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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 FY14

Approved Proposals FY14

Following are the approved user proposals for fiscal year 2014 including CSP and JGI-EMSL “Facilities Integrating Collaborations for User Science” (FICUS) initiative projects.

Community Science Program (CSP) Plans

Proposer Affiliation Project Description
Banfield, Jillian UC Berkeley, LBNL Community metagenomic and transcriptomic analyses of microbial carbon turnover in grassland soil profiles under two rainfall regimes
Bonito, Gregory Duke University Comparative genomics of early diverging terrestrial fungi and their bacterial endosymbionts
Brem, Rachel UC Berkeley Pioneering fungal mutagenesis using Tn-seq
Brutnell, Thomas Donald Danforth Plant Science Center Doubling the number of Panicoideae genome sequences
Canovas, David University of Seville, Spain Global genomic consequences of the deletion of the Aspergilli non-homologous end joining DNA repair mechanism employed as a genetic tool worldwide
Chen, Jay Oak Ridge National Laboratory RNA-seq-Enabled Expression Quantitative Trait Locus (eQTL) in Populus
Coleman, Jeffrey Alpert Medical School of Brown University/Rhode Island Hospital Exploring the supernumerary chromosomes of the Fusarium solani and Fusarium oxysporum species complexes: Reservoirs for functional genetic diversity
Duplessis, Sébastien INRA, France Combined population genomics and transcriptomics to decipher the molecular bases of virulence and host adaptation in the poplar leaf rust fungus Melampsora larici-populina
Goodwin, Stephen Purdue University Stress responses of fungal saprobes and plant pathogens of the Dothideomycetes
Hammond, Ming UC Berkeley Synthesis and parallel construction of a library of large binary vectors for the screening of suicide exons for multi-gene pathway engineering in plants
Hazen, Samuel University of Massachusetts Synthesis of grass transcription factors for functional characterization in the energy crop model system Brachypodium distachyon
Isaacs, Farren Yale University Harvesting recombinases from metagenomes to develop multiplex genome engineering technologies in microorganisms
Konstantinidis, Kostas Georgia Institute of Technology The microbiome of the upper troposphere and its role in the chemistry of the atmosphere.
Libault, Marc University of Oklahoma Use of a single cell type model, the root hair cell, to advance our understanding of the soybean and sorghum transcriptomic and epigenomic responses to various environmental stresses
Lilleskov, Erik USDA Forest Service, Northern Research Station Fungal, bacterial, and archaeal communities mediating C cycling and trace gas flux in peatland ecosystems subject to climate change
Mockler, Todd Donald Danforth Plant Science Center From sequence to function: Predicting physiological responses in Brachypodium to facilitate engineering of biofuel crops
Molnar, Istvan University of Arizona Leveraging the JGI MycoCosm to functionally characterize orphan polyketide synthase clusters and their predicted bioactive small molecule natural products using comparative metaparvomics and synthetic biology
Mullet, John Texas A&M University Sorghum GENCODE Project
Nelson, Rebecca Cornell University MetaMaize: Characterizing Aboveground Maize-Endophyte Associations Influenced By Host Genotype, Climatic Region, Seed Source, and Tissue Type
Pelletier, Dale Oak Ridge National Laboratory Defining the functional diversity of the Populus root microbiome
Pett-Ridge, Jennifer Lawrence Livermore National Laboratory Unraveling the rhizosphere carbon cycle: Using comparative metatranscriptomics to identify key processes involved in root-enhanced decomposition of organic matter
Schmitz, Robert University of Georgia Harnessing epigenomic reprogramming to improve bioenergy trait performance
Shaw, Jonathan Duke University Development of a Comparative Genomics Resource for Sphagnum magellanicum
Stepanauskas, Ramunas Bigelow Laboratory for Ocean Sciences Microbial Dark Matter project phase II – stepping deeper into unknown territory
Stewart, Frank Georgia Institute of Technology Microbial and viral regulation of community carbon cycling across diverse low-oxygen zones
Taylor, John UC Berkeley Fungal response to global change: Adaption to global change and determination of rates of mutation and recombination
Wagner, Michael University of Vienna, Austria Raman-based microcolony genomics and transcriptomics for studying microevolution and ecology of nitrifiers
Whitman, William University of Georgia Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains

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

Proposer Affiliation Project Description
Firestone, Mary Kathryn UC Berkeley Mapping soil carbon from cradle to grave: using comparative transcriptomics, proteomics and metabolite analysis to identify the microbial blueprint for root-enhanced decomposition of organic matter
Hansel, Colleen Woods Hole Oceanographic Institution Genome-enabled Investigations of the Role of Secreted Proteins and Reactive Metabolites in Carbon Degradation by Pure and Mixed Ascomycete Fungal Communities
Harris, Steven University of Nebraska-Lincoln Engineering morphology and secretion to enhance the productivity of fungal fermentations
Hess, Matthias Washington State University Tri-Cities FECB: A Functional Encyclopedia of Cyanobacteria – Building the knowledge framework for an enhanced understanding of carbon and nitrogen cycling
Hofmockel, Kirsten Iowa State University Development of novel approaches to target microbial drivers of C cycling in soil aggregates
Kistler, Harold USDA ARS Cereal Disease Laboratory Organelles promoting high level terpenoid biosynthesis in filamentous fungi
O’Malley, Michelle Ann UC Santa Barbara Identification and Regulation of Cellulases within Novel Anaerobic Gut Fungi
Weyman, Philip J. Craig Venter Institute Functional genomics of moss-cyanobacteria interactions in boreal forest ecosystems
  • Approved Proposals FY21
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  • 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
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