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    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.

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    (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.

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    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.

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    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.

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    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.

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    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.

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    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.”

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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Our Projects
Home › Our Projects › Approved User Proposals › Approved Proposals FY17

Approved Proposals FY17

Following are the approved user proposals for fiscal year 2017, including CSP, CSP Small-Scale, Synthesis, JGI-EMSL FICUS, and JGI-NERSC FICUS.

Community Science Program (CSP)

PI Affiliation Project Description
Aitken, Karen CSIRO (Australia) Understanding polyploidy through the generation of the first sugarcane genome sequence
Attwood, Graeme AgResearch Ltd (New Zealand) Defining gene function in rumen microbes
Bohlmann, Joerg University of British Columbia (Canada) Exploring the G3 “Gymnosperm Giga-Genomes” for Carbon Sequestration, Biofuels, and Bioproducts
Bonito, Gregory Michigan State University Functional gene network regulation in tripartite plant-fungal-bacterial mutualisms of bioenergy plants and algae
Bruns, Thomas University of California, Berkeley Functional genomics of pyrophilous fungi – determining the fate of pyrolyzed carbon in post-fire soils
Buchan, Alison University of Tennessee Knoxville Geo-metabolomics of a saltmarsh: Combining in situ, bulk, genomic, transcriptomic, and DOMeomic data streams
Coleman-Derr, Devin USDA-ARS Exploring the role of drought-induced plant associated microbes in promoting plant fitness in Sorghum bicolor and Oryza sativa
Cox, Michael University of Wisconsin-Madison Defining the Molecular Basis of Extreme Resistance to Ionizing Radiation
Crowe, Sean University of British Columbia (Canada) Mapping the global methanome
Cullen, Daniel Forest Products Laboratory Metatranscriptome analysis of fungal decay of Pinus contorta
Cushman, John University of Nevada Ice plant gene atlas resource development for Mesembryanthemum crystallinum, a facultative crassulacean acid metabolism (CAM) model for improved water-use efficiency of bioenergy feedstocks.
Des Marais, David Harvard University Perenniality, abiotic stress tolerance, and biomass allocation in Brachypodium, a model grass genus for bioenergy
Dijkstra, Paul Northern Arizona University Stress in Microbial Communities in Response to Changes in Carbon and Nitrogen Availability
Dopson, Mark Linnaeus University (Sweden) Exploring deep biosphere microbial communities by single-cell DNA sequencing
Doty, Sharon University of Washington Functional genomics of poplar endophytes for elucidation of mechanisms of improved plant growth under challenging conditions
Dudycha, Jeffry University of South Carolina Unlocking the photosynthetic diversity of cryptophyte algae through whole-genome sequencing.
Francis, Christopher Stanford University Spatiotemporal Characterization of Microbial Communities Controlling Estuarine Nitrogen and Carbon Cycling in the San Francisco Bay-Delta
Göker, Markus DSMZ (Germany) The One Thousand Microbial Genomes Phase 4 Project (KMG-4) – sequencing the most valuable type-strain genomes for metagenomic binning, comparative biology and taxonomic classification
Harris, Steven University of Nebraska – Lincoln Fungal interaction networks in biological soil crusts
Heyduk, Karolina University of Georgia Genome sequencing of C3 and CAM Yucca species
Johnson, Matthew Woods Hole Oceanographic Institute The role of acquired phototrophy in phytoplankton blooms: Insights from the Mesodinium rubrum genome
Kellogg, Elizabeth Donald Danforth Plant Science Center Pan-genomics of big bluestem, a broadly adapted dominant grass
LeBoldus, Jared Oregon State University RNAseq enabled metabolic modeling of disease resistance to Septoria canker in the DOE flagship P. trichocarpa
Lopez Peredo, Elena Marine Biological Laboratory Protecting photosynthesis during desiccation: do the genomes of desert-derived and aquatic Scenedesmus species hold the key to understanding extreme desiccation tolerance among green algae?
MacGregor, Barbara University of North Carolina Single-cell (meta-)genomics of uncultivable large sulfur bacteria and their epibionts: investigating host-microbe mediation of biogeochemical cycling
Mockler, Todd Danforth Center A Complete-Sequence Population for Pan-Genome Analysis of Sorghum
Moran, Mary Ann University of Georgia Dynamics of Bacterial Carbon and Sulfur Cycling in a Coastal Environment
Nguyen, Nhu University of Hawai’i at Manoa A genome atlas of the ectomycorrhizal genus Suillus: Phylogenetic diversity and population genomics of a keystone guild of symbiotic forest fungi
Nicholson, Wayne University of Florida Transcriptomic and methylomic responses of Carnobacterium species to extreme low pressure
Pett-Ridge, Jennifer Lawrence Livermore National Laboratory Microbial Carbon Transformations in Wet Tropical Soils: Effects of Redox Fluctuation
Raff, Jonathan Indiana University Combined Flux Chamber and Genomics Approach to Understanding Soil Emissions of Reactive Nitrogen Oxides in a Forested Environment
Shade, Ashley Michigan State University Greater than the sum of its parts? A synthetic microbial community approach to untangle member interactions and exometabolite production
Smart, Christine Cornell University Genetic diversity of shrub willow pathogen Melampsora americana aided by genome sequence
Stepanauskas, Ramunas Bigelow Laboratory for Ocean Sciences Expanding the dark matter reference catalog by targeting taxonomic blind spots
Whitman, William University of Georgia Core and pangenomes of soil and plant-associated prokaryotes
Yang, Xiaohan Oak Ridge National Laboratory Gene atlas for Kalanchoe laxiflora, a obligate crassulacean acid metabolism (CAM) model for genetic improvement of water-use efficiency in bioenergy feedstocks
Zhang, Chi University of Nebraska – Lincoln Genome sequencing of Zygnematales, the closest algal lineage to land plants, as a foundation for comparative genomic, transcriptomic, epigenetic, evolutionary, and biochemical studies

 

Small-Scale Microbial/Metagenome

PI Affiliation Project Description
Alvarez-Cohen, Lisa University of California, Berkeley Unraveling functional dynamics and regulation crucial for the stability of an anaerobic ammonium oxidizing (anammox) community via community metatranscriptomics and 16S rRNA sequencing
Andras, Jason Mount Holyoke College The effect of ecological restoration on the structure and function of soil microbial communities in coastal wetlands
Averill, Colin Boston University Molecular mechanisms of ectomycorrhizal interactions that stabilize soil carbon
Bell, Terrence Pennsylvania State University How interactions with soil microbiomes impact the survival and activity of a nitrogen-fixing soil surface consortium
Bowen, Jennifer Northeastern University Building a foundation for understanding carbon and nitrogen cycling in microbially diverse salt marsh sediments
Chistoserdova, Ludmila University of Washington Probing the role of electron transfer redox mediators in methane-oxidizing communities
Coleman, Maureen University of Chicago Teasing apart coexisting picocyanobacteria and their contributions to biogeochemistry
Cotner, James University of Minnesota-Duluth Translating stoichiometric diversity into genomic diversity: What elements are responsible for variability in bacterial biomass stoichiometry?
Craft, Chris Indiana University Microbial activity and community composition in a tidal freshwater marsh in response to sea level rise and saltwater intrusion: A field manipulation
D’Agostino, Paul Technische Universität München (Germany) Genome mining and synthetic biology of underrepresented organisms in the search for novel (bio-)chemistry
Dove, Nicholas University of California, Merced Immediate effects of prescribed fire on microbial communities, decomposition, and nitrification
Dynarski, Katherine University of California, Davis Microbial community composition and function throughout decomposition in temperate forests across a bedrock nitrogen gradient
Freedman, Zachary West Virginia University Assessing the recovery of microbial traits in bioenergy crop agroecosystems on reclaimed surface mines
Gutierrez, Tony Heriot-Watt University (UK) Genomic reconstruction to resolve the functional potential of oil-degrading bacteria in deep and surface waters of the Faroe-Shetland Channel
Hatzenpichler, Roland Montana State University Genomic characterization of cosmopolitan sediment-dwelling archaea hypothesized to be involved in anaerobic carbon cycling
Hatzinikolaou, Dimitris University of Athens (Greece) Genome sequencing of lignin and cellulose degrading isolates from Greek habitats
Hunt, Dana Duke University Seasonal and disturbance-related alterations in the biogeochemical cycling of estuarine carbon
Jensen, Paul University of California, San Diego Extracellular electron shuttles: A mechanism for obligate aerobes to survive anaerobic conditions
Kelly, Charlene West Virginia University Quantifying ecosystem changes following American chestnut restoration: From microbes to ecosystem function
Konstantinidis, Konstantinos Georgia Institute of Technology Real-time identification of horizontal gene transfer events using series metagenomes
Lebeis, Sarah University of Tennessee Characterizing functional chemotaxis receptors in different root zones
Lindemann, Steve Purdue University Identifying genome properties and environmental conditions governing the assembly of stable cyanobacterial-heterotroph consorta
Lindow, Steven University of California, Berkeley Trait-driven assembly of the leaf surface microbiome in an agricultural context
Maresca, Julia University of Delaware Light-induced gene expression in cosmopolitan freshwater Actinobacteria
Martens-Habbena, Willm Fort Lauderdale Research and Education Center Biogeochemistry of carbon and nitrogen cycling in subsiding subtropical soils
Mavrodi, Dmitri University of Southern Mississippi Transcriptomic responses of beneficial Pseudomonas rhizobacteria to Brachypodium root exudates
McMahon, Katherine University of Wisconsin-Madison Reference Genomes for Freshwater Bacteria – Alpha- and Beta-Proteobacteria
Müller, Henry Graz University of Technology (Austria) Elucidating the relevance of DNA methylation of strain-specific plant-microbe interactions
Myroid, David Oregon State University The metagenome of DIRT: How 20 years of altered carbon inputs have altered the functional potential of soil microbial communities
Oliveira, Rafael State University of Campinas (Brazil) Unravelling microbial communities associated with native plant species from P-impoverished soils of a global biodiversity hotspot
Ottesen, Elizabeth University of Georgia The genetic drivers and metabolic consequences of pelagic stream microbial community assembly
Pan, Chongle Oak Ridge National Laboratory Multi-cycle Selection of Sorghum Microbiomes for Biological Nitrogen Fixation
Richardson, Ruth Cornell University Metatranscriptomic responses of a butyrate-to-methane enrichment culture to sulfate and iron availability: elucidating the identities and strategies of metabolically versatile sulfate and iron reducing populations
Samuel, Buck Baylor College of Medicine Genomic analyses of the natural microbiome of Caenorhabditis elegans
Schmer, Marty USDA-ARS Nitrogen effects on soil microbial communities and soil organic carbon in a resilient bioenergy cropping system
Seyfferth, Angelia University of Delaware Impacts of rice cultivation practices on carbon and iron cycling: Unraveling functional microbial diversity in rice paddy rhizocompartments subject to silica-rich rice residue amendment
Valentine, David University of California, Santa Barbara Metagenomic reconstruction of novel archaeal genomes from energy-limited hypersaline sediments.
Veley, Kira Donald Danforth Plant Science Center Epigenetic and transcriptional changes that occur in populations of bacteria colonizing plant hosts.
Venturi, Vittorio International Centre of Genetic Engineering and Biotechnology (ICGEB) (Italy) Sequencing of a set of identified and characterized rice bacterial endophytes

Synthesis

PI Affiliation Project Description
Baker, David University of Washington Large scale de novo enzyme design for next generation metabolic engineering
Beisel, Chase North Carolina State University Profiling the functional diversity of CRISPR-Cas systems using cell-free transcription-translation systems
Bokinsky, Gregory Delft University of Technology (Netherlands) Plug adapters for biology: Activating heterologous iron-sulfur enzymes to fully exploit Nature’s catalytic potential
Chistoserdova, Ludmila University of Washington Establishing lanthanides as new life metals and understanding redox properties of lanthanide enzymes in metabolism of methane
Dueber, John University of California, Berkeley Identification of novel D-altronate dehydratases in the enolase superfamily enabling pectin utilization in S. cerevisiae
Huang, Possu Stanford University New protein platform for secondary metabolite detection
Jewett, Michael Northwestern University Reframing combinatorial assembly and rapid prototyping of biosynthetic pathways with cell-free systems
Juminaga, Alex LanzaTech, Inc. Advancing understanding of acetogenic CO2 fixation by generating a gene knock-out library to accelerate design of commercial strains for autotrophic production of fuels and bioproducts
Mead, David Varigen Biosciences Metagenomic mining for next generation DNA polymerases
Philmus, Benjamin Oregon State University Linking cyanobacterial orphan biosynthetic gene clusters to secondary metabolites
Redding, Kevin Arizona State University Chloroplastic CO2 reduction to formate supporting synthetic carbon xation
Schmeing, Thomas McGill University Synthetic DNA to facilitate structural and functional understanding of nonribosomal peptide synthetase production of secondary metabolites
Scott, Kathleen University of South Florida Creation of constructs for functional expression of recently described inorganic carbon transporters widespread among sulfur- and iron-oxidizing chemolithoautotrophic microorganisms
Subramanian, Venkatamaranan National Renewable Energy Laboratory Molecular engineering of Trichoderma reesei for improved cellulase production
Welander, Paula Stanford University Expression of novel triterpenoid biosynthesis proteins from environmental metagenomes

FY 2017 Facilities Integrating Collaboration for User Science (FICUS) JGI-EMSL Plans

Proposer Affiliation Project Description
Baldrian, Petr Institute of Microbiology ASCR (Czech Republic) The impacts of nitrogen availability and seasonal dynamics on plant-microbial interactions affecting C and N cycling in coniferous forest soils
Bartley, Laura University of Oklahoma Systems analysis of grass secondary cell wall development and regulation for biofuel production
Bianchi, Thomas University of Florida The role of priming effects on the conversion of blue carbon to CO2 in the coastal zone
Blanchard, Jeffrey University of Massachusetts Amherst Molecular mechanisms underlying changes in the temperature sensitive respiration response of forest soils to long-term experimental warming
Cattolico, Rose Ann University of Washington Global warming induced salinity shifts: metabolic responses by algal-bacterial consortia
Fendorf, Scott Stanford University Metabolic Constraints on Organic Matter Decomposition and Metal Cycling in Sediment Deposits
Liao, Hui-Ling Duke University Combined ‘omics approaches for the study of ectomycorrhizal symbiosis between Suillus and Pinaceae, with emphasis on their role in nutrient cycling
Rich, Virginia The Ohio State University Something old, something new: systems-level insights into plant-microbial-permafrost carbon dynamics by parallel high-resolution organic matter and microbial meta-omics
Skerker, Jeffrey University of California, Berkeley Understanding conversion of biomass-derived carbon into lipids and terpenoids in the oleaginous yeast Rhodosporidium toruloides
Wrighton, Kelly The Ohio State University Deciphering controls on plant decomposition in Arctic ecosystems: Identifying unknown microbial condensed tannin degradation pathways

 

FY 2017 Facilities Integrating Collaboration for User Science (FICUS) JGI-NERSC Plans

Proposer Affiliation Project Description
Babbitt, Patricia University of California, San Francisco Environmental Profiling of Enzyme Superfamilies for Function Prediction
Baker, David University of Washington Eukaryotic Protein Structure Determination Using Metagenome and Metatranscriptome Sequence Data
Brooks, Phillip University of California, Davis Advancing Metagenome Classification and Comparison by MinHash Fingerprinting of IMG/M Data Sets
DeLong, Edward University of Hawaii at Manoa Quantitative Analyses of Naturally Occurring Small RNAs in Global Metagenomic and Metatranscriptomic Datasets
Hallam, Steven University of British Columbia (Canada) Charting Global Biogeochemical Cycles using Fast Phylogenetic Mapping of Functional Anchor Genes
Konstantinidis, Konstantinos Georgia Institute of Technology Assessing Microbiomes at the Individual Population Level: Tool Development and Applications to Soil Carbon Cycling

 

  • Approved Proposals FY23
  • Approved Proposals FY22
  • Approved Proposals FY21
  • Approved Proposals FY20
  • Approved Proposals FY19
  • Approved Proposals FY18
  • Approved Proposals FY17
  • Approved Proposals FY16
  • Approved Proposals FY15
  • Approved Proposals FY14
  • Approved Proposals FY13
  • Approved Proposals FY12
  • Approved Proposals FY11
  • Approved Proposals FY10
  • Approved Proposals FY09
  • Approved Proposals FY08
  • Approved Proposals FY07
  • Approved Proposals FY06
  • Approved Proposals FY05
  • ETOP Projects

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