DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Science Highlights
    • Scientists
    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

    More

    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

    More

    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

    More

    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

    More

    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

    More

    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

    More

    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

    More

    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

    More

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

    More

    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

    More

    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

    More

News & Publications
Home › News Releases › DOE JGI Finishes 100th Microbial Genome

May 23, 2006

DOE JGI Finishes 100th Microbial Genome

ORLANDO, Florida — Microbes, thriving in even the world’s most extreme environments, are capable of performing myriad biological functions, learned over the billions of years they have inhabited the planet. Those lessons, and how they can be captured to render clean renewable sources of energy and to repair damaged environments, are among the many secrets encoded in their DNA sequence. On May 23, at the general meeting of the American Society of Microbiology (ASM), the U.S. Department of Energy Joint Genome Institute (DOE JGI) will announce that it has finished the sequence of 100 microbial genomes and released this information for the benefit of the global research community.

ASM President Dr. Stanley Maloy, who will touch on DOE JGI’s achievement in his President’s Forum remarks, said that the 100 microbes represent a rich portfolio of the vast and mostly uncharacterized microbial world. “DNA sequencing has opened a particularly productive vein to mine in exploring and expanding the frontier of microbiology. Especially where, through conventional culture methods, we are unable to shed light on the metabolic profiles of these microorganisms and their environmental implications, DNA sequencing provides us a welcome set of tools.”

“The power of DOE JGI sequencing microbes, and other organisms, is that it gives us the complete genomic ‘parts list’ of those organisms,” said Dr. Raymond L. Orbach, Director of the DOE Office of Science. “With this list in hand, we can explore how microbes use these parts to build and run their key functions, many of critical importance to DOE because they can break down plant materials to produce such useful sources of energy as ethanol and hydrogen, and clean up toxic waste sites. We know that microbes can perform these and a multitude of other amazing tasks and with the proper technology we can harness these capabilities.”

DOE JGI, a national user facility, has sequenced or is in the process of sequencing over 380 organisms, more than any other institution in the world. DOE JGI averages over 3.1 billion bases or letters of sequence generated per month, or roughly the equivalent of a human genome once over. As microbes range in size from typically five to tens of millions of bases, several microbes could be sequenced in one day. However, the sequencing process, in order to meet rigorous quality standards and to satisfy the demands of the scientific community, is an iterative one, requiring six- to eight-times coverage. The term “finished,” associated with the 100 microbial genomes accomplished by DOE JGI, is a technical designation referring to a standard of accuracy established for the Human Genome Project of tolerating no more than one mistake in 50,000 letters of genetic code with no gaps.

The microbes sequenced by DOE JGI, both single-celled and those multi-celled organisms invisible to the naked eye, cross all main branches of the tree of life: Eubacteria, Archaea, and even the Eukaryota, which include microscopic fungi, plants, and animals.

The 100th microbial genome, a project originally proposed by Dr. Kevin Sowers of the Center of Marine Biotechnology at the University of Maryland Biotechnology Institute (UMBI), is Methanosarcina barkeri fusaro, a methane-producing organism that exploits a unique metabolic pathway to do the job. This microbe, while isolated from a freshwater mud sample, also lives in the rumen of cattle where cellulose and other polysaccharides are digested.

“We are delighted that the DOE JGI’s 100th genome is a microorganism that one of our UMBI faculty members has been studying to evaluate its potential for bioremediation and as an alternative energy source,” said Dr. Jennie Hunter-Cevera, UMBI President. “By sequencing this and other important organisms, DOE JGI is helping to accelerate biotechnology discovery and innovation.”

Microbes are critical micromanagers in the balance of nature. DOE JGI collaborator Dr. Donald A. Bryant, Ernest C. Pollard Professor of Biotechnology and Professor of Biochemistry and Molecular Biology at Penn State University, elaborates.

“Green sulfur bacteria, Chlorobi, are extremely important players in the global cycling of carbon, sulfur, and nitrogen,” said Bryant. “Thanks to DOE JGI, the availability of multiple genome sequences for the Chlorobi has turbocharged our functional genomics studies. This has allowed us to make remarkable progress in understanding sulfur and ferrous iron oxidation, carotenoid and chlorophyll biosynthesis, photosynthetic light harvesting, oxygen tolerance, and many other aspects of the physiology and metabolism of the green sulfur bacteria.”

The search for microorganisms that can inform solutions to energy and environmental challenges can go to the extremes–the boiling hot pools in Yellowstone National Park, for instance–and lead to new biotechnology products.

“DOE JGI has played an invaluable and otherwise unavailable role in the development of new enzymes for industrial use,” said David Mead, President & CEO, of Lucigen Corporation. “The sequence acquisition of DNA from superheated thermal aquifers and other unique sources has resulted in the discovery of a new class of thermostable DNA polymerases and unique thermostable cellulase and hemicellulase enzymes. Without the DOE JGI these valuable molecules would not have made it into the marketplace.”

The list below features highlights of some of the finished 100 and references the collaborating institutions and the roles of the organisms in their environment.

Acidothermus cellulolyticus ATCC 43068. Alison Berry, University of California, Davis. Isolated from acid hot spring in Yellowstone; degrades cellulose, source of high-temperature enzymes.

Clostridium thermocellum. David Wu, University of Rochester; Mike Himmel, National Renewable Energy Laboratory. Cellulose degrader.

Cytophaga hutchinsonii ATCC33406. Mark McBride, University of Wisconsin Milwaukee. Cellulose degrader.

Frankia Cc13. Louis Tisa, University of New Hampshire. Fixes nitrogen; promotes formation of woody-biomass energy source.

Pichia stipitis. Thomas W. Jeffries, University of Wisconsin, Madison, USDA, Forest Service, Forest Products Laboratory, with José M. Laplaza; Volkmar Passoth, Swedish University of Agricultural Sciences (SLU), Yong-Su Jin, MIT: Ferments xylose to ethanol; potential to oxidize products of lignin degradation and plays a role in cellulose degradation.

Saccharophagus degradans 2-40. (formerly Microbulbifer degradans) Ronald Weiner, University of Maryland. Marine microbe degrades and recycles insoluble complex polysaccharides; potential for conversion of complex biomass to energy.

Thermobifida fusca YX. David Wilson and Diana Irwin, Cornell University. Major degrader of organic materials.

Moorella thermoacetica ATCC39073. Steven Ragsdale, University of Nebraska. Fixes carbon dioxide in absence of oxygen.

Nostoc punctiforme. Jack Meeks, University of California, Davis. Fixes carbon dioxide and nitrogen; produces hydrogen; survives acidic, anaerobic, and low-temperature conditions.

Burkholderia species. Jim Tiedje, Michigan State University. Outstanding degrader of polychlorinated biphenyls (PCBs).

Chromohalobacter salexigens DSM 3043 (formerly Halomonas elongate). Laszlo Csonka, Purdue University; Brad Goodner, Hiram College; Aharon Oren, The Hebrew University of Jerusalem. Extremely salt tolerant; displays metal resistance; degrades aromatic hydrocarbons and toxic organics.

Deinococcus geothermalis DSM11300. Michael Daly, Uniformed Services University of the Health Sciences, James K. Fredrickson, Pacific Northwest National Laboratory, Kira S. Makarova, National Institutes of Health. Resists radiation; can bioremediate radioactive mixed waste.

Desulfovibrio desulfuricans G20. Judy D. Wall, University of Missouri. Reduces sulfate, uranium, and toxic metals; corrodes iron piping; “sours” petroleum with hydrogen sulfide.

Geobacter metallireducens. Derek Lovley, University of Massachusetts. Important player in the carbon and nutrient cycles of aquatic sediments and in the bioremediation of organic and metal contaminants in groundwater.

Rhodobacter sphaeroides. Samuel Kaplan, University of Texas Health Sciences Center at Houston. Metabolically diverse, grows in wide variety of conditions; photosynthetic, providing fundamental insights into light-driven, renewable-energy production; can detoxify metal oxides.

Shewanella species. Jim Fredrickson, Pacific Northwest National Laboratory. Degrades metals including uranium, technetium, and chromium; important in carbon cycling in anaerobic environments.

DOE JGI provides the scientific community at large with access to DNA sequencing for DOE-relevant projects based on scientific merit as judged through independent peer review. Nominations, due August 10, 2006, are currently being sought for candidate microbes, microbial consortia, for draft genomic sequencing in support of DOE’s Office of Biological and Environmental Research (BER) Bioenergy Program element within its Genomics: GTL Program. Nominated candidates must be relevant to the BER mission to determine genomic sequences of microorganisms involved in energy production, particularly conversion of lignocellulosic material to ethanol, or hydrogen, or other biofuels.

The DOE Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories, Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest, along with the Stanford Human Genome Center to advance genomics in support of the DOE mission related to clean energy generation and environmental characterization and clean-up. DOE JGI’s Walnut Creek, Calif. Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.

Share this:

  • Click to share on Facebook (Opens in new window)
  • Click to share on LinkedIn (Opens in new window)
  • Click to share on Pinterest (Opens in new window)
  • Click to share on Twitter (Opens in new window)
  • Click to print (Opens in new window)

The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. JGI provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @jgi on Twitter.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Filed Under: News Releases

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles

Related Content:

Busting the Unbreakable Lignin

Pictured is a micrograph of Neocallimastix californiae.

Tracing the Evolution of Shiitake Mushrooms

A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.

JGI announces final round of 2022 Functional Genomics awardees

Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!

Introducing New Members of the JGI User Executive Committee

incoming 2023 UEC members

JGI at 25: Mapping Switchgrass Traits with Common Gardens

Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)

JGI Contributes Nine to 2022 Highly Cited Researchers List

Nine headshots, one for each researcher, laid out beside a purple ribbon reading, "Home to Highly Cited Researchers 2022 Clarivate"
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2023 The Regents of the University of California