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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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November 11, 2013

Macondo wellhead metagenomes

The 2010 Deepwater Horizon oil spill presented researchers with an opportunity to employ a variety of approaches to quantify and model the microbial community composition and activity through successive metabolic petroleum hydrocarbon degradation. The Macondo wellhead oil leak, in the Gulf of Mexico, released a complex mixture of hydrocarbons into the water column that stimulated… [Read More]

November 11, 2013

Extremophilic microbial mat communities

Found worldwide, microbial mat communities are often the pioneering species in perturbed environments and can represent the only biota in extreme habitats. These associations are well-adapted to a range of harsh conditions that include extremes of temperature, salinity, high or low oxygen levels, and nutrient deprivation. In many cases, microbial mats are highly productive biochemical… [Read More]

November 11, 2013

NutNet soil metagenomes

Terrestrial ecosystems worldwide are receiving elevated inputs of nitrogen and recent studies suggest that the additional nitrogen is impacting soil carbon sequestration rates. It has been speculated that nitrogen additions alter the microbial processing of organic carbon pools, inhibiting decomposition of certain pools and accelerating soil carbon sequestration. This project focuses on shotgun metagenomic sequencing… [Read More]

November 11, 2013

Single-cell sequencing of iron-oxidizing bacteria

Iron is the fourth most abundant element in the Earth’s crust and is potentially one of the most abundant energy sources on Earth. Deep sea hydrothermal vents deposit iron oxides into the oceans annually. Several decades ago, the first hints of unusual microbial communities associated with iron oxides at seamounts came from samples collected by… [Read More]

November 11, 2013

Bacterial symbionts of gutless marine worms

More than 100 species of gutless worms have been found in marine sediments around the world, and they have formed symbiotic relationships with bacteria that provide them with nutrition and have enabled them to colonize nutrient-poor environments. The symbionts are so efficient at feeding their hosts and recycling their waste compounds that the worms have… [Read More]

November 11, 2013

Carbon-storing bacteria in rhizosphere soils

Microbes are able to store carbon under suboptimal growth conditions in culture, but the extent to which they store carbon in bulk or rhizosphere soil are not well understood. One stress response observed in microbes is the production of carbon storage granules as a means of trapping the needed carbon in the soil. Understanding the… [Read More]

November 11, 2013

Assembling plant microbiomes

The relationships between plants and the microbes in the surrounding soil influences nutrient uptake, disease resistance and stress tolerance. Essentially all land plants grow in intimate association with complex microbial communities both above the ground (phyllosphere) and below the ground on roots and the immediately surrounding area (rhizosphere) and deep inside root intercellular spaces (endophytes)…. [Read More]

November 11, 2013

Fungal plant pathogens and energy feedstocks

The fungal genus Colletotrichum is one of the most common and destructive groups of plant pathogenic fungi, causing disease on plants from nearly every crop and natural ecosystem worldwide. Fourteen species are known pathogens of grasses and cereals, including several candidate bioenergy feedstocks. The impact of Colletotrichum on next-generation bioenergy feedstock production and yield could… [Read More]

November 11, 2013

Microbes in Antarctica’s Dry Valley

The Antarctic Dry Valley system represents one of the harshest and most extreme environments inhabited by microorganisms on Earth. The soils of these valleys contain microbes that must cope with cold temperatures, poor water and nutrient availability, high salinities, exposure to high doses of ultraviolet radiation, and lack of sunlight during polar winters. Such an… [Read More]

November 11, 2013

Boosting biomass of perennial grasses

Switchgrass and prairie cordgrass are candidate bioenergy feedstocks while Brachypodium distachyon is a model grass being used to study related candidate bioenergy feedstocks that was sequenced at the DOE JGI. All three plants have relationships with fungi that lead to benefits such as increased biomass and stress resistance. By studying the transcriptome –the tiny fraction… [Read More]
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