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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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    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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    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: bacteria

Content Tagged "bacteria"

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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]

November 1, 2013

Lost in symbiosis: genes dropped in piggy-backing bacterial strain

A genome comparison of two strains of a bacterium reveals gene loss as a result of a symbiotic relationship with a protist host. The Science The researchers sequenced the complete genome for a symbiotic strain of the bacterium, Polynucleobacter necessarius. They then compared the symbiont’s genome with the free-living strain in order to understand how… [Read More]

October 25, 2013

Root-dwelling denizen of Sheoak trees characterized

The complete genome of a novel nitrogen-fixing bacterium has been recently sequenced and analyzed. The Science The researchers isolated and sequenced the complete genome of a species of Micromonospora, bacteria that play a role in promoting plant growth and breaking down plant cell walls, from root nodules of Sheoak trees (Casuarina equisetifolia). The Impact Although… [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]

July 26, 2013

The Importance and Function of Nitrogen-Fixing Microbes

All organisms on Earth require nitrogen to survive, but most cannot use nitrogen unless it is combined with other elements. These compounds are formed by the process known as nitrogen fixation, which can only be carried out in nature with the help of microorganisms. In agriculture, fertilizers are often deployed to supplement nitrogen levels in… [Read More]

May 3, 2013

Marine metagenome offers clues to ocean nitrogen cycle

Nitrification is the process by which ammonia is converted first into nitrites and then into nitrates, a form of nitrogen that can then be used by plants to grow. However, understanding how the nitrogen cycle works in marine environments is equally crucial. Until 1977, scientists believed that ammonium could only be oxidized by aerobic bacteria…. [Read More]

June 21, 2012

Waves of Berkeley Lab Responders Deploy Omics to Track Deepwater Horizon Oil Spill Cleanup Microbes

In the aftermath of the Deepwater Horizon oil spill in the Gulf of Mexico two years ago, various strategies were deployed to prevent 4.9 million barrels of light crude oil from fouling the waters and reaching the shores. A team of Lawrence Berkeley National Laboratory (Berkeley Lab) researchers found that nature also played a role… [Read More]

June 1, 2012

Comparative genomics method to tag novel nitrogen-fixation genes

Nitrogen is crucial for plant growth but plants cannot harness it directly from the atmosphere. In the United States, legume crops such as soybeans and peas rely on nitrogen fertilizers to boost yields; in 2007, 13 million tons of industrially-produced fertilizers were applied. Soil bacteria such as Sinorhizobiummeliloti have a symbiotic relationship with plant hosts… [Read More]

March 2, 2012

Elucidating bacteria’s roles in ant fungal gardens

Leafcutter ants cultivate fungal gardens that serve as their primary food source. Working toward the goal of harnessing novel enzymes for breaking down plant biomass to produce cellulosic biofuels, Great Lakes Bioenergy Research Center (GLBRC) researchers have been studying the process by which the fungi break down the plant leaves harvested by the ants and… [Read More]

February 24, 2012

Analyzing enzymes for a PAH degradation pathway

Microbial activity is crucial for breaking down compounds, removing pollutants and chemically transforming organic compounds. Some of these pollutants are polycyclic aromatic hydrocarbons (PAHs) found in contaminated soils. The PAH phenanthrene, for example, can be broken down by the bacterium Arthobacterphenanthrenivorans, which was isolated from a creosote-polluted site in Greece, and used by the microbe… [Read More]
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