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 › Discovering diversity, one cell at a time

April 25, 2014

Discovering diversity, one cell at a time

The game where one has to guess how many jelly beans or marbles can fill a jar should never be played with the cyanobacterium Prochlorococcus. By some estimates, in a single liter of water as many as 100 million cells of this tiny bacterium can be found. These important organisms serve as the base of the ocean food chain and are thought to be responsible for providing about 20% of the oxygen produced by the planet each year.

Artist’s interpretation of Prochlorococcus diversity in a drop of seawater

MIT scientists discovered an amazing amount of diversity among a population of the marine microbe Prochlorococcus found in a few drops of water. Each subpopulation is characterized by a shared genomic “backbone” and a few flexible genes. The figurative backbone is depicted in this artist’s rendering of the bacteria and their diversity in a single drop of seawater. (Carly Sanker, MIT)

Though it is considered a single species, this unicellular organism can be classified into several distinct major ecotypes – characterized by variable factors such as seasonal, depth, and geographic patterns. However, even within these ecotypes, Prochlorococcus cells still display a wide range of genomic diversity. To learn more about the cyanobacterial populations at this level, MIT marine microbiologist Sallie Chisholm, a longtime collaborator of the U.S. Department of Energy Joint Genome Institute (DOE JGI), led a team that applied single-cell genomics to these cyanobacteria collected from the same environment at three separate times of the year.

As reported in the April 25, 2014 issue of Science, Chisholm, her post-doctoral fellow Nadav Kashtan, and their collaborators at the DOE JGI sequenced and assembled Prochlorococcus genomes from single cells collected at the Bermuda-Atlantic Time-series Study site in the northwestern Sargasso Sea between November 2008 and April 2009. They found cell clusters within known ecotypes that indicated that the relative abundance of cyanobacterial subpopulations shifted along with the seasons, likely in response to environmental changes. They then analyzed the cells on a finer scale, sequencing partial genomes from select clusters.

The team wondered if the Prochlorococcus subpopulations within the clusters were genomically distinct. The answer turned out to be yes, and each of these so-called “genomic backbones” is comprised of highly conserved core gene alleles, or alternative forms, and a smaller distinct set of flexible genes. “This covariation between the core alleles and flexible gene content, and its fine scale resolution, represents a new dimension of microdiversity within wild Prochlorococcus populations,” the team reported in their study. “Similar patterns have been identified in cultured isolates and metagenomic assemblies within coexisting members of a few other microbial species with very different ecologies, suggesting that differentiated genomic backbones may be a feature of diverse types of microbial populations.”

ocean sampling device

Sampling the ocean with a CTD. (Paul Berube, MIT)

The vast diversity of these abundant Prochlorococcus subpopulations was validated with help from the DOE JGI’s Rex Malmstrom. “My contribution was to provide the essential control data,” he explained. “We could do this based on our extensive R&D work on single cell genomics.”

Malmstrom said that the Chisholm lab found substantial sequence variation from cell to cell in wild Prochlorococcus populations, but needed controls to understand what fraction of the differences among individual Prochlorococcus cells was due to the genome amplification, sequencing, and assembly process. This could be determined from the analysis of many known-to-be-identical individual cells using the same sample analysis pipeline.

“This is a difficult and time consuming thing to do, but it’s the sort of thing we do regularly at the JGI when we test out changes to the single cell procedure,” he said. “So I looked through our R&D data on E. coli, our test organism of choice, and found a set of data that underwent similar treatment and had a similar sequence quality to the data used for the wild Prochlorococcus. We estimated the differences among the identical E. coli to be 100-fold lower than the differences among wild Prochlorococcus using our own assembly and analysis procedures. For good measure, the Chisholm lab also ran the raw E. coli sequence data through the same assembly and statistical analysis procedure they used for Prochlorococcus and found differences among the identical E. coli to be 100-fold lower than the differences among wild Prochlorococcus. This established that the magnitude of the differences they saw among the wild Prochlorococcus cells was by far the strongest signal in the data and technological artifacts were minimal.”

Electron micrograph of a cultured strain of Prochlorococcus

Electron micrograph of a cultured strain of Prochlorococcus, MED4. (N. Watson and L. Thompson, MIT)

The team noted that if each of the cyanobacterial backbone subpopulations were counted as distinct species, then Prochlorococcus consists of thousands of species. Further, they added, each of these groups likely helps maintain the “dynamic stability of the Prochlorococcus ‘collective’ in the global oceans.” Such a large set of coexisting subpopulations with distinct genomic backbones, the team concluded, may be characteristic feature of free-living bacterial species with huge populations in highly mixed habitats.

“It was heartening to work with JGI on part of this project because that is where the Prochlorococcus genomics story began about 15 years ago,” said Chisholm. “They sequenced the genomes of two of our strains that had been isolated from different oceans, giving us our first peek at the diversity within this group. Likewise, JGI’s current collection of a number of Prochlorococcus genomes has been an invaluable resource in our more recent work. These ‘reference genomes’ are key to unlocking the mysteries of the patterns we see in the genomes of wild populations.”

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:

Introducing New Members of the JGI User Executive Committee

incoming 2023 UEC members

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"

JGI announces first round of 2023 New Investigator awardees

Digital ID card with 10 headshots reads: Congratulations to our 2023 New Investigator recipients!

JGI at 25: Following Fungi that Pry Apart Plant Polymers

A brown goat with white horns looks at green hay

Exploring Possibilities: 2022 JGI-UC Merced Interns

2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)

JGI at 25: Using team science to build communities around data

  • 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