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February 17, 2004
A Gene-Sequencing First: Microbial Communities Collected
in the Environment

The first genomic characterization of a microbial community has been reported by researchers from the Department of Energy's Joint Genome Institute (JGI) and the University of California at Berkeley. They determined the genetic identities of several microorganisms that thrive in toxic conditions, known as "extremophiles," which were recovered from a natural biofilm growing at an Environmental Protection Agency Superfund site.

Up to this point, four out of every five microbes found in the wild have defied laboratory culture; they have only been studied in their natural habitat, in this instance runoff from an abandoned mine, or acid mine drainage. Jillian Banfield and her colleagues from UC Berkeley and Lawrence Berkeley National Laboratory, who have been studying this site for the past eight years, retrieved the sample from the depths of one of the nation's worst Superfund sites: Iron Mountain, California, near the northern town of Redding.

The genomes of several microbial species were sequenced from this pink biofilm community, collected from acid mine drainage in the Richmond Mine at Iron Mountain, California.

"For the first time we have managed to tease out genetic information directly from an environmental sample," says Eddy Rubin, director of the Joint Genome Institute. The traditional way DNA has been sequenced has been to cultivate an isolated organism in the laboratory. "In the community sequencing approach, we extract DNA directly from the environmental sample, which can contain millions of diverse organisms, a veritable microbial ecosystem."

Decades of earthmoving activity at the Richmond Mine in Iron Mountain created opportunities for microbes to colonize the site. The complex interactions of microbes, water, and exposed ore have generated dangerously high levels of sulfuric acid and toxic heavy metals that ultimately find their way into the upper Sacramento River ecosystem.

Banfield's team applied the screening technique known as FISH (fluorescence in situ hybridization), a microscopic technique for a gross assessment of the microbial composition before sequencing at the JGI. A panoply of bacteria and archaea emerged, including those from the Leptospirillum and Ferroplasma genera, which are implicated in mine leaching. Archaea are the remnants of an ancient group of organisms that bridge the gap in evolution between bacteria, prokaryotes, and the eukaryotes, those organisms whose cells have a nucleus.

"We extensively sampled the genomes of the dominant members of one of the microbial communities we were studying," says Banfield. "Our analyses of the assembled data have revealed a great deal about the population structure as well as the nature of pathways central to survival of the microbial community."

"This is our first look at a full microbial community using the powerful technologies pioneered by the Department of Energy," said Dr. Raymond L. Orbach, director of the Department of Energy's Office of Science. "Microbes thrive literally everywhere on earth, under all conditions, including extreme acidity, metal contamination and high radiation. Studies such as this by researchers from JGI and Berkeley will help DOE's Office of Science learn how microbes use inorganic materials as a source of energy that not only drives their cellular machinery but can also be used to clean up contaminated soil or water, capture carbon from the atmosphere, or produce potentially important sources of energy such as hydrogen and methane."

Shotguns and all that JAZZ

Microbial communities, though often undetected by the naked eye, play integral roles in the ecosystems where they reside. Examination of such actors, good or bad, has been difficult because the vast majority of microorganisms resist cultivation in the laboratory, so their actual function within the environment may remain cryptic. Now, however, by applying the shotgun-sequencing strategy to the problem, information about these communities and their interactions with their environment is surfacing.

The shotgun-sequencing process entails cutting up the long strands of DNA bound into the organism's genome into manageable pieces of approximately 3,000 base pairs. Then, methodically, these pieces are labeled and fed through sequencing machines to generate the exact order of nucleotide letters in the microbial genomes. By employing JAZZ, a computational tool developed at the JGI for the assembly of genomes, the ends of these fragments are compared and the genomic sequence reconstructed; other algorithms identify the genes and their possible functions.

"This work has provided a fascinating window, not only into the diversity of the species involved but their interdependency," says Rubin. "And just as we have found in our studies of vertebrate genomes, the individual differences within those species are coming to light."

Over the last ten years DOE has had an abiding interest in microbial genomics, a spin-off from its significant sequencing contribution to the Human Genome Project. "The current sequencing capacity of the JGI now approaches 2 billion bases per month—among the world leaders in this respect. We are now in a position to take the microbial genomes such as those described in the Nature paper and completely sequence them in a matter of days," says JGI Director Rubin.

"Community structure and metabolism through reconstruction of microbial genomes from the environment," by Gene Tyson, Philip Hugenholtz, Eric E. Allen, Rachna J. Ram, and Jillian F. Banfield of UC Berkeley's Department of Environmental Science, Policy and Management; the Joint Genome Institute's Paul Richardson and Victor Solovyev; and Jarrod Chapman and Daniel Rokhsar of both JGI and UC Berkeley's Department of Physics, appeared in Nature, 1 February, 2004.

Support for the project came from the DOE Microbial Genome Program within the Office of Science and the National Science Foundation's Biocomplexity in the Environment program.

The Joint Genome Institute (JGI), located in Walnut Creek, California, was established in 1997 by the three DOE national laboratories managed by the University of California: Lawrence Berkeley National Laboratory and Lawrence Livermore National Laboratory in California and Los Alamos National Laboratory in New Mexico.

In addition to its microbial sequencing projects, JGI has whole-genome sequencing programs that include vertebrates, fungi, and plants. Funding for the JGI is predominantly from the Office of Biological and Environmental Research in DOE's Office of Science.

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