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“Comparative Metagenomics of Microbial Communities”
Science, April 22, 2005

Environmental Genomics: Opening a New Window into Microbial Diversity and Function
U.S. Department of Energy Office of Science

First Genomes Revealed from Environmental Microbial Communities
DOE Joint Genome Institute Press Release, Feb. 2, 2004

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  Contact: David Gilbert
  Phone: (925) 296-5643
April 21, 2005

Genetic fingerprints yield insights
into health of diverse ecosystems

WALNUT CREEK, Calif. — Groundbreaking research led by the U.S. Department of Energy Joint Genome Institute (DOE JGI) demonstrates for the first time that the signatures of the genes alone in terrestrial and aquatic samples can accurately diagnose the health of the sampled environments.

Whale Skeleton on Ocean Bottom
DNA from this whale skeleton provides researchers with information about environmental conditions in the Santa Cruz Basin. The photo was taken about one mile below sea level, four and one-half years after the whale died in 1998.

The study, published in the April 22 edition of the journal Science, positions large-scale genome sequencing to accelerate advances in environmental sciences akin to the contributions DNA sequencing has made to biomedical sciences.

“These DNA sequence fingerprints can be used to provide highly accurate assessments of the vitality of extremely diverse environments,” said Dr. Raymond L. Orbach, Director of the DOE Office of Science, which supported the research. “These fingerprints can be used to reveal environments under stress as well as signal progress in remediating contaminated environments. This may well develop environmental ecology into a fully quantitative science.”

Dubbed environmental genomic tags, or EGTs, the indicators capture a DNA profile of a particular ecological niche and reflect the presence and levels of nutrients, pollutants, and other environmental features.

The EGT approach employed in the study shares similarities with aspects of the Human Genome Project research. In the early 1990s, incomplete fragments of human genes called expressed sequence tags (ESTs) were used as diagnostic fingerprints for human tissues to determine their unique features and disease status. These information-rich data allowed researchers to forge ahead with studying genes important in disease processes, long before the completion of the entire human genome.

“EGT fingerprints may be able to offer fundamental insights into the factors impacting on various environments,” said DOE JGI Director Eddy Rubin, who led the research team. “With EGTs we don’t actually need a complete genome’s worth of data to understand the functions required of the organisms living in a particular setting. Rather, the genes present and their abundances in the EGT data reflect the demands of the setting and, accordingly, can tell us about what’s happening in an environment without knowing the identities of the microbes living there,” Rubin said.

Silage Farm in Minnesota
Aerial view of the farm in Waseca County, Minnesota, where researchers gathered soil samples from the drainage area of a silage bunker for large-scale genome sequencing.

The EGT fingerprints capture a DNA profile of a particular ecological niche and reflect the presence and levels of nutrients and pollutants, as well as features like light and temperature. For example, genes involved in breaking down plant material are over-represented in soil and absent in sea water; while in sea water, genes involved in the passage of sodium, a major chemical component of salt water, are particularly abundant. As light is a major energy source for microbes living in surface water, there was an abundance of genes involved in photosynthesis in samples collected from shallow water. These differences in the abundances of genes involved in particular functions provide DNA clues to features of the environments where the samples were taken. Importantly, the DNA clues were easy to find despite the vast numbers of different individual microbial species within the samples.

Rubin argues that the genes and their relative abundance as gleaned from EGTs reflect the intricate physical and biochemical details of a given environment even if the actual identities of the resident microbes are unknown. This finding is crucial for studies of microbes in the wild, since the sheer number of different organisms present in nearly all environments makes it a daunting task to sequence this multitude of organisms one at a time. With the EGT approach, an abbreviated sequencing effort enables scientists to piece together the information and form a useful metabolic picture of an entire complex environment.

The study was done in collaboration with Diversa Corporation of San Diego, Calif., which provided the DNA from environments ranging from soil from a Minnesota farm to samples of several whale skeletons collected from the Pacific and Arctic ocean depths separated by thousands of miles. The DNA was then sequenced and analyzed by the DOE JGI. While different environments present different metabolic pictures, this research, Rubin said, facilitates a holistic perspective on environmental systems – an approach that many scientists will welcome.

Toxic Runoff from Iron Mine
Site of the first microbial community to have its genetic identities revealed by large-scale genome sequencing. Microorganisms thriving in toxic conditions, known as "extremophiles," were recovered from a natural biofilm growing at the Richmond Mine in Iron Mountain, California. The complex interaction of microbes, water, and exposed ore has generated dangerously high levels of sulfuric acid and toxic heavy metals that ultimately find their way into the upper Sacramento River ecosystem.

“Environmental systems are extremely complex, harboring numerous diverse species coexisting in a single locale,” said Rubin. “By focusing on the information encoded in the DNA fragments sequenced, independent of the organisms from which they derived, we were able to get around the problem of species diversity.”

Very little is known about the microbes since the vast majority of them, some 99 percent, are resistant to being grown under standard laboratory conditions. The EGT strategy’s particular utility is that it offers an easily accessible window into that important part of the biosphere with significant impact on the environment.

DOE JGI postdoctoral fellow Susannah Green Tringe was first author on the Science paper that, in addition to other DOE JGI scientists, included collaborators from Diversa Corporation and the European Molecular Biology Laboratory, Heidelberg, Germany.

The DOE Joint Genome Institute, supported primarily by the Department of Energy’s Office of Biological and Environmental Research in the DOE Office of Science, is among the world leaders in whole-genome sequencing projects devoted to microbes and microbial communities, model system vertebrates, aquatic organisms, and plants. Established in 1997, JGI now unites the expertise of four national laboratories – Lawrence Livermore, Lawrence Berkeley, Los Alamos, and Oak Ridge – along with the Stanford Human Genome Center to advance the frontiers of genome sequencing and related biology. More information about JGI can be found at the JGI Website.

Founded in 1952, Lawrence Livermore National Laboratory is a national security laboratory that develops science and engineering technology and provides innovative solutions to our nation's most important challenges. Lawrence Livermore National Laboratory is managed by Lawrence Livermore National Security, LLC for the U.S. Department of Energy's National Nuclear Security Administration.