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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 FY18

Approved Proposals FY18

Following are the approved user proposals for fiscal year 2018, including CSP, CSP Small-Scale, CSP Synthesis, and JGI-EMSL FICUS.

Community Science Program (CSP)

PI Affiliation Project Description
Banfield, Jill University of California, Berkeley LBNL Watershed Function SFA: Biogeochemical dynamics from genome to watershed scales
Beam, Jake Bigelow Laboratory for Ocean Sciences Emergent properties of marine and freshwater sediment chemolithoautotrophic microbial communities
Berka, Randy Novozymes Genus-wide Genomics of the Biomass-Degrading and Plant-Beneficial Trichoderma
Bhaya, Devaki Stanford University Cyanophages and Cyanobacteria in Extreme Environments
Buckley, Dan Cornell University Microbial Metabolic Dependency and its Impacts on the Soil Carbon Cycle
Catalan, Pilar Universidad de Zaragoza, Spain Genomic Characterization of the Brachypodium Polyploid Model to Unravel Bases of Success of Polyploidy in Flowering Plants
Coleman, Maureen University of Chicago Integrated Ecosystem Genomics across a Vast and Vital Freshwater System
Crump, Byron Oregon State University Combined Metagenomics and Metatranscriptomics to Evaluate Dissolved Organic Matter Metabolizing Microbes in Big Rivers of the U.S.
Cullen, Daniel Forest Products Laboratory Gene Expression in the Unusual White Rot Fungus Phlebiopsis gigantea
Dijkstra, Paul Northern Arizona University Partitioning Flux between Entner-Douderoff and Embden-Meyerhof-Parnas Glycolysis in Soil Communities
Duplessis, Sebastien INRA (France) Rust Pangenomics: Understanding the Diversity and Potential Impact of Rust Fungi – a Systematic Collection of Genomes & Transcriptomes
Fukami, Tadashi Stanford University Genomic Basis of the Ecological Success of Nectar Yeasts in their Carbon-Stressed and Nitrogen-Limited Environments
Garre, Victoriano University of Murcia (Spain) Exploring the Role of DNA Methylation in Biofuel Production, Environmental Sensing and Development in Basal Fungi
Huffaker, Alisa University of California, San Diego Systems Analysis of Secondary-Metabolism-Mediated Microbial Community Interactions in Sorghum and Maize Enabled by Comparative Metabolomic and Transcriptomic Genome-Wide Association Studies
Kalluri, Udaya Oak Ridge National Laboratory Reciprocal Impacts of Modified Plant Cell Wall and Associated Microbiome
Kistler, Harold USDA ARS Cereal Disease Lab, University of Minnesota Mechanisms of Co-Evolutionary Adaptation of Soil Microbes
Leebens-Mack, James University of Georgia Open Green Genomes: a Framework for Comparative Plant Genomics
Liu, Yu UT Southwestern Medical Center Determination of Fungal Chromatin Regulatory Network and Its Impact on Gene Expression
Mandadi, Kranthi Texas A&M University Gene Atlas of Diverse Grass-Microbe Interactions in Brachypodium and Setaria
Martinez-Gomez, Norma Michigan State University Dissecting the Genetic and Functional Diversity of Rare Earth-dependent Plant-Microbiome Interactions by Sequencing Analysis
Martiny, Jennifer University of California, Irvine Investigation of diel variation in microbial decomposition processes
Reese, Brandi Texas A&M University-Corpus Christi Dynamics of Seasonal and Diurnal Fluctuations in a Wetland Mangrove Ecosystem
Stuart, Rhona Lawrence Livermore National Laboratory Flipping the Switch: the Molecular Mechanisms Underlying Trophic Strategy Versatility in Parasitic Chytrids
Sullivan, Matt Ohio State University Elucidating Viral “Dark Matter” and Biogeochemical Impacts in Extreme Environments
Tas, Neslihan Lawrence Berkeley National Laboratory Deciphering Microbial Functions at Soil-Aquatic Interfaces: Fate of Carbon Exports into High-Elevation Streams
Tiffin, Peter University of Minnesota Leveraging Natural Diversity to Identify the Genetic Basis of Microbial Success in Legume-Rhizobia Mutualism and Non-Host Environments
U’Ren, Jana University of Arizona Comparative and Population Genomics of Xylariaceae: Exploring the Roles of Endophytic Fungi in Lignocellulose Degradation, Nutrient Cycling, and Secondary Metabolite Production
Umen, James Donald Danforth Plant Science Center Comparative Genomics and Germ Plasm Diversity in Acutodesmus, a Green Microalgal Bioenergy Feedstock Candidate with Potential for Breeding and Hybridization
Yang, Xiaohan Oak Ridge National Laboratory High Quality Genome Sequencing of Agave tequilana, a Bioenergy Crop with High Drought Tolerance and Low Biomass Recalcitrance
Zhang, Ru Donald Danforth Plant Science Center High-Throughput Sequencing and Metabolomics Enabled Phenomics to Investigate Integration of Heat and Circadian Responses in the Model Green Alga Chlamydomonas reinhardtii

Small-Scale Microbial/Metagenome

PI  Affiliation Project Description
Atsumi, Shota University of California, Davis Genomic Analysis, and Reconstruction of Isobutyl Acetate Tolerance in Escherichia coli
Barnhart, Elliott U.S. Geological Survey Multi-omic Sequencing of Sulfate Transition Zones in the Terrestrial Subsurface with Recalcitrant Carbon
Epstein, Slava Northeastern University Microbial Stem Cell Hypothesis
Högfors-Rönnholm, Eva Novia University of Applied Sciences (Finland) Microbial Community Structure and Function of an Actual and Potential Acid Sulfate Soil
Izquierdo, Javier Hofstra University Plant Growth-Promoting Bacteria from the Rhizosphere of the Beachgrass Ammophila breviligulata
Liu, Xiao-Jun Allen University of Massachusetts Amherst Disentangling the Relative Contributions of the Microbiome and Physical Protection in Soil Response to Long-Term Environmental Stress
Mason, Olivia Florida State University Coupled Plant:Microbe Interactions Mediate carbon and biogeochemical cycling in the marsh rhizosphere
McMahon, Katherine University of Wisconsin-Madison Biogeochemical gradients structure mercury-methylating microbial communities in a reservoir system
Nicol, Graeme Ecole Centrale de Lyon (France) Determining the interaction of viruses with prokaryotic hosts controlling nitrogen cycling in soil
Peay, Kabir Stanford University How does precipitation impact the taxonomic and functional diversity of the Populus trichocarpa soil microbiome?
Potnis, Neha Auburn University Unraveling the diversity of plant-associated saprophytic/non-pathogenic bacteria and their role in plant health and plant-pathogen interactions
Richardson, Ruth Cornell University Metagenomic Exploration of Microbial Communities involved in Carbon and Sulfur Cycling in Two Central New York State Peatlands
Selbmann, Laura University of Tuscia (Italy) Metagenomic Reconstruction of Endolithic Communities from Victoria Land, Antarctica
Thamatrakoln, Kim Rutgers University The Role of Light and Nutrient Limitation on Algal Host-Virus Interactions in Natural Populations and Subsequent Impacts on Carbon Export and the Biological Pump
Treusch, Alexander University of Southern Denmark (Denmark) Impacts of Climate Change Induced Flooding of Coastal Soils on Carbon Cycling and Sequestration – 3.0
Voges, Mathias Stanford University Elucidating the Biological Role of Root Exudates: Investigating the Transcriptional Response of Pseudomonas simiae WCS417 to Novel Specialized Plant Metabolites.
Ziels, Ryan University of British Columbia (Canada) Genome-Centric Metagenomics and Metatranscriptomics to Resolve Adaptive Capacities of Methane-Producing Biofilms to High Salinity Concentrations

Synthesis

PI Affiliation Project Description
Ando, Nozomi Cornell University Evolution of Allosteric Regulation in the Ribonucleotide Reductases: Investigating a Family of Ancient Enzymes
Berlemont, Renaud CSU Long Beach ProtHunt: Environmental multi activity proteins for improved biomass deconstruction, from sequenced metagenomes to protein biochemistry
Chang, Michelle UC Berkeley Mining the diversity of environmental organisms to discover novel halogenation catalysts
Donia, Mohamed Princeton University A natural model system for studying functional evolution and synthetic design principles of non-ribosomal peptide synthetases

FY 2018 Facilities Integrating Collaboration for User Science (FICUS) JGI-EMSL Plans

Proposer Affiliation Project Description
Bowen, Jennifer Northeastern University Combining High Resolution Organic Matter Characterization and Microbial Meta-Omics to Assess the Effects of Nutrient Loading on Salt Marsh Carbon Sequestration
Mayes, Melanie Oak Ridge National
Laboratory
Linking Proteogenomics, Metabolomics, and Soil Organic
Chemistry of Tropical Wetlands to a Soil Nutrient Cycling Model
Onstott, Tullis Princeton University Detecting Seismically-Sustained Deep Subsurface CH4-Cycling Chemolithoautotrophic Microbial Communities Using Multi-Omic Analyses and NanoSIMS
Saleska, Scott University of Arizona Investigating the Carbon Cycling Implications of Changing Microbial Leaf Litter Decomposition across a Permafrost
Thaw Gradient
Talbot, Jennifer Boston University Scaling Molecular Mechanisms of Mycorrhizal-Decomposer
Interactions to Emergent Ecosystem Carbon Balance
Tiemann, Lisa Michigan State University Tracking Switchgrass Photosynthate via 13CO2 Pulse-Chase into the Rhizosphere Microbiome and Metabolome
  • Approved Proposals FY23
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  • 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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