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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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Home › Our Projects › Approved User Proposals › Approved Proposals FY21

Approved Proposals FY21

Following are the approved user proposals for CSP, FICUS JGI-EMSL-NEON, CSP Functional Genomics and CSP New Investigator calls.

Community Science Program

Proposer Affiliation Proposal Description
Bahram, Mohammad Swedish University of Agricultural Sciences (Sweden) Evolution of Nutritional Modes of Ceratobasidiaceae (Basidiomycota, Fungi)
Bhattacharya, Debashish Rutgers University Extreme Solutions to Extreme Problems: Studies of Life at the Edge Using Cyanidiophyceae Red Algae
Chopra, Ratan University of Minnesota Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
Cosgrove, Daniel Pennsylvania State University Synthesizing Microbial Expansins with Unusual Activities
D’Agostino, Paul Technische Universität Dresden (Germany) Expanding Genomic Knowledge of Unexplored Symbiotic and Terrestrial Cyanobacteria
Hammond, Ming University of Utah High-Throughput Functional Discovery of Bacterial Sensory-Enzymes
Hanschen, Erik University of Arizona A Genomic Approach to Understanding Mechanism and Consequences of Life Cycle Evolution in Green Algae to Understand Reproduction in Biofuel and Feedstock Relevant Algae
Harkess, Alex Auburn University The Brassicales Genome Initiative
Hatzenpichler, Roland Montana State University Taxonomic, Genomic, Metabolic, and Functional Heterogeneity in Yellowstone Geothermal Features
Hurley, Amanda Wisconsin Institute for Discovery Novel Secondary Metabolite-Producing Bacteria for Plant Disease Control
Larkin-Swartout, Alyse University of California, Irvine Detecting Nutrient Limitation and Coastal Biogeochemical Responses to El Nino Using Microbial Eco-Genomic Biomarkers
Looney, Brian Duke University Metatranscriptomic Study of Ectomycorrhizal Fungal Communities of Populus Across a Diversity Gradient
Lopes dos Santos, Adriana Nanyang Technological University (Singapore) New Green Genes
Ma, Li-Jun University of Massachusetts Amherst Genome Dynamics, Chromosomal Rearrangements and Potential Functional Impacts in Fusarium, A Genus of Endophytic, Plant Pathogenic and Saprophytic Fungi
McDaniel, Stuart University of Florida The Metabolic Basis of Bryophyte-Microorganism Interactions
McKay, John Colorado State University Enabling Reverse Genetics in the Oil Seed Crop Camelina sativa Through Mutant Population Sequencing
Mock, Thomas University of East Anglia (United Kingdom) 100 Diatom Genomes Project
Moran, Mary Ann University of Georgia Temperature Effects on Metabolite-Mediated Autotroph-Heterotroph Carbon Transfer
Nuccio, Erin Lawrence Livermore National Laboratory Deeply Rooted: Using Metagenomics and Isotope-Assisted Metagenomics to Determine How Switchgrass Alters Subsoil Carbon Sequestration
Ozias-Akins, Peggy University of Georgia Sequencing of Apomictic Relatives of Switchgrass for Apomixis Gene Discovery and Comparative Genomics
Schuppenhauer, Michael Lawrence Berkeley National Laboratory SMARTFARM Metagenome Analysis of Carbon and Nitrogen Cycling in Commercial Bioenergy Crop Soils
Shen, Ben The Scripps Research institute Large-Scale Genome Sequencing for Establishing a Natural Products Genomics Resource Center
Slotkin, R. Keith Donald Danforth Plant Science Center Transcript Annotations of Repetitive Elements Enable Investigation of Previously Inaccessible Dark Matter Regions of Complex Bioenergy Plant Genomes
Spietz, Rachel Montana State University Impacts of Viral Infections Upon Microbial Carbon Cycling in the Samail Ophiolite
White III, Richard University of North Carolina at Charlotte Elucidating the Role Of Bacteriophage Lifestyle Strategy in Microbially-Mediated Perennial Rhizosphere Nitrogen Transformations
Willis, John Duke University Genomic Resources for Mimulus, a Powerful Plant System for Analyses of Environmental Adaptations
Wommack, Eric University of Delaware Deducing Gene to Function Linkages Within Virioplankton Populations Through the Lens of Ecosystem Gradients

FY 2021 Facilities Integrating Collaboration for User Science (FICUS) JGI-EMSL Proposals

Proposer Affiliation Proposal Description
Bailey, Vanessa Pacific Northwest National Laboratory Characterization of simplified soil communities with high and low carbon use efficiency across differing moisture treatments
Bhatnagar, Jennifer Boston University Plant-mycorrhizal-decomposer interactions under climate change: the role of shifting plant carbon allocation
Blanchard, Jeff University of Massachusetts, Amherst Integrative analysis of multi-omic data across NEON eco-climatic regions
Glass, N. Louise University of California, Berkeley Nuclear cooperation, sharing of public goods and coordination of plant biomass utilization: probing functions unique to multinucleate syncytial fungi
Hatzenpichler, Roland Montana State University Ecophysiology, inter-domain interactions, and biogeochemical impact of an aerobic methane-producing freshwater bacterium
Heyduk, Karolina University of Hawaii Characterizing the molecular and metabolic regulation of drought-tolerant CAM photosynthesis
Mouser, Paula University of New Hampshire Membrane adaptations in response to environmental and engineered perturbations: Implications on attachment and carbon cycling in the deep terrestrial subsurface
Selbmann, Laura University of Tuscia (Italy) Metabolic processes and trophic interactions in Antarctic cryptoendolithic communities
Swaminathan, Kankshita HudsonAlpha Institute for Biotechnology Characterization of self-incompatibility in the bioenergy grass Miscanthus
Ziels, Ryan University of British Columbia (Canada) Resolving carbon fluxes within microbial communities inhabiting full-scale bioenergy facilities

CSP Functional Genomics

Proposer Affiliation Proposal Description
Alper, Hal University of Texas at Austin Accessing an expanded transport-ome through a transporter protein library
Geddes, Barney North Dakota State University Synthetic symbiotic gene clusters for engineering designer rhizobium-legume symbioses
Henrissat, Bernard Technical University of Denmark Large scale functional exploration of the Carbohydrate-Active Enzymes sequence space
Lowe-Power, Tiffany University of California, Davis Synthesis and functional analysis of type VI secreted secretion (T6SS) genes from plant symbiotic bacteria
Mahadevan, Radhakrishnan University of Toronto Transcription Factor Biosensor Libraries for Community Use in Metabolic Engineering
Mueller, Alex LanzaTech, Inc. Cell-free combinatorial assessment of the genomic landscape of gas-fermenting Clostridium autoethanogenum for use in biosynthetic design
Narayan, Alison University of Michigan Profiling chemical function across sequence space
Nayak, Dipti University of California, Berkeley Functional Characterization of Energy Conservation Pathways in Methanogenic Archaea within the Methanosarcina Genus
Robinson, Serina Eawag Swiss Federal Institute of Aquatic Science and Technology Functional characterization of metagenomic hydrolases from stream biofilms enabling access to alternative organic carbon pools
Woolston, Ben Northeastern University Development of a Robust Genome Engineering Toolbox for the Model Acetogen Eubacterium limosum

CSP New Investigator

Proposer Affiliation Proposal Description
Carey, Sarah Auburn University Transcriptomic analyses of the high-seed oil halophyte Batis maritima
Evans, Rebecca Washington State University Metagenomes of the developing soils of Mount St Helens responding to nitrogen deposition and invasive species and the impact on soil carbon storage and cycling
Fairbanks, Dawson University of Arizona Determining seasonal trait based microbial responses to moisture pulse events in the Jemez River Basin Critical Zone
Fernandes, Vanessa The University of New Mexico Unraveling the genomes of novel genera in the Microcoleus steenstrupii complex to understand climate change responses in biocrusts
Fulweiler, Robinson Boston University Relating microbial community function to methane emissions in temperate seagrass meadows
Garrigues Cubells, Sandra Westerdijk Fungal Biodiversity Institute (Netherlands) Study of the functional conservation and diversity of fungal transcriptional regulators involved in plant biomass degradation.
Geddes, Barney North Dakota State University Elucidating the genetic determinants of rhizobial effectiveness at symbiotic nitrogen fixation
Ghimire, Sabita Miami University High ammonium toxicity in ammonia-oxidizing bacteria
Glassman, Sydney University of California, Riverside Using metagenomics to elucidate microbial mechanisms of altered carbon and nitrogen cycling post-fire in southern California Chaparral
Igwe, Alexandria University of Miami Local adaptation of nitrogen-fixing bacteria, Microvirga, to high-stress serpentine soils
Jackrel, Sara University of California, San Diego Bacterial drivers of the Home-Field Advantage and the role of locally accelerated litter decomposition in the carbon cycle
Leisner, Courtney Auburn University Genomic regulation of plant biomass and nutrient responses to elevated atmospheric carbon dioxide levels in soybean
Lopez Pozo, Marina University of Colorado at Boulder Influence of rhizosphere microbes on duckweed transcriptome under elevated CO2
McGonigle, Julia Bigelow Laboratory for Ocean Sciences Linking Genomes to Phenomes in Extremophilic Microorganisms with Advanced Single Cell Approaches
Prenni, Jessica Colorado State University Investigating the Relationship Between Cover Crop Species Diversity, the Composition and Function of the Soil Microbiome, and Soil Health
Sandaa, Ruth-Anne University of Bergen (Norway) Metatranscriptomic analysis of the different steps in a marine giant virus-algae infection
Sillo, Fabiano Institute for Sustainable Plant Protection, National Research Council (Italy) Mining ectomycorrhizal genomes and transcriptomes: from pan-genome to adaptive evolution in a climate change scenario
Su, Wei Wen University of Hawaii at Manoa RNA-seq analysis of Yarrowia lipolytica to decipher synthesis of acetyl-CoA derived oleochemicals from waste lipid feedstock for biomanufacturing of biofuels and bioproducts
Vimercati, Lara University of Colorado at Boulder Transcriptomic studies of the polyextremophilic yeast Naganishia friedmannii exposed to freeze-thaw stress
Xie, Meng Brookhaven National Laboratory Exploring transcriptional responses to iron bioavailability in Populus
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  • Approved Proposals FY10
  • Approved Proposals FY09
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  • Approved Proposals FY06
  • Approved Proposals FY05
  • ETOP Projects

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