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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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Home › Items tagged with: carbon cycle

Content Tagged "carbon cycle"

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November 7, 2011

Permafrost soil metagenome study on LiveScience

“Nobody has looked at what happens to microbes when the permafrost thaws,” said Janet Jansson, a senior staff scientist at Lawrence Berkeley National Laboratory in California. She led a study that recorded what happened when chunks of Alaskan permafrost thawed for the first time in 1,200 years. Read more on LiveScience [Read More]

November 7, 2011

Permafrost soil metagenome study in UK Press Association

At the testing laboratories, US researchers extracted almost 40 billion elements of raw DNA, reflecting high microbial diversity in the soil.The scientists were also able to piece together the genetic code, or genome, of a previously unknown methane-producing “methanogen” that was present in large numbers. Reporting their findings in an early online edition of the journal… [Read More]

November 7, 2011

Permafrost soil metagenome study in GenomeWeb

“Currently in climate models, it’s not really taken into account adequately what the microorganisms are doing,” senior author Janet Jansson, a researcher affiliated with the Lawrence Berkeley National Laboratory and the US Department of Energy’s Joint Genome Institute, told GenomeWeb Daily News. “The hope is to get enough information at the microscopic level that we’ll have… [Read More]

November 5, 2011

DOE JGI science in the Washington Post

JGI director and geneticist Eddy Rubin is a pioneer in the field of “metagenomics,” the study of how the DNA in many creatures can work together to create ecosystems. Right now, he and his team are studying microbes that live in a cow’s rumen, the stomach-like organ that the animals use to break down grasses… [Read More]

November 4, 2011

CSP 2012 announcement in GenomeWeb Daily News

The Department of Energy’s Joint Genome Institute has chosen 41 research projects out of 152 applicants to use its sequencing services under its 2012 Community Sequencing Program, JGI said Thursday.Researchers for this year’s CSP program, which provides the scientific community with access to JGI’s high-throughput sequencing technologies, proposed projects to study plant-microbe interactions, how microbes… [Read More]

October 6, 2011

Of Soil Carbon and Climate Change

Thanks to genome sequencing techniques such as those at the Department of Energy’s Joint Genome Institute in Walnut Creek, California, we now have a much better idea of what microbes are in soil, what they’re doing, and what proteins they’re producing. That’s important, because a handful of soil can teem with millions of microbes, some… [Read More]

September 20, 2011

DOE JGI’s Tringe in PopSci’s Brilliant 10

Susannah Green Tringe of the DOE Joint Genome Institute (DOE JGI) has been named one of 2011’s “Brilliant 10,” the annual list compiled by Popular Science magazine of top young researchers. In adding her name to the list, which appears in the October issue, the magazine recognized her $2.5 million grant from the DOE Early… [Read More]

September 16, 2011

Soil biocrust microbial genome

One of the DOE JGI’s 2011 Community Sequencing Program projects involves studying biological soil crusts to understand their role in the global carbon cycle. Found in arid lands which make up nearly half of the planet’s total land mass, communities of lichens, mosses and cyanobacteria use soil particles to form biocrusts less than half an… [Read More]

September 6, 2011

Dark ocean project in Climate Action

To understand the world’s climate, we must understand how the 70% of the Earths surface that is covered with water behaves. Very little is known about the processes below 200m, or the area where photosynthesis is not possible due to the lack of light penetration. Scientists from the U.S. Department of Energy Joint Genome Institute… [Read More]

September 2, 2011

Capturing carbon in the dark ocean

Using single cell genomics, researchers identified bacteria in the “twilight zone” that are involved in capturing carbon. [Read More]
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