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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

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    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

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    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

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    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

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    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

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

Approved Proposals FY21

Following are the approved user proposals for CSP, FICUS JGI-EMSL-NEON 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 Plan

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 Michael University of British Columbia (Canada) Resolving carbon fluxes within microbial communities inhabiting full-scale bioenergy facilities

CSP New Investigator

Proposer Affiliation Proposal Description
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
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
Glassman, Sydney University of California, Riverside Using metagenomics to elucidate microbial mechanisms of altered carbon and nitrogen cycling post-fire in southern California Chaparral
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
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
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
  • Approved Proposals FY21
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  • Approved Proposals FY19
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  • Approved Proposals FY17
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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
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