New Catalytic Pathway for the Reduction of CO2 to CO Under Mild Conditions
Bay Area Air District, California Free Up Additional $3M For Oakland Port Trucks

Researchers Publish First Volume of Genomic Encyclopedia of Bacteria and Archaea; Resource for Optimizing Biofuels, Bioremediation and Carbon Capture

Genome researchers from the US and Germany have published the initial “volume” of the Genomic Encyclopedia of Bacteria and Archaea (GEBA)—an analysis of the first 56 genomes sequenced from the two domains. The paper appeared in the 24 December edition of the journal Nature.

The 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. Close to 2,000 microbes have been and are being decoded to date. The GEBA pilot was launched in May 2007 in collaboration with 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.

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

“Microbes run the world. It’s that simple.”
—2007 NAS report on Metagenomics

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

Comments

Jonathan Eisen

In case anyone is interested, have posted some additional details about the paper, some more links to discussions on the web, and the story behind the work, on my blog (I was the senior author of the study): here and here .

Stan Peterson

Taxonomy is a necessary prerequiste to being able to describe and measure the population and healht of the Worl's flora and fauna.

Wild exagerations of massive die-off of species are just that. When taxanomic evidence is requested, none is forthcoming. So it is massive exageration based on no valid Science. Just fearsome proprosals and fear mongering without foundation, to increase donations from the gullible.

The reality is that Science has determined the existence of massive increases in the Terran biota over the past half decade. Biota estimated to equal the entire tonnage of all life on Earth has been discovered.

All this life living in the very rocks for miles beneath the sea, was previously unknown. This biota also explains much of the sources of petroleum. It is not only from dead dinosaurs; this living biota equal to at least all the weight of all other life on Earth, create it every single day of their lives.

It just goes to show that we have catalogued far from even half of the species on the Earth, so there is no way to establish species die-off.

The sky-is-falling doomsayers can't name 25 species doccumented to have gone extinct in the past decade. This even as we have found at least a million more species of microbes. Yet it serves their interest to scare the wits out of the gullible to augment their cushy lifestyles.


Jerry

Fools have no interest in understanding;
they only want to air their own opinions.
Proverbs 18:2

Verify your Comment

Previewing your Comment

This is only a preview. Your comment has not yet been posted.

Working...
Your comment could not be posted. Error type:
Your comment has been posted. Post another comment

The letters and numbers you entered did not match the image. Please try again.

As a final step before posting your comment, enter the letters and numbers you see in the image below. This prevents automated programs from posting comments.

Having trouble reading this image? View an alternate.

Working...

Post a comment

Your Information

(Name is required. Email address will not be displayed with the comment.)