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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 FY12

Approved Proposals FY12

Following are the approved user proposals for fiscal year 2012.

Community Science Program (CSP) Plans

Proposer Affiliation Project Description
Acinas, Silvia ICM-CSIC, Spain Microbial metagenomics and transcriptomics from a global deep-ocean expedition
Andresson, Olafur University of Iceland Sequencing of the three cultured partners of the lichen Lobaria pulmonaria and the sequencing of the transcriptomes from the natural tripartite lichen under selected and controlled conditions.
Banfield, Jill University of California, Berkeley Terabase sequencing for comprehensive genome reconstruction to assess metabolic potential for environmental bioremediation
Brodie, Eoin DOE JGI Mediterranean Grassland Soil Metagenome (MGSM): Enabling a systems view of soil carbon and nitrogen biogeochemistry under a changing climate.
Brutnell, Thomas Boyce Thompson Institute for Plant Research Development of sequence-based community tools for Setaria viridis-a model genetic system for C4 grasses
Bucking, Heike South Dakota State University Exploring the transcriptome of perennial grasses in association with beneficial microorganisms to increase biomass production and environmental sustainability of bioenergy production
Cary, Stephen University of Delaware Understanding terrestrial microbial biocomplexity in an Antarctic desert landscape: resolving universal drivers of community structure and function in a trophically simple system
Crouch, Jo Anne USDA-ARS Genomic signatures of pathogenicity and endophytism in five species of grass-associated Colletotrichum impacting the health and production of bioenergy feedstocks, agriculture and the environment
Dangl, Jeff University of North Carolina at Chapel Hill Plant associated metagenomes–Microbial community diversity and host control of community assembly across model and emerging plant ecological genomics systems.
DeAngelis, Kristen University of Massachusetts Microbial ecology and genomics of carbon-storing bacteria in rhizosphere soils
Dubilier, Nicole & Kleiner, Manuel Max Planck Institute for Marine Microbiology, Germany Understanding novel pathways for energy and carbon use in bacterial symbionts of gutless marine worms
Emerson, David Bigelow Laboratory for Ocean Sciences Single cell genome sequencing of biomineralizing bacteria
Fierer, Noah University of Colorado Cross-site metagenomic analyses to assess the impacts of experimental nitrogen additions on belowground carbon dynamics
Fredrickson, Jim Pacific Northwest National Laboratory Microbial Interactions in Extremophilic Mat Communities
Gilbert, Jack Argonne National Laboratory Creating a successional model for carbon remediation in the Gulf of Mexico
Gross, Stephen DOE JGI The Agave Microbiome: Exploring the role of microbial communities in plant adaptations to desert environments
Hazen, Samuel University of Massachusetts Creating a multi-functional library of grass transcription factors for the energy crop model system Brachypodium distachyon
Hess, Matthias Washington State University Expression profile of biomass-degrading fungi inhabiting the cow rumen
Kelly, William AgResearch, New Zealand The Hungate 1000. A catalogue of reference genomes from the rumen microbiome.
Kerfeld, Cheryl DOE JGI Enhancing Bacterial Carbon Capture and Sequestration: Synthesis of Building Blocks for the Carboxysome, A Metabolic Module for CO2 Fixation
Kyrpides, Nikos DOE JGI Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project
Laplaze, Laurent Institut de Recherche pour le Developpement (IRD), France Transcriptome Analysis of Salt Tolerance in Casuarina trees
Martin, Francis INRA, France Metatranscriptomics of Soil Forest Ecosystems
McKay, Robert Bowling Green State University Metagenomics and metatranscriptomics of the Lake Erie ‘dead zone’: a seasonal source of greenhouse gases
McMahon, Katherine University of Wisconsin, Madison Dynamics of microbial carbon processing pathways across a decade in a freshwater eutrophic lake revealed through metagenomic sequencing
Mock, Thomas University of East Anglia, UK Sea of Change: Eukaryotic Phytoplankton Communities in the Arctic Ocean
Mohn, William University of British Columbia, Canada Metagenomic and metatranscriptomic analysis of forest soil communities across North America
Moran, Mary Ann University of Georgia The Genetic Basis for Heterotrophic Carbon Processing in the Sea
Murray, Alison Desert Research Institute Lake Vida brine microbial community (LVBMCo) genomics and transcriptomics – a window into diversity, adaptation and processes in extreme cold
Gerard Muyzer Delft University of Technology Genome sequencing of 100 strains of the haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacterium Thioalkalivibrio
Nealson, Kenneth University of Southern California Life at the edge: community cooperation and success in a very extreme (ultrabasic and ultra-reducing) environment
Ohm, Robin DOE JGI Towards functional genomics: development of Schizophyllum commune as a model system to study lignocellulose degradation
Pester, Michael University of Vienna, Austria Targeted metagenomics and metatranscriptomics of a sulfate-reducing rare biosphere member and potentially novel sulfate reducers that impact methane emission from peatlands
Powell, Amy Sandia National Laboratories A Phylogenomic Framework to Investigate Fungal Thermophily
Pukkila, Patricia University of North Carolina at Chapel Hill Functional genomics in the model mushroom Coprinopsis cinerea
Rodrigues, Jorge University of Texas at Arlington Profiling metagenomic consequences of Amazon deforestation at different spatial scales
Schadt, Christopher Oak Ridge National Laboratory Defining the Populus Microbiome: Role of Genotype by Environment Interactions in Shaping the Rhizosphere Microbiome of Populus trichocarpa
Schrenk, Matthew East Carolina University Metagenome-enabled Investigations of Carbon and Hydrogen Fluxes within the Serpentinite-hosted Subsurface Biosphere
Spatafora, Joseph Oregon State University 1000 Fungal Genomes
Stepanauskas, Ramunas Bigelow Laboratory for Ocean Sciences Dark ocean microbial single cell genomics
Wing, Rod University of Arizona Empowering functional plant genomics with genomes and transcriptomes of the top 20 Brassicales
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