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 › Expanding Research Communities and Collaborations: 2014 CSP Portfolio Announced

October 28, 2013

Expanding Research Communities and Collaborations: 2014 CSP Portfolio Announced

From the depths of ocean dead zones, to wide swaths of forests, and rising up to the troposphere, where most weather changes occur, the U.S. Department of Energy Joint Genome Institute (DOE JGI) 2014 Community Science Program portfolio seeks to parse functional information extracted from complex ecosystems to address urgent energy and environmental challenges.  These massive, data-intensive undertakings require interdisciplinary approaches, many leveraging additional expertise through a new inter-DOE-Facility partnership.

Photo: Terry Lathem, a graduate student in Georgia Tech’s School of Earth and Atmospheric Sciences, takes notes aboard a NASA DC-8 gathering samples of microorganisms in the atmosphere. Credit: NASA

Photo: Terry Lathem, a graduate student in Georgia Tech’s School of Earth and Atmospheric Sciences, takes notes aboard a NASA DC-8 gathering samples of microorganisms in the atmosphere. Credit: NASA

Reflecting its vision of serving the scientific community as a next-generation genome science user facility, the DOE JGI has joined forces with the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory to provide complementary scientific resources to significantly expand genomic understanding to cellular function. The inaugural round of eight accepted proposals showcases the synergy between these two DOE user facilities.

Photo: Influx is a one-of-a kind flow cytometer/cell sorter located at EMSL

Photo: Influx is a one-of-a kind flow cytometer/cell sorter located at EMSL

Five of the eight new DOE JGI-EMSL proposals going forward will focus on carbon cycling and three relate to improvements in biofuels production. Each of these projects will tap the capabilities at both facilities to further the research in ways that would not otherwise be possible, and all are targeted for completion within an 18-month time window.

Two of the carbon cycling projects focus on soil microbial communities. Mary Firestone from the University of California, Berkeley will study the plant-soil-microbial interactions of an annual grass Avena fatua with soil from a California grassland, a model ecosystem for further exploration of the rhizosphere, the soil and microbial community around plant roots. By combining DNA sequencing with the study of unique chemical traces that the cells produce (metabolomics) and the large-scale study of their protein structures and functions (proteomics), this project will lend insights into how changing climate conditions might influence carbon cycling and carbon sequestration in terrestrial ecosystems.  According to the U.S. Department of Agriculture, grasslands and rangelands account for approximately 50 percent of such areas and provide forage for livestock and native herbivores, habitat for native flora and fauna, watersheds for rural and urban uses, ecosystem goods and services, areas for recreation, and potentially for renewable and nonrenewable energy sources as well.

Kirsten Hofmockel from Iowa State University will combine the DOE JGI’s high-throughput sequencing capabilities and EMSL’s cell sorting technologies to conduct a large-scale comparative analysis of soil microbial communities. With an eye toward linking microbial community dynamics to ecosystem-scale biogeochemical models, the samples come from a study comparing four bioenergy cropping systems being conducted at Iowa State University’s South Reynoldson Farm.  Among the goals of this project is to develop novel labeling and cell sorting approaches to shed light on the structure and function of carbon cycling microbial communities within soil and to identify key soil carbon cycling organisms and their relationship with other community members and soil characteristics.

Another CSP 14 project, led by Marc Libault of the University of Oklahoma explores a single cell type model, the root hair cell, to advance our understanding of the response of soybean and sorghum plants to various environmental stresses.

Photo: Mar- Libault; Aleksandr Jurkevic, University of Missouri

Photo: Mar- Libault; Aleksandr Jurkevic, University of Missouri

Two other carbon cycling projects involve the study of cyanobacteria. Matthias Hess at Washington State University-Tri Cities will build off the DOE JGI’s pioneering work in filling in gaps in the tree of life through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) pilot project  and a recent spin-off focused specifically on cyanobacteria (http://genome.jgi.doe.gov/programs/bacteria-archaea/GEBA-Cyano.jsf). The GEBA-Cyano project has doubled the amount and diversity of cyanobacterial genome sequence data in the public databases. Hess’ project will develop a Functional Encyclopedia of Cyanobacteria with the help of samples provided by the Culture Collection of Microorganisms from Extreme Environments, to better understand photosynthetic microbial communities and their central role in carbon and nitrogen cycling. Another project comes from the J. Craig Venter Institute’s Philip Weyman, who will study the interactions between the Pleurocarpous feathery moss and cyanobacteria found in boreal forests. Since these ecosystems are enormous carbon sinks, their health and productivity is of vital importance to monitoring and moderating future increases in CO2.

Photo: The boreal moss (Hylocomium splendens). Credit Jeroen Gillard from JCVI

Photo: The boreal moss (Hylocomium splendens). Credit Jeroen Gillard from JCVI

Another carbon cycling project involves a family of wood-degrading fungi known as Ascomycetes, which include molds and mildews. Colleen Hansel at the Woods Hole Oceanographic Institute will focus on these organisms, which take leading roles in breaking down lignocellulose in contaminated sites. The initial focus will be on sequencing samples that are isolated from contaminated freshwater lake sediments and coal mine drainage treatment systems, and then by using the metabolomic and proteomic analyses capabilities at EMSL she seeks to identify the metabolic pathways that are involved in breaking down carbon in these organisms.

Three projects focus on biofuels and the role of fungi improving production of them. Steve Harris from the University of Nebraska-Lincoln will build upon previous DOE JGI sequencing of the industrially important filamentous fungi Aspergillus niger and Trichoderma reesei. A strain of A. niger is critical to the large-scale production of citric acid while other strains provide enzymes that can break down plant cell walls to free up sugars that can then be fermented and distilled into biofuel.  T. reesei is the workhorse organism for a number of industrial enzyme companies for the production of cellulases that can be used to break down plant biomass. The Harris team plans to harness genomic, proteomic, and microscopy data in order to facilitate the breeding of improved production strains for both fungi.

The proposal from Michelle O’Malley from the University of California, Santa Barbara also builds from a previous DOE JGI project, one that characterized the microbial communities in the cow rumen. In this new proposal, however, the researchers will target anaerobic fungi in communities isolated from large herbivores (elephant, giraffe, goat, horse, and sheep) that are involved in breaking down plant biomass. Novel isolates that possess desirable enzymatic properties will be used for the construction of metabolic models to drive improvements in bioprocessing strategies.

Photo: One of the objectives of the MetaMaize project, led by Rebecca Nelson and Alice Churchill of Cornell University, is to look for protection against mycotoxigenic ear-rot fungi. Credit: Laura Morale

Photo: One of the objectives of the MetaMaize project, led by Rebecca Nelson and Alice Churchill of Cornell University, is to look for protection against mycotoxigenic ear-rot fungi. Credit: Laura Morale

Photo: One of the objectives of the MetaMaize project, led by Rebecca Nelson and Alice Churchill of Cornell University, is to look for protection against mycotoxigenic ear-rot fungi. Credit: Laura Morale

Photo: One of the objectives of the MetaMaize project, led by Rebecca Nelson and Alice Churchill of Cornell University, is to look for protection against mycotoxigenic ear-rot fungi. Credit: Laura Morale

Photo: Endophytes, shown here, are microbes that can live within plants (such as these maize plants), without causing immediately apparent symptoms. Credit: Alice Churchill

Photo: Endophytes, shown here, are microbes that can live within plants (such as these maize plants), without causing immediately apparent symptoms. Credit: Alice Churchill

Finally, Harold Kistler from the U.S. Department of Agriculture-Agricultural Research Service will focus on compounds known as terpenoids that are produced by plants and filamentous fungi including Fusarium graminearum. The goal is to determine a way to efficiently and abundantly produce terpenoids in filamentous fungi, so that they can be evaluated as renewable biofuels that have higher energy content than ethanol and could be more compatible with existing fuel infrastructure. Aside from using the DOE JGI’s RNA sequencing

The remaining 29 accepted projects, more traditional DOE-JGI sequencing projects, were chosen for their relevance to other goals of the CSP 2014 call, and will be carried out entirely at DOE JGI. Farren Isaacs from Yale University is leading a DNA synthesis project that will identify and synthesize metagenome-derived enzymes that can be introduced into microbes to address challenges in bioremediation, global carbon cycling and development of alternative energy strategies. “Recent advances in synthetic biology increase the prospect of using engineered microorganisms for a myriad of these challenges,” he noted in his proposal. “Developing genome engineering technologies to drive high-throughput genetic modifications across genomes of diverse microorganisms, would vastly expand our ability to utilize microorganisms for DOE mission objectives.”

Photo: Mass Spectrometer, Proteomics Lab @ EMSL

Photo: Mass Spectrometer, Proteomics Lab @ EMSL

Another selected project will explore airborne microbial communities and their influences on the Earth’s biogeochemical cycles. Kostas Konstantinidis from Georgia Tech and his colleagues are concentrating on airborne microbes in the upper trophosphere, a region that contains almost all the water vapor of the atmosphere. In particular, they are seeking to characterize the conditions enabling the survival of microbes in this layer and their roles in cloud formation and the water cycle. This linkage of microbial processes and climate change processes is a bold new direction for DOE JGI.

The DOE JGI Plant Flagship Genomes initiative is another area of emphasis for the 2014 CSP call. These are plants sequenced for their potential as feedstock crops for biofuel production or else as comparators that will assist in the interpretation of feedstock crop genomes and potentially lead to their improvement for purposes of biofuel development. Many of the six selected projects focus on the poplar (black cottonwood) tree—the first tree ever sequenced—and published by the DOE JGI in the journal Science back in 2006. For example, Jay Chen from Oak Ridge National Laboratory will investigate gene expression in poplar populations. The goal is to use the information to identify genetic elements and transcriptional networks involved in plant cell wall development to improve the development of poplar as a feedstock for cost-effective, sustainable biomass production and conversion into biofuels. Another project, from Jonathan Shaw of Duke University, will leverage the first moss genome sequenced – Physcomitrella patens – and expand the moss/bryophyte knowledgebase by sequencing peat moss (Sphagnum magellanicum) to learn more about its role on the global carbon budget.

Photo: Four-year-old poplar trees grown in the field that will be used for sampling. Credit: Jay Chen

Photo: Four-year-old poplar trees grown in the field that will be used for sampling. Credit: Jay Chen

Another area of interest in this year’s CSP call is microbial diversity and function. Among the approved projects is one from Michael Wagner from Austria’s University of Vienna, who will test a novel method for identifying ammonia-oxidizing bacteria and nitrite-oxidizing bacteria in wastewater sludge. These bacteria are key drivers of the nitrogen cycle and essential in wastewater treatment plants for the removal of nitrogen from sewage.

Photo: Rosette deployment to collect ocean microbes from the Eastern Tropical North Pacific oxygen minimum zone aboard the R/V New Horizon. Samples collected during this voyage will be used for the project proposed by Frank Stewart of Georgia Tech

Photo: Rosette deployment to collect ocean microbes from the Eastern Tropical North Pacific oxygen minimum zone aboard the R/V New Horizon. Samples collected during this voyage will be used for the project proposed by Frank Stewart of Georgia Tech

A total of eight fungal projects were approved from this year’s call. One is led by Istvan Molnar from the University of Arizona and focuses on gene clusters from sequences in the DOE JGI’s fungal portal MycoCosm. The researchers will identify genes involved in producing compounds that play a role in plant-microbial interactions, plant stress tolerance or plant/fungal symbioses.

A third area of emphasis this year was microbial emission and capture of greenhouse gases in terrestrial systems. These projects focus on carbon capture, nitrogen processing and methane reduction. From the 10 prokaryotic projects approved out of the CSP 2014 call, many of them focus on understanding the roles of soil microbial communities on the carbon cycle in a number of environments. For example, Erik Lilleskov from the USDA Forest Service will study microbial communities involved in carbon cycle in peatland ecosystems. Peatlands, his proposal noted, represent up to five percent of the land surface but sequester as much as one third of the soil organic carbon.

The final area of emphasis for the call focused on the DOE JGI’s DNA synthesis capabilities, and many of the six projects approved, including the one from Isaacs described earlier, primarily focus on exploring pathways that could lead to bioenergy and environmental applications. For example, the proposal from UC Berkeley’s Ming Hammond will build and characterize a modular system for multi-gene regulation in plants. One application of this system is improving the cost-effective production of lignocellulosic biofuels as they focus on modifying gene expression to increase biomass density while reducing lignin—an integral part of the secondary plant cell wall, but a bottleneck to biofuels production.

Photo: An aerial shot of the SPRUCE (Spruce-Peatland Response Under Climate and Environmental Change) site at the US Forest Service Marcell Experimental Forest in Minnesota.]

Photo: An aerial shot of the SPRUCE (Spruce-Peatland Response Under Climate and Environmental Change) site at the US Forest Service Marcell Experimental Forest in Minnesota.]

All 37 projects selected by an external review panel out of 123 full proposals reflect the emphasis on collaboration between researchers and the potential of further expanding research communities working on these topics. Additionally, the projects selected combine sequence data generation with large-scale experimental and computational capabilities and the total allocation for the CSP 2014 portfolio is expected to be more than 30 trillion bases (terabases or Tb).

Together, all of these projects are the first selected under a new aegis as the DOE JGI’s primary user program changes names from the Community Sequencing Program to the Community Science Program, a title that more accurately reflects the work being done by and at the DOE JGI. “The DOE JGI offers access to high throughput DNA sequencing, analysis of DNA sequence, and, recently, DNA synthesis for investigators who have questions of relevance to DOE mission areas,” said Deputy Director of Programs Jim Bristow. The change, he added, aligns with the Institute’s 10-year Strategic Vision to transition from a sequencing facility to a fully-fledged genomic analysis resource offering researchers the opportunity to submit a DNA sample of their organisms of interest and receive not just raw DNA sequence but detailed functional annotations that can be parlayed into a foundation for collaborative science.

The full list of projects that make up the CSP 2014 portfolio, supported by the DOE Office of Science, may be found here “Community Science Program
Sequencing Plans for 2014″. The DOE JGI Community Science Program also accepts proposals for smaller-scale microbial and resequencing projects and reviews them twice a year.

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