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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 FY20

Approved Proposals FY20

Following are the approved user proposals for fiscal year 2020, including CSP, CSP New Investigator, and FICUS JGI-EMSL.

Community Science Program

Proposer Affiliation Proposal Description
Alcami, Antonio Spanish National Research Council (Spain) Diversity of DNA and RNA viruses in Antarctica
Anderson, Rika Carleton College Microbial and Viral Mediation of Biogeochemical Cycles from Source to Sink in Hydrothermal Vent Systems
Bowler, Chris Institut de Biologie (France) New Diatom Genome Sequences from the Most Abundant Genus in the Global Ocean
Brodie, Eoin Lawrence Berkeley National Laboratory Scaling Microbial Traits from Genomes to Watersheds Through Combined Airborne Hyperspectral Imaging, Soil Biogeochemistry, and Metagenome Assembled Genomes
Bushley, Kathryn University of Minnesota Defensive Mutualisms Between Fungal Root Endophytes and Soybean
Cullen, Daniel Forest Products Laboratory Mechanisms of Wood Decay by Soft Rot Fungi
diCenzo, George Queen’s University (Canada) Constructing a Functional and Regulatory Gene Atlas of a Nitrogen-Fixing Legume Symbiont to Instruct Genome Annotation and Synthetic Biology Applications
Dick, Richard The Ohio State University Exploring Microbial Roles in Plant Drought Tolerance in the Sahel
Gerlach, Robin Montana State University Deciphering Cross-Domain Interactions in High-Productivity, High-pH, High-Alkalinity Microalgae Communities
Hanson, Thomas University of Delaware Groundtruthing And Expanding Our Metabolic Understanding of Important C And S Cycling Microbes
Hess, Matthias University of California, Davis Detangling the Inter-Organismal Interactions During Anaerobic Biomass Degradation And Methane Production in the Rumen Ecosystem
Hori, Chiaki Hokkaido University (Japan) Elucidating the Plant-Microbe Interactions of the Wood Decay Fungus Perenniporia fraxinea, a Serious Pathogen Of Hardwood Trees
Juenger, Tom University of Texas at Austin Resequencing a Fast-Neutron Mutant Population of a C4 Perennial Grass (Panicum hallii)
Kliebenstein, Daniel University of California, Davis Pangenomic Comparison of Structural Variation Driving Recurrent Network Evolution in Brassicaceae Metabolism
Mock, Thomas University of East Anglia (United Kingdom) The International Arctic Ice Drift Experiment MOSAiC: Seasonal Changes of Microbial Communities Across the Arctic Ocean
Polle, Juergen Brooklyn College of CUNY Exploring the Diversity of Parasitic and Commensal Chytrids of Microalgae
Rodrigues, Jorge University of California, Davis Is the Soil Aggregate a Biogeofunctional Island? Unifying Two Theories to Explain Multiple Biological Processes
Selbmann, Laura University of Tuscia (Italy) Shed Light in The daRk lineagES of the Fungal Tree Of Life (FTOL) Acronym: (STRES)
Sullivan, Matt The Ohio State University Inferring Virus-Host Interactions Through Multi-Omics High-Resolution Time Series
Uehling, Jessie University of California, Berkeley Evaluating the Role of Fungal Endosymbionts in Fungal Mating and Evolution
Woods, Daniel University of California, Davis Genetic Tools in Brachypodium Distachyon to Identify Genes Regulating Bioenergy Relevant Traits in Grasses
Wrighton, Kelly Colorado State University Creating the GROW (Genome Resolved Open Watershed) Database: Leveraging Distributed Research Networks to Understand Watershed Systems
Ziels, Ryan University of British Columbia (Canada) Mapping Methanogenic Metabolic Networks in Full-Scale Bioenergy Facilities Using Functionally-Targeted Multi-Omics
Zuccaro, Alga University of Cologne (Germany) Host-Specific Regulation of Effector Gene Expression In Mutualistic Root Endophytic Fungi

CSP New Investigator

Proposer Affiliation Proposal Description
Anantharaman, Karthik University of Wisconsin-Madison Paired viral-microbial metagenomes from anoxic freshwaters to inform biogeochemical cycling and hypolimnion dynamics associated with a long-term time series
Branco, Sara Montana State University Mechanisms of heavy metal tolerance in Suillus luteus
Brzezinski, Mark University of Califorina Unraveling the genetic basis of silica formation and fatty acid biogenesis in freshwater vs. marine diatoms
Ciric, Milica Institute of Molecular Genetics and Genetic Engineering (IMGGE) De-novo sequencing of 82 selected strains with biomass-degrading and bioremediation potential
Collins, Gavin National University of Ireland Galway Growth and development of methanogenic biofilms for bioenergy production
Eyice, Ozge Queen Mary University of London Microbial dimethylsulfide degradation in anoxic sediments
Harkess, Alex Donald Danforth Plant Science Center The phylogeny and evolution of rapidly reproducing duckweeds
Krukenberg, Viola Montana State University Revealing the extent of microbial methane cycling in geothermal features of Yellowstone National Park
Louis, Joe University of Nebraska-Lincoln Temporal transcriptomic analysis to understand the host and non-host aphid feeding on sorghum
Martinez Garcia, Manuel University of Alicante Tackling complex paradigms in marine virology: what are we missing with current viral metagenomics?
Monteoliva, Mariela Oklahoma University Transcriptomic and metabolomic analysis of stems of switchgrass lignin mutants under drought stress
Paape, Tim University of Zurich Molecular strategies for adaptation by legumes to toxic environments
Perryman, Clarice University of New Hampshire Characterizing the Pathways and Potential for Methane Oxidizing Bacteria to Mitigate Emissions from Thawing Permafrost
Rhee, Seung Carnegie Institution for Science Leveraging genomics and metabolomics to reveal mechanisms of thermoadaptation in a desert extremophile Tidestromia oblongifolia
Santoro, Alyson University of California, Santa Barbara Interactions between chemoautotrophic and heterotrophic bacteria investigated using combined transcriptomics and metabolomics
Sharp, Jonathan Colorado School of Mines Depth-resolved metagenomic inquiry of coupled nitrogen, carbon and sulfur biogeochemistry within a temporally dynamic photosynthetic wetland biomat
Techtmann, Stephen Michigan Tech University Diversity of carbon monoxide-based metabolisms and the role of carbon monoxide in sediment carbon cycling
Trivedi, Pankaj Colorado State University Effect of climate warming on the temporal functional scaling of boreal forest soil microbiome?
Wakao, Setsuko Lawrence Berkeley National Laboratory Mining for genes required for silica biomineralization in stramenopiles
Ward, Lewis Harvard University Metagenomic characterization of novel phototrophic microbial mats from an organic carbon-rich hot springs

FY 2020 Facilities Integrating Collaboration for User Science (FICUS) JGI-EMSL Plans

Proposer Affiliation Proposal Description
Beliaev, Alex Pacific Northwest National Laboratory Understanding Genomic Underpinnings of High-Biomass Productivity Phenotypes in Industrially Relevant Microalgae
Brodie, Eoin Lawrence Berkeley National Laboratory Beyond the Rhizosphere: Microbial Functional Traits Through the Whole Soil Profile and Their Response to Warming
Chain, Patrick Los Alamos National Laboratory Bacterial:Fungal Interactions in Soil: Developing a Mechanistic Understanding of Nutrient Exchange Between Soil Microbes and the Resulting Consequences for C/N Cycling
Crump, Byron Oregon State University Sunlight Exposure Replaces the Function of Microbial Enzymes Needed to Degrade DOM
Dunbar, John Los Alamos National Laboratory Carbon Cost of Plant-Microbe Interactions Under Drought
Gerlach, Robin Montana State University Deciphering Interactions Hypothesized to Lead to High Productivity in High Ph-High Alkalinity Phototrophically Driven Microbial Communities
Hallam, Steven University of British Columbia Expanding the Functional Metagenomics Toolkit with CRAGE and CRISPR-Cas9 In Taxonomically Diverse Microbial Host Chassis
Liao, Hui-ling University of Florida Discover Ectomycorrhizal Fungi-Triggered Macro- and Micronutrient Reactions and Movements: From Cell to Ecosystem Function
McDermott, Jason Pacific Northwest National Laboratory Prediction of Response in Soil Microbiome Carbon Utilization to Changing Moisture Conditions
Merchant, Sabeeha University of California, Berkeley Gene Function Discovery in Photosynthesis: A Multi-Omics Approach
Tfaily, Malak University of Arizona Rhizosphere Effects on Soil Organic Matter Decomposition and Microbial Activity in a Tropical Rainforest Under Drought: Unearthing Aggregate- to Ecosystem-Scale Contributions to Carbon Cycling Through Whole-Ecosystem Stable Isotope Labeling
  • Approved Proposals FY21
  • Approved Proposals FY20
  • Approved Proposals FY19
  • Approved Proposals FY18
  • Approved Proposals FY17
  • 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
  • ETOP Projects

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