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    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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    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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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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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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    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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    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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    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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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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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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    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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    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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Home › Items tagged with: archaea

Content Tagged "archaea"

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November 8, 2013

New tool helps find gene markers in microorganisms

Researchers have devised a novel method to exploit relationships between bacteria and archaea for a new set of gene markers The Science The researchers developed a new way to identify gene markers in bacteria and the primitive microorganisms classified in the kingdom known as Archaea. Dubbed, PhyEco (for phylogenetic and phylogenetic ecology) this strategy can… [Read More]

August 30, 2013

Subsurface Sediment Yields Novel Organism

Metagenomic analysis emphasizes the “extraordinary microbial novelty” of poorly-explored subsurface ecosystems The Science Through metagenomics, researchers reconstructed a dominant organism and member of a new phylum-level lineage from an aquifer sediment in Colorado. The Impact Analysis of the complete microbial genome led to a detailed metabolic model with evidence for multiple new enzymes and pathways…. [Read More]

November 16, 2012

Yellowstone yields novel achaeon and candidate Archaea phylum

When a third branch to the Tree of Life was proposed several decades ago, the evidence used to support the need to recognize the kingdom Archaea came in the form of two divisions of organisms that could not be categorized as Eukaryotes or Bacteria. Since then, several more archaeal phyla have been recognized, many of them… [Read More]

November 15, 2012

DOE JGI Director Rubin’s keynote at the UCSF Institute for Human Genetics 2012 Symposium

The [UCSF Institute for Human Genetics 2012] symposium led off with geneticist Eddy Rubin, MD, PhD, whose presentation demonstrated that genetic studies are being applied to human problems that extend even beyond the realm of medicine. Rubin – a scientist who oversaw the sequencing and analysis of 13 percent of the human genome as part of the… [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]

July 6, 2011

UCLA microbiologists find energy-efficient structures in archaeon

a type of Archaea known as Methanosprillum hungatei contains incredibly efficient energy-storage structures. The findings are published in the July 5 issue of the journal Environmental Microbiology. M. hungatei is of considerable environmental significance because of its unique ability to form symbiotic relationships with syntrophic bacteria to break down organic matter and produce methane gas. Yet while their important role in… [Read More]

July 1, 2011

DOE JGI/JBEI collaboration in Green Car Congress

Such salt-tolerant enzymes, particularly cellulases, offer significant advantages for industrial utility over conventional enzymes, they said. The group plans to expand this research to develop a full complement of enzymes that is tailored for the ionic liquid process technology with the goal of demonstrating a complete biomass-to-sugar process, one they hope can enable the commercial… [Read More]

March 23, 2011

Earth Microbiome Project in Sacramento Bee

To understand microbes (Bacterial, Archaeal, Eukaryal and Viral) in terms of whom they are and what they do is the challenge of microbial ecology. The EMP presents a revolution in how this problem is tackled and defines both questions and potential suite of tools to provide answers.  Key participants in this unprecedented project include BGI,… [Read More]

August 13, 2010

Syntrophic communities sequencing project on SciGuru

In work published in the advanced online version of the International Society for Microbial Ecology (ISME)’s Journal on August 5, an international team of scientists including DOE JGI researchers report the first metagenome analysis of a microbial community grown in an anaerobic methanogenic (methane producing) bioreactor. The microbial community is syntrophic, i.e., certain organisms live… [Read More]
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