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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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    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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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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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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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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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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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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    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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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 FY23
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  • 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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