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 › 2018 DOE JGI Community Science Program Allocations Announced

September 26, 2017

2018 DOE JGI Community Science Program Allocations Announced

Proposals encompass multiple capabilities of the national user facility

Mucor circinelloides sporangiophore. (S. Torres-Martínez. University of Murcia, Spain.)

Mucor circinelloides sporangiophore. Fungal responses to DNA methylation in the context of developmental signals is just one aspect of Victoriano Garre‘s proposal. (S. Torres-Martínez. University of Murcia, Spain.)

Though organisms can be studied in isolation, a more comprehensive picture emerges when their environmental interactions are taken into account. Along the same lines, many of the 30 proposals selected for the 2018 Community Science Program (CSP) of the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, aim to utilize multiple genomic and analytical capabilities, along with scientific expertise, to users focused on the underlying mechanisms involved in bioenergy generation and biogeochemical processes.

“These new CSP projects demonstrate further growth into multi-omics, with nearly all requesting functional genomics technologies including transcriptomics, epigenomics and metabolomics, and roughly half spanning more than one of our Science Programs,” said Susannah Tringe, DOE JGI User Programs Deputy. “They bring exciting new investigators, ideas and approaches to the application of genomics to DOE mission science.”

East River, CO, USA (Courtesy of Jill Banfield)

East River in Colorado is where watershed studies are being conducted as part of a proposal from Jill Banfield. (Courtesy of Jill Banfield)

The CSP 2018 proposals were selected from 76 full submissions based on 94 letters of intent. Click here to see the full list of approved CSP 2018 proposals. Additionally, 60 percent of the accepted proposals come from new DOE JGI primary investigators.

Among this year’s accepted proposals:

  • Dan Buckley of Cornell University aims to dissect soil microbial food webs using stable isotope probing, a method that traces nutrient fluxes by providing labeled substrates that are consumed and incorporated into DNA. This will allow his group to identify and characterize uncultivated microbes that have crucial roles in the soil carbon cycle.
  • Virus-infected Brachypodium (Courtesy of Kranthi Mandadi)

    Developing gene atlas maps to study  grass-microbe interactions that can lead to either healthy or virus-infected Brachypodium is a partial aim of Kranthi Mandadi‘s proposal. (Courtesy of Kranthi Mandadi)

    Boulos Chalhoub of the French National Institute for Agricultural Research (INRA) will explore how DNA methylation and repeated hybridization have shaped the polyploid Brachypodium hybridum, a relative of candidate bioenergy grasses such as switchgrass. Polyploid plants contain multiple sets of chromosomes, which makes sequencing and assembling these genomes more challenging, but can also make the plants more stress tolerant.

  • Maureen Coleman of the University of Chicago will apply integrated ecosystem genomics across the Great Lakes, which hold 20 percent of the Earth’s surface freshwater. She will characterize the metabolic diversity and activity of microbes participating in nutrient cycling in these important aquatic systems.
  • Yellowstone National Park, Octopus hot spring biofilms (Courtesy of Devaki Bhaya)

    The interactions between cyanobacteria – such as those found in Octopus hot spring biofilms at Yellowstone National Park – and viruses is the topic of Devaki Bhaya‘s proposal. (Courtesy of Devaki Bhaya)

    Byron Crump of Oregon State University aims to apply metagenomics and metatranscriptomics to microbes that metabolize dissolved organic matter in river ecosystems, critical conduits for land-to-ocean transfer of materials including terrestrial organic matter.

  • Alisa Huffaker of the University of California (UC), San Diego will harness the DOE JGI’s diverse capabilities in the plant, metagenome, and synthesis programs, and use metabolomics to produce systems analysis of the metabolic diversity of sorghum and maize to better understand microbiome interactions and how these grasses tolerate various stresses.
  • James Leebens-Mack of the University of Georgia will develop a comparative plant genomics framework involving high-quality genome assemblies and annotations for 35 species. The Open Green Genomes Initiative, which lists 98 co-primary investigators along with Leebens-Mack, will improve comparative analyses of the genes, regulatory networks and metabolic pathways influencing plant growth and responses to environmental stress, and inform engineering of plants for efficient production of biofuels and bioproducts. In the proposal, the team noted that the large number of investigators “is a testament to the importance and broad interest in developing infrastructure – including strategically sampled reference-quality genome sequences – to aid comprehensive comparative analyses across the green tree of life.”
  • Illustration of disease symptoms caused by rust fungi on different host plants (photos by M. Catherine Aime)

    Illustration of disease symptoms caused by rust fungi, the topic of Sebastien Duplessis‘ proposal, on different host plants. (photos by M. Catherine Aime)

    Udaya Kalluri of Oak Ridge National Laboratory wants to know how modifying plant cell walls in the candidate bioenergy feedstock crop poplar, one of the DOE JGI’s Plant Flagship Genomes, impacts plant-microbe interactions and the utility of poplar for biofuel production.

  • Corby Kistler of the USDA-ARS Cereal Disease Lab and the University of Minnesota targets the mutually antagonistic relationships between bacteria and fungi in native prairie soil, and how their system of checks and balances allow perennials to thrive. His proposal will harness the DOE JGI’s fungal, microbial, metagenome and metabolomics capabilities.
  • Yu Liu of the University of Texas Southwestern Medical Center plans to define the global regulatory network of DNA chromatin structures in the filamentous fungus Neurospora crassa, an important model organism for the fungal conversion of biomass.
  • Norma Martinez-Gomez of Michigan State University aims to identify the rare earth element-dependent enzymes involved in plant-microbe interactions that can boost crop yields such as candidate bioenergy feedstocks while reducing the need for fertilizers.
  • Nectar yeast, Metschnikowia gruessii. (Manpreet Dhami, Tadashi Fukami, and Lydia-Marie Joubert)

    Nectar yeasts including Metschnikowia gruessii are the focus of Tadashi Fukami‘s proposal. (Manpreet Dhami, Tadashi Fukami, and Lydia-Marie Joubert)

    Jennifer Martiny of UC Irvine will explore the activity of surface soil microbes on leaf litter in an arid ecosystem to understand how daily cycles in moisture and temperature impact nutrient cycling.

  • Neslihan Tas of Lawrence Berkeley National Laboratory, recently named a DOE Early Career Research Program awardee, plans to use sequencing and metabolomics to explore microbial functions over time in watershed ecosystems. Her team is already collecting samples from soil-aquatic interfaces at two Colorado high-elevation streams.
  • Ru Zhang of the Donald Danforth Plant Science Center is investigating how the model green alga Chlamydomonas reinhardtii – genome sequenced and assembled by the DOE JGI – regulates its responses to heat stress and day length with the aid of metabolomics. The information could lead to algal strains that produce more biomass for conversion to biofuel. 
Morphological diversity of Xylariaceous endophytes. (J.M. U'Ren)

A proposal by Jana U’Ren calls for a genomic survey of Xylariaceae fungi. The morphological diversity of Xylariaceous endophytes is shown here. (J.M. U’Ren)

These projects, as well as the other 17 selected in this round of the CSP, represent new ways of incorporating DNA sequencing with other analytic approaches to explore biological relationships that underpin bioenergy and biogeochemical processes. Understanding how microbes live in association with other microbes and plants, how plant genome diversity results from DNA modifications, how microbes exploit available local nutrient resources, and how metabolic plasticity can be understood and potentially exploited, among other questions, will help scientists leverage high throughput analytic methods for DOE mission purposes.

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 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

JGI at 25: Expanding Metagenomics to Capture Viral Diversity

Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
  • 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