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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 FY16

Approved Proposals FY16

Following are the approved user proposals for fiscal year 2016 including CSP, CSP Small-Scale, Synthesis, and FICUS projects.

FY 2016 Community Science Program (CSP) Plans

PI Affiliation Project Description
Catcheside, David Flinders University (Australia) Acquisition of the sequestrate (truffle like) habit by basidiomycete macrofungi
Cooper, Elizabeth Clemson University Comparative transcriptomics of sweet and grain sorghum to understand the mechanism and timing of sugar accumulation in an important bioenergy crop
de Vries, Ronald CBS-KNAW Fungal Biodiversity Centre (Netherlands) Dissecting the different approaches of ascomycete fungi to degrade plant biomass
DeLong, Ed University of Hawaii at Manoa Going long and going deep: Comprehensive open ocean community single cell genome sequencing at the model open ocean time series study site, station ALOHA
Dollhofer, Veronika Bavarian State Research Center for Agriculture (Germany) Anaerobic fungi and assessment of their potential for biogas production
Duplessis, Sebastien INRA (France) Sequencing a reference genome for Phakopsora pachyrhizi, the fungal pathogen responsible for the Asian Soybean Rust
Francis, Christopher Stanford University Metagenomic characterization of nitrogen-cycling microbial communities impacting uranium release in the Upper Colorado River Basin
Hamelin, Richard University of British Columbia (Canada) Pathobiome of bioenergy trees
Hibbett, David Clark University Comparative and functional genomics of shiitake mushrooms: an international collaboration to resolve evolutionary relationships, substrate specificity, growth profiles, and routes to domestication in the amphi-Pacific genus Lentinula
Juenger, Tom University of Texas at Austin Exploring natural genetic diversity in switchgrass (Panicum virgatum) and its microbiome
Kalyuzhnaya, Marina University of Washington Systems level insights into methane cycling in arid and semi-arid ecosystems via community metagenomics and metatranscriptomics
Lorito, Matteo University of Naples (Italy) Supporting the development of microbial probiotics for grasses useful in sustainable bioenergy production
Martin, Francis INRA (France) 1KFG: Deep sequencing of ecologically-relevant Dikarya
Mayali, Xavier Lawrence Livermore National Laboratory Influence of phycosphere-associated bacteria on microalgal biofuel production
McMahon, Katherine University of Wisconsin-Madison Diel cycles of gene expression in oligotrophic, dystrophic, and eutrophic lakes to identify new gene functions and dissect carbon cycling metabolisms
Merchant, Sabeeha University of California, Los Angeles Comparative genomics and expression profiling of snow algae Chlamydomonas cribrum and Chloromonas nivalis
Niyogi, Kris University of California, Berkeley Functional genomics of photosynthesis in Chlamydomonas, JGI’s flagship alga
O’Malley, Michelle University of California, Santa Barbara Genomic basis for syntrophic interactions between anaerobic gut fungi and methanogenic archaea
Pires, J. Chris University of Missouri-Columbia Investigating the diversity of mycorrhizal fungi to understand the evolution and function of symbiosis with orchids
Plett, Jonathan University of Western Sydney (Australia) Exploring the genomic basis for the global diversification by the ectomycorrhizal genus Pisolithus
Poland, Jesse Kansas State University The Intermediate Wheatgrass Genome: A resource for understanding mechanisms of perenniality and accelerating the development of perennial crops
Rappe, Michael University of Hawaii at Manoa Metagenomics of viral and microbial communities inhabiting warm, anoxic fluids of the sediment-buried deep ocean crust
Schachtman, Daniel University of Nebraska Systems analysis of the physiological and molecular mechanisms of Sorghum nitrogen use efficiency, water use efficiency and interactions with the soil microbiome
Spatafora, Joey Oregon State University Genomics of the early diverging lineages of fungi and their transition to terrestrial, plant-based ecologies
Umen, James Donald Danforth Plant Science Center Single cell and population dynamics of chromatin across the diurnal cycle in the model alga Chlamydomonas
Walsh, David Concordia University (Canada) Microbial metagenomics of carbon cycling communities in northern aquatic ecosystems
Wrighton, Kelly Ohio State University Life in the extreme deep terrestrial subsurface: microbial metabolism before and after shale gas extraction

Small-Scale Proposals

Proposer Affiliation Project Description
Beman, J Michael University of California, Merced Metagenomics of methane production and oxidation in high altitude lakes of Yosemite National Park
Chistoserdova, Ludmila University of Washington Understanding methane cycling through manipulation of synthetic methane-oxidizing communities
Cullings, Ken NASA Ames Extreme endosymbiosis: An investigation into a unique fungal microbiome found in geothermal ecosystems in Yellowstone National Park and New Zealand
DeAngelis, Kristen University of Massachusetts, Amherst Expanding genomic diversity of terrestrial bacteria: linking genes to metabolism in the slower-growing members of forest soil bacterial communities
Kostka, Joel Georgia Institute of Technology The role of the Sphagnum microbiome in carbon and nutrient cycling in peatlands
McMahon, Katherine University of Wisconsin-Madison Reference genomes for abundant freshwater taxa – Actinobacteria and Verrucomicrobia phase 2
Meredith, Laura Stanford University Microbial, chemical, and physical drivers of COS fluxes and 18O-CO2 exchange rates in soils
Miller, Christopher University of Colorado, Denver Developing a systems-level understanding of biotic and abiotic controls on microbial methane cycling in freshwater wetlands
Redmond, Molly University of North Carolina, Charlotte Metagenomic sequencing of methane-oxidizing mesocosms from the Gulf of Mexico and Hudson Canyon
Rich, Jeremy Brown University Metagenomic sequencing of an uncultivated bacterial phylum in marine sediments amended with organic carbon and nitrate
Saito, Mak Woods Hole Oceanographic Institution Characterizing Synechococcus dominated populations from the Costa Rica dome and surrounding waters
Shade, Ashley Michigan State University Response and recovery of surface soil microbial communities to an ongoing underground coalmine fire
Simister, Rachel University of British Columbia Linking microbial genomic capacity to geochemical process in the deep terrestrial biosphere
Slonczewski, Joan Kenyon College Cyanobacterial communities of Antarctic Lake Fryxell liftoff mats and glacier meltwater
Tolar, Bradley Stanford University Monitoring the transcriptional response of a representative low-salinity ammonia-oxidizing thaumarchaeote to shifts in environmental conditions
Walsh, Davi Concordia University Metagenomics of western Arctic Ocean microbial communities
Wilkins, Michael Ohio State University Seasonal sulfur cycling as a control on methane flux in carbon-rich prairie pothole sediment ecosystems
Wrighton, Kelly Ohio State University Identifying key genomes and metabolisms responsible for near-surface methane cycling in freshwater wetlands

Synthesis Proposals

Proposer Affiliation Project Description
Chang, Jui-Jen Biodiversity Research Center,Academia Sinica Designer Operons-A biomimic approach to the regulation of an enzyme cocktail for an artificial enzyme complex
Chen, Brandon Genomatica, Inc. Engineering efficient methanol utilization for renewable chemicals
McCourt, Peter University of Toronto Exploring the perception landscape of the strigolactone receptor
Prather, Kristala Massachusetts Institute of Technology Combinatorial assembly, screening and functional characterization of a recombinant glucaric acid pathway in S. cerevisiae
Shen, Ben The Scripps Research institute Construction of bacterial artificial chromosome (BAC) vector libraries for comparative genomics, elucidation of gene functions and heterologous expression of targeted genes
Smanski, Mike University of Minnesota Towards a mechanistic understanding of disease suppressive soils: Refactoring natural product gene clusters
Wang, Clay University of Southern California Identification of fungal secondary metabolites with novel structures
Zimmer, Jochen University of Virginia Synthesis of cellulose synthase genes implicated in primary and secondary plant cell wall formation for structural and functional analyses of plant cellulose biosynthesis

FY 2016 Facilities Integrating Collaboration for User Science (FICUS) JGI-EMSL Plans

Proposer Affiliation Project Description
Bell-Pedersen, Deborah Texas A&M University Specialized Ribosomes: A New Frontier in Gene Regulation
Cardon, Zoe Marine Biological Laboratory 3D Reality Check: Developing Structural Support for Predicting Microbial Function and Interpreting Microbial “Omics” Data
Doty, Sharon University of Washington Nitrogen fixation in Populus: Identification and localization of the key diazotrophs in planta
Duhaime, Melissa University of Michigan Building the phage-host-environment interaction data to scale from genes-to-ecosystems: Towards predictive modeling of wild microbial and viral community dynamics
Eastwood, Dan Swansea University (UK) Genomes to dynamic decay communities: Understanding fungal interactions during early decomposition events in natural lignocellulosic substrate
Neumann, Rebecca University of Washington A Rhizosphere-Scale Investigation of the Relationship Between Plant Productivity and Methane Emissions from Wetlands
Orphan, Victoria California Institute of Technology Fluorescence-based cell sorting and targeted proteomic analysis of active methane-oxidizing syntrophic consortia from environmental samples
Pan, Chongle Oak Ridge National Laboratory Integrated Omics Analyses of a Populus Pedigree for Crop Improvement
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