DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Science Programs
    • Science Highlights
    • Scientists
    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

    More

    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

    More

    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

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    A panoramic view of a lake reflecting a granite mountain.
    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

    Listen

    A light green shrub with spiny leaves, up close.
    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

    Listen

    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    iPHoP image (Simon Roux)
    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

    More

    Abstract image of gold lights and squares against a black backdrop
    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

    More

    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

    More

    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

    More

    croppe image of the JGI helix sculpture
    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

    Listen

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

    More

    image from gif that shows where in the globe JGI fungal collaborators are located.
    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

    More

    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

    More

News & Publications
Home › News Releases › DNA of Uncultured Organisms Sequenced Using Novel Single-Cell Approach

April 21, 2009

DNA of Uncultured Organisms Sequenced Using Novel Single-Cell Approach

WALNUT CREEK, CA—Scientists from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Bigelow Laboratory for Ocean Sciences have assembled high quality, contamination-free draft genomes of uncultured biodegrading microorganisms using a novel single cell genome sequencing approach. This proof of principle study, published in the April 23 edition of the journal PLoS One, offers researchers a new method to access and decipher the information embedded in genomes of interest with only minute quantities of DNA.

“Most of the microbial genomes sequenced to date are derived from organisms cultured in the laboratory,” said DOE JGI Director Eddy Rubin. “We estimate that roughly 99.9 percent of the microbes that exist on this planet currently elude standard culturing methods, denying us access to their genetic material, so we have to explore other methods to characterize them. The power of single cell genomics is that it offers us the ability to sort out one cell from a complex environmental sample, liberate the DNA from that cell, and enzymatically produce millions of copies of that genome so that we have enough DNA to sequence it and characterize its metabolic potential.

“In its capacity as a national user facility, DOE JGI is dedicated to helping our users expand the utility of genomic information to advance DOE mission-relevant science—and in this particular case, building on our understanding of how the carbon balance is maintained in the ocean.  The single cell approach will be of great interest to many of our users that have problems with accessing their particular target genomes.”

Woyke

Research Scientist Tanja Woyke with a list of single cell sequencing projects at the JGI.

 

Tanja Woyke and her colleagues at the DOE JGI sequenced genomes of two uncultured flavobacteria, marine microorganisms known for their biopolymer degradation capacity. The environmental sample for this work – surface ocean water – was collected in Maine’s Boothbay Harbor. The two flavobacteria were chosen by Bigelow Laboratory collaborators Ramunas Stepanauskas and Michael Sieracki, who are particularly interested in genes encoding proteorhodopsins.

“Proteorhodopsins enable some microbial cells to harness the energy from sunlight in a process that is very different from photosynthesis,” said senior author Stepanauskas.  “Recent metagenomic studies revealed that proteorhodopsins are very abundant and diverse in the ocean. Using our single cell sequencing technology, we are starting to identify the specific group of microorganisms that carry proteorhodopsin genes, and to analyze the genomic context that may shed light on the role of proteorhodopsins in the ocean and their potential in biotechnology.”

A technique called fluorescence activated cell sorting was used by the Bigelow scientists to pick out individual bacterial cells directly from the environmental sample. The single cells were then lysed (blown open) and a process called multiple displacement amplification was applied to make millions of copies of the bacterial genomes for sequencing. The resulting flavobacterial genome sequences are approximately 80 to 90 percent complete, a level sufficient, Woyke said, to prove the utility of the technique. Woyke credited DOE JGI’s Cliff Han and his team at Los Alamos National Laboratory (LANL), which worked on closing gaps in the assembly.

Even though the flavobacteria sequenced are marine organisms, Stepanauskas pointed out that the single cell sequencing approach can be applied to organisms from a number of environments, including those microbial communities inhabiting extreme environments, such as hot pools, contaminated soil, and those constituting the human microbiome. The technique bypasses the need for culturing before sequencing, he said, because only one cell is needed to decode a genome.

“As long as you can isolate a single cell, pick it from the environment, lyse it, you can generate millions of copies of that genome and gain access to the information inside that organism,” Woyke confirmed. “One of the key issues that still needs refining is the lysis step, since many microbes will not lyse with alkaline solutions, the most common agent for the job. But we are actively working on that.”

OLYMPUS DIGITAL CAMERA

Coastal water sample from Boothbay Harbor, Maine collected by Bigelow Laboratory team. Photo courtesy of Ramunas Stepanauskas (Bigelow Laboratory).

The capacity to sequence DNA from a single, uncultured cell was first documented in 2005 at Roger Lasken’s team while he was at the New Haven-based company Molecular Staging, but the technique has yet to yield a completed genome. “If one copy of the genome stays intact, you should theoretically be able to finish a genome from a single cell,” Woyke said. She also noted that other groups are working on pooling identical cells to have a better chance of achieving that goal.

“However, each microbial cell may turn out to be different, that’s just one of the unanswered, basic questions in biology that may be finally addressed by single cell genomics,” added Stepanauskas. “Even without completed genome assemblies, single cell sequencing offers radically new opportunities for the basic research and biotechnology applications of the microbial ‘uncultured majority’.”

Woyke said they are currently working with several DOE JGI collaborators to apply the single cell approach to other organisms of interest. One of the projects involves examining the microbial communities within cow rumen to identify enzymes that break down cellulose from plant material that can be used for next-generation biofuels production.

Other authors on the study include DOE JGI’s Gary Xie, Cliff Han, Hajnalka Kiss, Jimmy Saw, Pavel Senin, and Chi Yang, Alex Copeland and Jan-Fang Cheng. Other collaborating institutions are the University of La Laguna (Spain), the University of Hawaii at Manoa and the National Yang-Ming University (Taiwan).

The U.S. Department of Energy Joint Genome Institute, supported by DOE’s Office of Science, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup.  DOE JGI, located in Walnut Creek, Calif., 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:

You can move, but you can’t hide

Illustration of a magnifying glass identifying viruses and plasmids.

JGI announces second round of 2023 New Investigator awardees

From left to right: [above] Emma Bell, Mallory Choudoir, Sneha Couvillion, Tobin Hammer, Christina Hazard, Rachel Mackelprang, Brook Moyers, Mei, Ran,; [below] Benjamin Peterson, Dacheng Ren, Allison Rober, Neal Scott, Chikae Tatsumi, Vojtech Tlaskal, Fernando Torralbo, Luis Felipe Valdez-Nuñez

A Collaboration to Improve Plant Genome Annotations Across Species

A tiled collage of square photos of different plants - soybeans, and sorghum, for example.

From Berkeley to Binghamton: Tracking Strawberry Evolution

iPHoP: A Matchmaker for Phages and their Hosts

iPHoP image (Simon Roux)

Supercharging SIP in the Fungal Hyphosphere

Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
  • 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