  To date about 2,000 microbes have been and are being decoded.  The idea to get this going was launched in 2007 in a collaboration with Department of Energy Joint Genome Institute and the non-profit German Collection of Microorganisms and Cell Cultures, DSMZ, to sequence 100 bacterial and archaeal genomes based on the phylogenetic positions of organisms.

DOE JGI Director Eddy Rubin says, “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.”

Most studies in microbiology have exploited a narrow subset of the evolutionary diversity of bacteria and archaea known to exist. The choices 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 world in more depth with a project to sequence little-studied microbial species that will inform about other microbes and complex microbial communities.

Senior author Jonathan Eisen, DOE JGI Phylogenomics Program Head and University of California, Davis Professor says, “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.”  There, the point he’s trying to make is to get a working inventory of what sequences can do what.

Eisen goes on explaining 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.

It’s getting possible soon that a fully designer organism will be within reach.

The U.S. DOE has a well-established tradition of contributing to the advancement of microbial genomics for energy and environmental applications.  A 2007 National Academy of Sciences report on this study of microbial communities or “Metagenomics” said, “Microbes run the world. It’s that simple.”  That’s a pretty wide-ranging comment, but from a biological viewpoint – accurate.  Microbes do the massive and complex work of changing out waste molecules of one step into the foods and fuels for the next steps in the food chain for all life on earth.

Several of the characterized microbes from the first GEBA “volume” are already 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 the listed GEBA organisms.  The researchers synthesized the genes and have begun to characterize them.  The 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.

Hans-Peter Klenk, Head of the Department of Microbiology at DSMZ says, “The GEBA project perfectly fits with our vision for the future of microbial taxonomy and the collection of type strains in general. DSMZ will provide easy and affordable access to biological material, cultures as well as DNA, of all GEBA pilot project strains to the worldwide scientific community – without any strings attached. Moreover, participation in the GEBA pilot project provides an excellent opportunity to train the next generation of genome scientists.”

Nikos Kyrpides, JGI Genome Biology Program Head, who helped launch the project and whose group designed and administers the GEBA data management and analysis system in collaboration with the Biological Data Management and Technology Center of LBNL says, “GEBA is a triumph of edgy science from two government institutions with perfect complementarities, forming an international partnership for the benefit of the entire community.”

Eisen says this is only the start so 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.

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

Now this is progress in the making.


2 Comments so far

  1. Wing Chun on January 6, 2010 6:38 AM

    […] The First Genome for Bacteria And Archaea Goes Online | New Energy … […]

  2. What are the three Domains and the types of organisms in Biology? | BingSite on May 10, 2010 3:42 PM

    […] The First Genome for Bacteria And Archaea Goes Online | New Energy and Fuel […]

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