DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • 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 › A Functional Genomics Database for Plant Microbiome Studies

December 18, 2017

A Functional Genomics Database for Plant Microbiome Studies

Catalog of candidate genes involved in plant-microbe relationships.

Phylogenetic tree of 3,837 high quality and non-redundant bacterial genomes. Outer ring denotes the taxonomic group, central ring denotes the isolation source, and inner ring denotes the root-associated genomes within plant-associated genomes. Taxon names are color-coded based on phylum: green – Proteobacteria, red – Firmicutes, blue – Bacteroidetes, purple - Actinobacteria. (Asaf Levy)

Phylogenetic tree of over 3,800 high quality and non-redundant bacterial genomes. Outer ring denotes the taxonomic group, central ring denotes the isolation source, and inner ring denotes the root-associated genomes within plant-associated genomes. Taxon names are color-coded based on phylum: green – Proteobacteria, red – Firmicutes, blue –Bacteroidetes, purple – Actinobacteria. (Asaf Levy, JGI and Isai Salas Gonzalez, University of North Carolina)

As the global population rises, estimated to hit nearly 10 billion by 2050, so does the need to boost crop yields and produce enough plant material for both food and sustainable alternative fuels. To help improve crop breeding strategies and overcome challenges such as making plants more tolerant of marginal lands, and stresses such as drought and low nutrient availability, researchers are focusing on understanding and promoting beneficial plant-microbe relationships.

Published December 18, 2017 issue in Nature Genetics, a team led by researchers at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility, and the Howard Hughes Medical Institute at the University of North Carolina at Chapel Hill (UNC) have exploited a catalog of bacterial genomes to identify and characterize candidate genes that aid bacteria in adapting to plant environments, specifically genes involved in bacterial root colonization.

Most of the studies in the field to date have focused on the community structure of the plant microbiome, i.e. “who is there,” and less on the function, i.e. “what they are doing, how and when they are doing it.” Previous studies that have considered function have mainly looked at a single host-microbe interaction, such as the one between an Arabidopsis plant and a pathogen.

“If we want to engineer the right microbiome to support plant growth, we need to understand the real function of the microbiome and not just sequence marker genes,” said study co-first author Asaf Levy, a research scientist at the JGI. “Here we used a massive genomic and computational effort to address the fundamental and important question: ‘How does the plant microbiome interact with the plant?’”

Most of the interaction between microbes and plants occurs at the interface between the roots and soil. Researchers from UNC, Oak Ridge National Lab, and the Max Planck Institute isolated novel bacteria from the root environment of Brassicaceae (191), poplar trees (135), and maize (51). The genomes of these 377 bacterial isolates, plus an additional 107 single bacterial cells from roots of A. thaliana, were then sequenced, assembled, and annotated at the JGI.

The authors then combined the new genomes with thousands of publicly available genomes that represent the major groups of plant-associated bacteria, and included bacteria from multiple plant and non-plant environments, such as the human gut, for comparison. The resulting database of 3837 genomes, 1160 of which are from plants, was used in a comparative genomics analysis.

The researchers then identified genes that are enriched in the genomes of plant-associated and root-associated organisms.

“It’s very important for us to understand what genes and functions microbes use to colonize plants because only then might we have a chance to rationally devise useful ‘plant probiotics’ to help us raise more food and energy crops with fewer chemical inputs such as fertilizers and pesticides or fungicides,” said study senior author Jeff Dangl, a Howard Hughes Medical Institute investigator and the John N. Couch Professor of Biology at the University of North Carolina at Chapel Hill

Among the key insights gained from the study was that plant- and soil-associated genomes tend to be larger than control genomes from the same clade. This was found to be due in part to enrichment of genes involved in sugar metabolism and transport, likely an adaptation to photosynthesis-derived plant carbon, generated by nature’s “candy factories,” said Asaf Levy. Up to 20% of the carbon fixed by plants through photosynthesis is exuded through the roots as sugars to attract microbes.

Numerous genes that seem to mimic plant functions—by encoding “Plant-Resembling PA and RA Domains” or PREPARADOs—were also identified. “It is well known that plant pathogens use proteins that mimic plant domains required for immune function,” said Dangl. “Imagine that the pathogen injects directly into the plant cell a protein that mimics part of a particular immune system machine. It’s like putting a partly defective cog into a wheel—the wheels can’t turn anymore. We reckon that the plant-associated protein domains that we identified might work in the same way.”

Rapidly evolving genes are often a signature of a molecular arms race between organisms sharing an environment. These genes are often used in offense or defense against another organisms. Two new rapidly evolving protein families associated with different “lifestyles” of related plant-associated bacteria were identified in the study. One, found in commensal bacteria, was dubbed “Jekyll”; the other, found in pathogenic bacteria, was named “Hyde.” With collaborators from Virginia Tech and ETH (Switzerland), JGI scientists discovered that the latter are very efficient in killing competing bacteria, potentially to help these “Hydes” take over the leaf niche. Berkeley Lab’s Innovation and Partnerships Office (IPO) has filed a patent application for this family as a potential antibacterial mechanism for controlling phytopathogens. IPO seeks industry partners with the capabilities, experiences and resources to bring a product to market that advances the discoveries by JGI and its research collaborators. Interested parties should email ipo@lbl.gov and visit IPO’s Industry Partnerships webpage for details on partnering with Berkeley Lab.

The complete catalog of new genomes and plant-associated genes is available to the research community through a dedicated web portal: Genomic Features of Bacterial Adaptation to Plants.

“The database is a precious resource for the research community studying plant-microbe interactions as it is an unbiased way to identify potentially interesting genes involved in interaction with a plant—including many totally novel genes. We are currently experimentally studying the function of many of these genes to gain a better functional understanding of the plant microbiome.” Levy said.

Collaborating institutions on this work included Oak Ridge National Laboratory, University of Washington, and the Max Planck Institute. In addition to the DOE Office of Science, funding for this work was provided through the NSF INSPIRE Program to Jeff Dangl (UNC), Ruth Ley (MPI) and Susannah Tringe (JGI). Additional funding was provided by the DOE-USDA Feedstocks Program to the Dangl lab and Dale Pelletier (ORNL).

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