DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Science Highlights
    • Scientists
    (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

    Algae growing in a bioreactor. (Dennis Schroeder, NREL)
    Refining the Process of Identifying Algae Biotechnology Candidates
    Researchers combined expertise at the National Labs to screen, characterize, sequence and then analyze the genomes and multi-omics datasets for algae that can be used for large-scale production of biofuels and bioproducts.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    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

    Ian Rambo, graduate student at UT-Austin, was a DOE Graduate Student Research Fellow at the JGI
    Virus-Microbe Interactions of Mud Island Mangroves
    Through the DOE Office of Science Graduate Student Research (SCGSR) program, Ian Rambo worked on part of his dissertation at the JGI. The chapter focuses on how viruses influence carbon cycling in coastal mangroves.

    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
    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

    Integrating JGI Capabilities for Exploring Earth’s Secondary Metabolome
    Natural Prodcast podcast: Nigel Mouncey
    JGI Director Nigel Mouncey has a vision to build out an integrative genomics approach to looking at the interactions of organisms and environments. He also sees secondary metabolism analysis and research as a driver for novel technologies that can serve all JGI users.

    More

News & Publications
Home › News Releases › Boldly Illuminating Biology’s “Dark Matter”

July 14, 2013

Boldly Illuminating Biology’s “Dark Matter”

Photo: There are more microbes in, on and around the Earth than there are stars in the sky, and we only know about a small fraction of the microbial diversity around us. In an effort to learn more about the "microbial dark matter," researchers are sequencing and analyzing samples collected from around the world. (Composition by Zosia Rostomian, Berkeley Lab)

Photo: There are more microbes in, on and around the Earth than there are stars in the sky, and we only know about a small fraction of the microbial diversity around us. In an effort to learn more about the “microbial dark matter,” researchers are sequencing and analyzing samples collected from around the world. (Composition by Zosia Rostomian, Berkeley Lab)

Is space really the final frontier, or are the greatest mysteries closer to home?  In cosmology, dark matter is said to account for the majority of mass in the universe, however its presence is inferred by indirect effects rather than detected through telescopes. The biological equivalent is “microbial dark matter,” that pervasive yet practically invisible infrastructure of life on the planet, which can have profound influences on the most significant environmental processes from plant growth and health, to nutrient cycles in terrestrial and marine environments, the global carbon cycle, and possibly even climate processes. By employing next generation DNA sequencing of genomes isolated from single cells, great strides are being made in the monumental task of systematically bringing to light and filling in uncharted branches in the bacterial and archaeal tree of life.  In an international collaboration led by the U.S. Department of Energy Joint Genome Institute (DOE JGI), the most recent findings from exploring microbial dark matter were published online July 14, 2013 in the journal Nature.

“Instead of wondering through the starkness of space, this achievement is more like the 21st Century equivalent of Lewis and Clark’s expedition to open the American West,” said Eddy Rubin, DOE JGI Director.  “This is a powerful example of how the DOE JGI pioneers discovery, in that we can take a high throughput approach to isolating and characterizing single genomes from complex environmental samples of millions of cells, to provide a profound leap of understanding the microbial evolution on our planet.  This is really the next great frontier.”

This microbial dark matter campaign targeted uncultivated microbial cells from nine diverse habitats: Sakinaw Lake in British Columbia; the Etoliko Lagoon of western Greece; a sludge reactor in Mexico; the Gulf of Maine; off the north coast of Oahu, Hawaii, the Tropical Gyre in the south Atlantic; the East Pacific Rise; the Homestake Mine in South Dakota; and the Great Boiling Spring in Nevada.  From these samples, the team laser-sorted 9,000 cells, from which they were able to reassemble and identify 201 distinct genomes, which then could be aligned to 28 major previously uncharted branches of the tree of life.

Photo: Crab Spa is a diffuse-flow hydrothermal vent site on the East Pacific Rise and one of the nine sampling sites for this study. (Photo courtesy of Stefan Sievert, Woods Hole Oceanographic Institution)

Photo: Crab Spa is a diffuse-flow hydrothermal vent site on the East Pacific Rise and one of the nine sampling sites for this study. (Photo courtesy of Stefan Sievert, Woods Hole Oceanographic Institution)

“Microbes are the most abundant and diverse forms of life on Earth,” said Tanja Woyke, DOE JGI Microbial Program Head and senior author on the Nature publication.  “They occupy every conceivable environmental niche from the extreme depths of the oceans to the driest of deserts.  However, our knowledge about their habits and potential benefits has been hindered by the fact that the vast majority of these have not yet been cultivated in the laboratory.  So we have only recently become aware of their roles in various ecosystems through cultivation-independent methods, such as metagenomics and single-cell genomics.  What we are now discovering are unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the domains of life.”

To get around the difficulty of growing most microbes in the lab, recent efforts have focused on conducting surveys based on sequencing marker or 16S ribosomal RNA genes that are conserved across microbial lineages because of their essential role as “housekeeping” genes—critical for the organism’s survival.  Genome sequencing of the rest of the genomes of most of these lineages is however proceeding much more slowly. “Microbial genome representation in the databases is quite skewed,” said Chris Rinke, DOE JGI postdoctoral fellow and first author of the study.  “More than three-quarters of all sequenced genomes fall into three taxonomic groups or phyla but there are over 60 phyla we know of.”  For the majority of them, however, there are no cultivated members available.

“Based on 16S surveys we know they’re out there, but we don’t know much about them—that’s why we call them microbial dark matter,” Woyke added. “Using modern single-cell techniques allowed us to access the genetic make-up for some of them, even without growing them in the lab.”

In this effort to “seek out new life,” the team’s findings fell into three main areas.  The first was the discovery of unexpected metabolic features.  They observed certain traits in Archaea that previously only were seen in Bacteria and vice-versa.  One such trait involves an enzyme that bacteria commonly use for creating space within their protective cell wall, which is needed so the cell can, for example, expand during cell division.  As it rather generically cleaves the protective bacterial cell envelope, it needs to be very tightly regulated. For the first time, a group of Archaea was found to encode this potent enzyme and the authors hypothesize that Archaea may deploy it as a defense mechanism against attacking Bacteria.

Photo: Study first author Chris Rinke shows off the DOE JGI’s single-cell genomics capabilities during the annual Genomics of Energy & Environment Meeting. (Roy Kaltschmidt, Berkeley Lab)

Photo: Study first author Chris Rinke shows off the DOE JGI’s single-cell genomics capabilities during the annual Genomics of Energy & Environment Meeting. (Roy Kaltschmidt, Berkeley Lab)

The second contribution arising from the work was the correct reassignment, or binning, of data of some 340 million DNA fragments from other habitats to the proper lineage.  This course correction provides insights into how organisms function in the context of a particular ecosystem as well as a much improved and more accurate understanding of the associations of newly discovered genes with resident life forms.

The third finding was the resolution of relationships within and between microbial phyla—the taxonomic ranking between domain and class—which led the team to propose two new superphyla, which are highly stable associations between phyla.  The 201 genomes provided solid reference points, anchors for phylogeny—the lineage history of organisms as they change over time. “Our single-cell genomes gave us a glimpse into the evolutionary relationships between uncultivated organisms – insights that extend beyond the single locus resolution of the 16S rRNA tree and are essential for studying bacterial and archaeal diversity and evolution,” Woyke said.  “It’s a bit like looking at a family tree to figure out who your sisters and brothers are.  Here we did this for groups of organisms for which we solely have fragments of genetic information.  We interpreted millions of these bits of genetic information like distant stars in the night sky, trying to align them into recognizable constellations. At first, we didn’t know what they should look like, but we could estimate their relationship to each other, not spatially, but over evolutionary time.” Woyke and her colleagues are pursuing a more accurate characterization of these relationships so that they can better predict metabolic properties and other useful traits that can be expressed by different groups of microbes.

Phil Hugenholtz, Director of the Australian Centre for Ecogenomics at The University of Queensland, a former DOE JGI researcher, and another one of the paper’s authors reinforced the motivation for taking on this expedition of sorts.  “For almost 20 years now we have been astonished by how little there is known about massive regions of the tree of life. This project is the first systematic effort to address this enormous knowledge gap. One of the most significant contributions is that based on these data, we provided names for many of these lineages which, like most star systems, were just numbered previously. For me, taxonomic assignment is important as it welcomes in strangers and makes them part of the family.  Yet this is just a start.  We are talking about probably millions of microbial species that remain to be described,” Hugenholtz said.

Cosmologists have only mapped half of one percent of the observable universe and the path ahead in environmental genomics is similarly daunting.  “There is still a staggering amount of diversity to explore,” Woyke said.  “To try to capture 50 percent of just the currently known phylogenetic diversity, we would have to sequence 20,000 more genomes, and these would have to be selected based on being members of underrepresented branches on the tree.  And, to be sure, these are only what are known to exist.”

The Nature publication “Insights into the phylogeny and coding potential of microbial dark matter” builds upon a DOE JGI pilot project, the Genomic Encyclopedia of Bacteria and Archaea (GEBA: and closely articulates with other international efforts such as the Microbial Earth Project which aims to generate a comprehensive genome catalog of all archaeal and bacterial type strains (http://www.microbial-earth.org), and the Earth Microbiome Project (http://www.earthmicrobiome.org).  More information about GEBA-MDM is available at http://genome.jgi.doe.gov/MDM/.

Joining the DOE JGI in authorship on the MDM paper are researchers from Bielefeld University, Germany, the University of California, Davis, the University of Technology Sydney, the Bigelow Laboratory for Ocean Sciences, University of British Columbia, the University of Nevada, Las Vegas, the University of Western Greece, Woods Hole Oceanographic Institution, University of Illinois at Urbana-Champaign, and the Australian Centre for Ecogenomics of the University of Queensland, Australia.

Publication:

Rinke C et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 499, 431–437 (2013). https://doi.org/10.1038/nature12352

Relevant Links:

  • University of Illinois news release: http://engineering.illinois.edu/news/2013/07/25/genome-sequencing-work-illuminates-microbial-dark-matter

 

 

 

Byline: David Gilbert

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:

JGI at 25: Solving the Mystery of the Missing Oil

A surface slick in the Gulf of Mexico, taken ~1.5 km from the Deepwater Horizon wellhead (Olivia Mason, LBNL).

JGI at 25: The Human Genome Project, or the JGI’s Origin Story

JGI contributions detailed in DOE Human Genome Project poster

JGI at 25: A Single Cell, Myriad Microbial Discoveries

Artistic rendering of a microbial genome layered over a dark forest. (Composition by Zosia Rostomian/Berkeley Lab)

Calculating the Costs of Multiple Switchgrass Gene Copies

: Documented occurrences of different switchgrass cytotypes (4X in blue and 8X in orange) throughout the United States. One of the early interests in exploring 8X switchgrass was because the noticeable occurrence of 8X in 4X distribution gaps. (Joseph Napier)

The Power of One, Amplified

One of the pools at Dewar Creek hot springs in British Columbia, Canada. (Allyson Brady)

JGI at 25: Roots of a Mutualist Relationship

Laccaria bicolor
  • 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

© 1997-2022 The Regents of the University of California