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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 › CSP Plans
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September 22, 2017

Bacteria and Fungi in Native Prairies

Despite the persistent presence of potentially harmful fungi and bacteria, America’s native prairies are healthy, thriving communities of perennial herbaceous plants. How do these communities maintain a balance with these microbes? Bacteria and fungi found in native prairie soil, are mutually antagonist and thus may keep each other in check. Each produces antibiotic compounds when… [Read More]

September 22, 2017

Dynamics of Wetland Mangrove Ecosystems

Wetland mangroves are among the most productive ecosystems on the planet, generating a substantial amount of methane each year. Researchers know very little about how the microbial communities responsible for methanogenesis respond to climatic shifts. Since these communities experience strong subtropical seasonal and diurnal changes in light and temperature, the team aims to track temporal… [Read More]

September 22, 2017

Elucidating Viral “Dark Matter”

This proposal seeks to study viruses and microbes in nearly unexplored extreme environments including hydrothermal vents, glacial sea ice, and modern and ancient sea brines. The team will develop catalogs of which viruses are there, and use these to explore their genomes to identify genes the viruses have ‘stolen’ to augment a key microbial metabolism… [Read More]

September 22, 2017

Microbial Success in Legume-Rhizobia Mutualism

Recent advances have revealed the importance of microbes on plant and animal health. For plant productivity, no microbe-plant association is more important than that between rhizobia bacteria and legume plants. This symbiosis is the major natural contributor of nitrogen, a nutrient that limits plant growth in agricultural and natural systems. This work will identify genes… [Read More]

September 22, 2017

Quantifying Cyanobacteria Interactions

Yellowstone National Park, Octopus hot spring biofilms (Courtesy of Devaki Bhaya)Photosynthetic microbes play a major role in the Earth’s complex biogeochemical cycles. The vast populations of photoautotrophic cyanobacteria in the oceans, terrestrial and freshwater environments fix significant amounts of carbon and nitrogen. These phototrophic hosts are prey to viruses that release carbon and other nutrients, so the long term objective is to quantify dynamic interactions… [Read More]

September 22, 2017

Iron- and Sulfur-Oxidizing Sediment Bacteria

Iron and sulfur are important elements to all life on Earth. Some groups of bacteria use iron and sulfur as energy sources and make organic carbon (sugars) from carbon dioxide in the atmosphere. These bacteria, known as iron- and sulfur-oxidizing bacteria, are found in the sediments and waters of the ocean and on land. They… [Read More]

September 22, 2017

Dynamic Behavior of Soil Ecosystems

By incubating soil with position-specific 13C-labeled glucose and determining the isotope distribution in the pyruvate that is produced, researchers will distinguish between two forms of glycolysis that may occur in intact microbial communities. Additionally, they will sequence DNA and RNA from soils and use that information to improve metabolic models. Improved understanding of microbial energy… [Read More]

September 22, 2017

Metabolic Diversity Across the Great Lakes

The Laurentian Great Lakes hold 20 percent of Earth’s surface freshwater and provide inestimable ecosystem services, yet surprisingly little is known about the structure and activity of microbial communities in this ecosystem. This project seeks to characterize the metabolic diversity and activity of microbes across the Great Lakes, and to understand how these microbes control… [Read More]

September 22, 2017

Gene Expression in Phlebiopsis gigantea

This project seeks to exploit the unique ability of the fungus Phlebiopsis gigantea to rapidly colonize freshly cut loblolly pine. Investigations will advance understanding of the early and exclusive deconstruction of coniferous wood by P. gigantea, provide a framework for functional analyses of hitherto unknown proteins, develop effective biocontrol strategies against economically important root rot… [Read More]

September 22, 2017

Genus-Wide Genomics of Trichoderma

Trichoderma is a genus of fungi that has a broad impact on mankind. There are approximately 270 species of Trichoderma fungi that have varied interactions with other fungi, animals, plants, and efficiently degrade plant biomass material. One species in particular (T. reesei) is well-established for production of enzymes used in the biofuel and biorefinery industries…. [Read More]
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