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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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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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    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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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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    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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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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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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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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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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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 FY23
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  • Approved Proposals FY14
  • Approved Proposals FY13
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  • Approved Proposals FY09
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  • Approved Proposals FY07
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  • Approved Proposals FY05
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