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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 FY10

Approved Proposals FY10

Following are the approved user proposals for fiscal year 2010.

Community Science Program (CSP) Plans

Eukaryotes

Proposer Affiliation Organism
Collier, Jackie Stony Brook University Four Labyrinthulomycete species
Cullen, Daniel US Forest Service, Forest Products Laboratory Homkaryotic derivative of Postia placenta
Cullen, Daniel US Forest Service, Forest Products Laboratory Lignin-degrading fungus Phlebiopsis gigantea
Goodwin, Stephen USDA-ARS and Purdue University Dothideomycetes plant pathogens
Grossniklaus, Ueli University of Zurich Apomictic plant Boechera holboellii
Koppisch, Andy Los Alamos National Laboratory Colony forming microalga Botryococcus braunii var Showa
Kubisiak, Thomas US Forest Service, Southern Research Station Fusiform rust fungus Cronartium quercuum f.sp. fusiforme
Martin, Francis Institut National de la Recherche Agronomique Pan-global basidiomycetes Pisolithus tinctorius and Pisolithus microcarpus
Moreau, Herve CNRS and UPMC Resequencing Ostreococcus tauri
Paterson, Andrew University of Georgia Resequencing sorghum
Phister, Trevor North Carolina State University Completion of the Dekkera (Brettanomyces) bruxellensis genome sequence
Pringle, Anne Harvard University Cellulose degrading fungus Amanita thiersii
Quatrano, Ralph Washington University in St. Louis Ceratodon purpureus(moss)
Reeve, Wayne Murdoch University Phytopathogenic oomycete Phytophthora cinnamomi
Roossinck, Marilyn Samuel Roberts Noble Foundation Alteration of Curvularia protuberata transcripts due to presence of Curvularia thermal tolerance virus
Vyverman, Wim Ghent University Diatom transcriptome and genome
Weeks, Donald University of Nebraska-Lincoln Transcriptome analyses of Chlamydomonas and Chlorella
Zhong, Shaobin North Dakota State University Fungal pathogen Cochliobolus sativus

Bacteria and Archaea

Proposer Affiliation Organism
Auchtung, Jennifer Michigan State University Role of population microdiversity in adaptation to environmental redox gradients
Anderson, Iain DOE Joint Genome Institute Xylan degraders
Anderson, Iain DOE Joint Genome Institute Genomic survey of haloarchaeal genomes
Bayer, Travis University of California, San Francisco Actinotalea fermentans
Bollmann, Annette Miami University Five isolates from the contaminated subsurface sediment of Oak Ridge’s FRC area
Brown, Igor NASA Johnson Space Center Two strains of Cyanobacteria for biological remediation
Bryant, Donald Penn State University Representative photosynthetic purple sulfur bacteria
Cavicchioli, Rick University of New South Wales Novel haloarchaea from Deep Lake
Coleman, Nicholas University of Sydney Ethene and vinyl chloride-oxidizing Mycobacterium strains
Cooper, Vaughn University of New Hampshire Adaptive mechanisms in Burkholderia biofilms
Copley, Shelley University of Colorado at Boulder Sphingobium chlorophenolicum
Daly, Michael Uniformed Services University of the Health Sciences Radiation-resistant bacterium Deinococcus grandis
Dopson, Mark Umeå University Psychrotolerant Acidithiobacillus species
Dvornyk, Volodymyr University of Hong Kong Nostoc linckia from “Evolution Canyon”
Edwards, Elizabeth University of Toronto Novel acetogenic bacterial isolates from dechlorinating microbial mixed cultures
Emerson, David Bigelow Laboratory for Ocean Sciences Two novel ‘Zetaproteobacteria’ from the ocean
Green, Stefan Florida State University Denitrifying bacterial isolates
Grzymski, Joseph Desert Research Institute Microbes integral to the cycling of sulfate and iron
Haggblom, Max Rutgers University Acidobacterium species from Arctic tundra soils
Hedlund, Brian University of Nevada Las Vegas Thermophiles in Great Basin hot springs
Kappler, Ulrike The University of Queensland Alkaliphilic sulfur oxidizing bacteria for sulfur pollution remediation
Lewis, Gillian University of Auckland Freshwater manganese depositing β-proteobacterium (Siderocapsaceae)
Liao, James University of California, Los Angeles Reverse metabolic engineering of Escherichia coli
Liu, Wen-Tso University of Illinois at Urbana-Champaign Comparison of novel methanogens from peatlands and bioreactors
Liu, Wen-Tso University of Illinois at Urbana-Champaign Obligate syntrophic bacteria capable of phthalate isomer compound degradation in methanogenic conditions
Martinez, Robert University of Alabama ORFRC Rahnella sp. Y9602
Mavrommatis, Konstantinos DOE Joint Genome Institute Cyanobacteria (Synechocystis) transcriptome
Mayali, Xavier Lawrence Livermore National Laboratory Marine Roseobacter RCA cluster bacterial strain LE17
Mills, David University of California, Davis Acetobacter aceti ATCC 23746
Muyzer, Gerard Delft University of Technology Haloalkaliphilic chemolithoautotrophic Thioalkalivibrio bacteria
Nesbø, Camilla University of Oslo Thermotogales strain mesG1.Ag.4.1
Norton, Jeanette M. Utah State University Nitrosomonas cryotolerans and Nitrosospira briensis for comparative phylogenomics of ammonia-oxidizing bacteria
Pappas, Katherine University of Athens Zymomonas mobilis transcriptomes and resequencing Z. mobilis industrial strain ZM4
Reeve, Wayne Murdoch University Rhizobia of clover, pea/bean and
lupin microsymbionts
Robb, Frank Center of Marine Biotechnology Carbon monoxide oxidizing thermophiles
Rodrigues, Jorge University of Texas at Arlington Genome closure of lignocellulosic degrader Verrucomicrobium sp. strain TAV2.
Sanchez Amat, Antonio University of Murcia Marine bacterial genus Marinomonas
Sello, Jason Brown University Biomass-degrading bacteria Streptomyces viridosporus ATCC 39115 and Streptomyces setonii ATCC 39116
Smidt, Hauke Wageningen University Halorespiring Firmicutes
Stabb, Eric The University of Georgia Research Foundation Mutations in Vibrio fischeri
Stein, Lisa University of Alberta Methanotrophic Bacteria from diverse environments
Stepanauskas, Ramunas Bigelow Laboratory for Ocean Sciences Single cell genome sequencing of mesopelagic bacterioplankton
Tisa, Louis University of New Hampshire An atypical Frankia isolate and Non-Frankia Actinobacteria from Actinorhizal Plants
Vieille, Claire Michigan State University Resequencing of Actinobacillus succinogene
Ward, David Montana State University Synechococcus cyanobacterial isolates

Metagenomes

Proposer Affiliation Organism
Breitbart, Mya University of South Florida Modern freshwater microbialites
Chistoserdova, Ludmila University of Washington Functional metagenomics of methane and nitrogen cycles in freshwater lakes
Davidson, Seana University of Washington Metagenome function of the Earthworm egg capsule bacterial community
Deng, Li University of Arizona Viruses that infect freshwater cyanobacteria
Edwards, Elizabeth University of Toronto Dehalobacter-containing dechlorinating community
Hedlund, Brian University of Nevada, Las Vegas Great Boiling Spring sediment and water microbial communities
Kirchman, David University of Delaware Metagenomic analysis of methane degradation in Arctic coastal waters and sediments
Madsen, Eugene Cornell University Naphthalene biodegrading microbial community
Mincer, Tracy Woods Hole Oceanographic Institute Natural microbial community associated with the cyanobacteria Trichodesmium
Moon, Christina AgResearch Limited Lignocellulolytic enzyme discovery from the rumen
Powell, Amy Sandia National Laboratories Eukaryotic microbial metatranscriptome of blue grama grass rhizosphere soils
Sullivan, Matthew University of Arizona Viral community in the Subarctic Pacific Ocean
Sullivan, Matthew University of Arizona Viral community in the Mediterranean Sea
Taylor, Mike University of Auckland Microbial symbionts of New Zealand’s endemic wood-degrading insects
Waldrop, Mark US Geological Services Permafrost Soil Microbiota
Ward, Naomi University of Wyoming Metatranscriptomic analysis of bacterial-algal interactions
Warnecke, Falk Friedrich Schiller University of Jena Desert locust (Schistocerca gregaria)
Worden, Alexandra Monterey Bay Aquarium Research Institute Metagenomics of uncultured marine eukaryotes
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