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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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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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    A panoramic view of a lake reflecting a granite mountain.
    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

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    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

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    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    iPHoP image (Simon Roux)
    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

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    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    image from gif that shows where in the globe JGI fungal collaborators are located.
    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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All JGI Features
Home › Items tagged with: biogeochemistry

Content Tagged "biogeochemistry"

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March 8, 2013

Comparing extremophile isolates from Yellowstone

Researchers isolated and sequenced four species of Hydrogenobaculum. [Read More]

November 30, 2012

A photosynthetic pathway for mats under anoxic conditions

Many microbes are unculturablebecause they do not thrive when extracted from their habitats. Studies conducted within the context of a group allows researchers to see the interactions taking place and use the clues provided to identify the individual roles of the microorganisms. Photosynthetic microbial mats fix carbon in the day, but it turns out that… [Read More]

January 13, 2012

1000 Fungal Genomes project in The Daily Barometer

Joey Spatafora, an associate professor at Oregon State University, is leading an international project to sequence the genomes of a thousand fungi, a project aptly named 1000 fungal genomes.    “It’s a really, really exciting time in fungal biology because we can sequence fungal genomes more easily than we could ten years ago,” Spatafora said. The Daily Barometer [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]

May 16, 2011

DOE JGI microbes on space shuttle Endeavour per Wired UK

there are also some other passengers on the shuttle, who might not receive the same media attention, sew-on patches and victory parades. Alongside the all-male crew of mission STS-134, six types of microorganism and a bobtail squid will strap in their seat-belts and head into space. Read more in Wired UK but head for the DOE… [Read More]

March 16, 2011

DOE JGI’s Community Sequencing Program Project Call in GenomeWeb

The Department of Energy’s Joint Genome Institute said today that it is now accepting letters of intent from researchers seeking to use the genomics technologies available through its Community Sequencing Program (CSP). JGI’s sequencing program provides the scientific community with access to a range of high-throughput technologies for use in large-scale sequence-based genomic projects that… [Read More]

January 8, 2011

A highly adaptable bacterium that can thrive alone or in symbiosis

Variovorax paradoxus is a β-proteobacterium typically found in the region where the plant roots interact with soil and has the ability to engage in mutually beneficial interactions with both plants and other bacterial species. The bacterium also has the ability to break down a wide range of contaminants including pesticides and crude oil compounds, and… [Read More]

September 16, 2010

A bacterium for breaking down dioxins

Isolated from the River Elbe in Germany, Sphingomonas wittichii RW 1 belongs to a family of bacteria that play a role in breaking down complex aromatic compounds associated with decaying plant mater and chemical pollution. S. wittichii itself is capable of completely breaking down toxic dioxin pollutants, and was selected for sequencing by the DOE… [Read More]

June 6, 2010

DOE JGI’s use of Isilon scale-out NAS on EarthTimes

Leveraging Isilon’s X-Series, featuring its OneFS® operating system, JGI has unified 25 genome sequencers onto a single, high performance, highly scalable, shared pool of storage, reducing storage management. The JGI is also using the Isilon IQ 5000S-SSD, which combines SAS and Solid State Disk (SSD) drives as an additional storage resource for its team. With… [Read More]

June 6, 2010

DOE JGI’s use of Isilon scale-out NAS on San Diego, CA’s CBS 8

Prior to deploying Isilon scale-out NAS, the JGI used more than six network file system (NFS) servers to power its 25 DNA sequencers. As the JGI’s genomic sequencing operations expanded, its NFS servers were unable to scale in-line with demand, fragmenting data across its separate file systems and limiting the performance of both the JGI’s… [Read More]
Page 1 of 212»

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