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

Our Projects
Home › Our Projects › Approved User Proposals › Approved Proposals FY15

Approved Proposals FY15

Following are the approved user proposals for fiscal year 2015 including CSP and JGI-EMSL Collaborative Science Initiative projects.

FY 2015 Community Science Program (CSP) Plans

Proposer Affiliation Project Description
Baliga, Nitin Institute of Systems Biology Genome-wide analysis of chromatin accessibility and miRNA-mediated transcriptional regulation of lipid accumulation in Chlamydomonas reinhardtii
Banfield, Jill University of California, Berkeley Genome-resolved metagenomic analysis of microbial function in the subsurface
Banfield, Jill University of California, Berkeley Tree-driven diel microbial carbon dynamics in the vadose zone
Barrasa, Jose Maria University of Alcala  (Spain) Study of the lignocellulolytic machinery in saprobic wood and leaf litter degrading Agaricales
Busby, Posy University of Washington Mechanisms of interaction in the foliar fungal microbiome of Populus trichocarpa
Cadillo-Quiroz, Hinsby Arizona State University Microbial composition and metagenomic functional potential across tropical peatlands: comparative evaluation and modeling of C decomposition to greenhouse gases
Campbell, Barbara Clemson University Biogeochemical cycling links between terrestrial and marine systems
Cavicchioli, Rick University of New South Wales (Australia) Seasonal variation in Antarctic microbial communities: ecology, stability and susceptibility to ecosystem change
Chistoserdova, Ludmila University of Washington Methane oxidation as a community function: defining partnerships and strategies through sequencing metagenomes and metatranscriptomes of laboratory manipulated microcosms
DiFazio, Steven West Virginia University Sex determination in the Salicaceae
Frank, Carolin University of California, Merced Diazotrophic aboveground endophytes in native pines, poplar and willow
Fredrickson, Jim PNNL Spatio-temporal functional profiling in model microbial communities
Hallam, Steven University of British Columbia (Canada) Microbial engines driving organic matter transformations in the dark ocean: an integrated biological and chemical perspective
James, Timothy University of Michigan Revealing the ecological function of uncultured fungal dark matter in freshwater ecosystems using single cell genomics
Klassen, Jonathan University of Connecticut Metagenomic mining of natural product diversity and understanding its contribution to ecosystem function in the cellulolytic fungus-growing ant symbiosis
Klenk, Hans-Peter; Goker, Markus University of Newcastle (UK); DSMZ (Germany) Exploiting the genomes of the Actinobacteria: plant growth promoters and producers of natural products and energy relevant enzymes united in a taxonomically unresolved phylum
Lamendella, Regina Juniata College Systems biology approach to fracking for environmental monitoring
Laudencia-Chingcuanco, Debbie USDA-ARS Creating a genome-wide sequence-indexed collection of grass mutants
Liu, Wen-Tso University of Illinois Shedding light on the anaerobic wastewater treatment “black-box” in anthropogenic carbon cycling: exploring the uncharted ecological function of uncultured microbial taxa through next-generation sequencing technology
Loper, Joyce USDA-ARS Exploring the genomic diversity of the Pseudomonas fluorescens group
Medina-Munoz, Monica Penn State University How do coral hosts communicate with their associated microbial community?
Peay, Kabir Stanford University Coprophilous fungi as a model system for understanding the metagenomics of carbon cycling in microbial eukaryote communities
Simon, Holly Oregon Health & Science University A systems approach to evaluate physical constraints and microbial controls on fluxes of nutrients and energy in a coastal ecosystem
Sorek, Rotem Weizmann Institute of Science (Israel) Comparative genomics of a single organism: In search of acquired immunity in trees
Swaminathan, Kankshita University of Illinois Understanding variance in allele specific expression in the polyploid Saccharinae
Thon, Michael University of Salamanca (Spain) Evolution and adaptation of carbohydrate utilization in the Colletotrichum acutatum species complex
Treseder, Kathleen University of California, Irvine Genomes and transcriptomes of decomposer fungi responding to warming in Alaskan boreal forest
Wildermuth, Mary University of California, Berkeley Comparative genomics of powdery mildews and associated host plants
Wosten, Han Utrecht University (Netherlands) Functional genomics of lignocellulose degradation by Agaricomycete fungi
Wurzbacher, Christian IGB (Germany) Whole genome sequencing of aquatic fungi responsible for the degradation of recalcitrant substrates in liquid environments
Young, Erica University of Wisconsin Metagenome and metatranscriptome of complex algal communities growing in wastewater: Bioremediation, nutrient transformation, carbon sequestration
Zhang, Baohong East Carolina University Panicum virgatum small RNA sequencing to identify gene expression changes related to biofuel traits

JGI-EMSL Facilities Integrating Collaborations for User Science (FICUS) Plans

Proposer Affiliation Project Description
Colwell, Frederick Oregon State University Integrated Biogeochemical Modeling of Microbial Consortia Mediating Anaerobic Oxidation of Methane in Dynamic Methane Hydrate-bearing Sediments
Crump, Byron Oregon State University Decoding DOM Degradation: How Does Carbon Source and Sunlight Exposure Alter Microbial Metabolism and Expression of Genome-Encoded Metabolic Degradation of Permafrost Organic Matter?
Cumming, Jonathan West Virginia University Mapping the Metabolism of Nutrient and Carbon Exchange in the Plant-Microbe Symbiosis
de Vries, Ronald CBS-KNAW Fungal Biodiversity Centre Dissecting Intraspecies Diversity in Fungal Wood Decay
DiChristina, Thomas Georgia Institute of Technology Sensing External Metals by Outer Membrane Beta-Barrel Proteins
Lebeis, Sarah University of Tennessee Uncovering the Composition and Function of the Aquatic Microbiome for Duckweeds
Luthey-Schulten, Zaida University of Illinois at Urbana-Champaign Quantifying Differential Expression and Identifying Bottlenecks in Methanogenic Pathways
Magnuson, Jon Pacific Northwest National Laboratory Elucidating the Influences of Engineered N-glycosylation Motifs in Bacterial Biomass Hydrolyzing Enzymes upon Heterologous and Native Gene Expression, Secretion and Degradation in Aspergillus niger
Rich, Virginia University of Arizona Systems-level Insights into Carbon Transformations in Thawing Permafrost by Parallel High-resolution Organic Matter and Microbial Community Characterizations
Stegen, James Pacific Northwest National Laboratory Coupling Microbial Communities to Carbon and Contaminant Biogeochemistry in the Groundwater-Surface Water Interaction Zone
Vilgalys, Rytas Duke University Integrated Genomic/Transcriptomic/Secretomic Study of Plant-Fungal Interactions Between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Mushroom Genus Suillus
Wrighton, Kelly The Ohio State University Microbial Controls on Biogeochemical Cycling in Deep Subsurface Shale Carbon Reservoirs
  • 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

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles
  • 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