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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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    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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March 6, 2017

Nitrogen Uptake Between Fungi and Orchids

Researchers investigated Tulasnella calospora as both a free-living mycelium and in symbiosis with the photosynthetic orchid long-lipped serapias. (Ziegler175, Wikimedia Commons, CC BY-SA 3.0)Fungal and plant gene expression provides clues to nitrogen pathways. The Science Orchids are an example of an experimentally tractable plant that is highly dependent on its relationship with its mycorrhizal fungal partners for nutrient supply. In this recent study, researchers for the first time identified some genetic determinants potentially involved in nitrogen uptake and… [Read More]

February 6, 2017

Metagenomics Leads to New CRISPR-Cas Systems

The newly discovered CRISPR-CasY system was found in bacteria from deep underground at Crystal Geyser in California. (Jill Banfield, UC Berkeley)First CRISPR-Cas9 system in archaea discovered The Science Through metagenomic data generated by the DOE Joint Genome Institute, researchers analyzed 155 million protein coding genes from uncultivated microbial communities, leading to the discovery of the first CRISPR-Cas9 protein in the archaeal domain, and of two previously unknown simple bacterial CRISPR-Cas systems. The Impact Microbes play… [Read More]

December 19, 2016

Of Mutualism and Lipid Metabolism in Fungi

Hyphae and asexual sporangia of Rhizopus microsporus (photo by Stephen Mondo). Inset shows a hypha with YFP-labeled Burkholderia endobacteria in green and DAPI-stained fungal nuclei in blue; scale bar, 5 um (photo by Olga Lastovetsky)Novel mechanism in bacterial-fungal symbiosis could have biodiesel production applications The Science To answer the challenge of producing renewable, sustainable alternative fuels, researchers aren’t just looking at developing candidate bioenergy crops but are also reviewing other natural sources of energy-dense oils such as fungi. To learn more about how bacteria interact with fungi in a… [Read More]

December 9, 2016

DOE JGI Database of DNA viruses and retroviruses debuts on IMG platform

This graphic depicts the geographic distribution of GOLD biosamples and organisms. Organism location of isolation is marked in pink while Biosample location of collection is denoted with blue dots. Updates to the Genomes OnLine Database (GOLD) are reported in the upcoming Database issue of Nucleic Acids Research. (Image from Supratim Mukherjee et al. Nucl. Acids Res. 2016;nar.gkw992)The Science In a series of four articles published in the Database issue of the Nucleic Acids Research journal, DOE JGI researchers report on the latest updates to several publicly accessible databases and computational tools that benefit the global community of microbial researchers. One report focuses on a new database dedicated global viral diversity. [Read More]

September 26, 2016

Modeling Microbial Networks in an Oxygen Minimum Zone

Collecting sampled waters from Saanich inlet into carboys for large volume filtration of microbial biomass. (Image courtesy of Steven Hallam, UBC)UBC team develops predictive marine microbiome math model. The Science With help from two DOE national user facilities, a team at the University of British Columbia (UBC) has developed a math model that could help researchers and policy makers track the impact of climate change on the microbial networks that drive the world’s marine ecosystems…. [Read More]

September 6, 2016

Microbial Metabolism Impacts Sustainability of Fracking Efforts

This is not one of the wells used in the study, but it shows what a site looks like during the drilling process. (Image courtesy of the MSEEL (Marcellus Shale Energy and Environment Laboratory www.mseel.org), where the Wrighton Lab is also conducting research.)Team finds surface microbes are colonizing the deep subsurface. The Science Through a collaborative science program involving two DOE national user facilities, DOE-supported researchers have been able to reconstruct microbial genomes for the first time from shale formations that are being drilled to extract natural gas. Coupled with microbial metabolic information, the data shed light… [Read More]

August 4, 2016

Identifying the Microbial Culprits Initiating Oceanic Nitrogen Loss

In the Nature paper, the team found functional nitrate reductase pathways, shown on the left-hand side of the nitrogen cycle, in SAR11 microbes. (Nitrogen cycle graphic by Zosia Rostomian, Berkeley Lab)Novel lineages of SAR11 clade reveal adaptations to oxygen-poor ocean zones. The Science Oxygen minimum zones (OMZs) extend over about 8 percent of the oceanic surface area, but account for up to 50 percent of the total loss of bioavailable nitrogen and thus play an important role in regulating the ocean’s productivity by substantially impacting… [Read More]

June 20, 2016

Insights into How Soil Microbes Regulate Carbon & Sulfur Cycling

German fen with Phragmites australis by Paul Schulze, CC-BY 4.0 (https://www.flickr.com/photos/paulschulze/14351953065/)Researchers find rare sulfate reducers substantially affect methanogenesis in peatlands. The Science Utilizing microcosms of peat soil, researchers mimicked naturally fluctuating conditions to study sulfate-reducing microbes and how they regulate methane production in peat microbial communities. The Impact Numbers by themselves don’t tell the whole story. Microbes found in low abundance can play key roles… [Read More]

May 20, 2016

Evaluating the cost of accuracy of sequencing approaches

Sakinaw Lake UBCResearchers perform benchmark study for improving microbial community profiling. The Science Researchers use synthetic and natural microbial lake communities to compare the microbial community profiles generated from high throughput short-read sequencing and high throughput long-read sequencing approaches. The Impact Microbes play key roles in maintaining the planet’s biogeochemical cycles, but only a fraction of them… [Read More]

May 3, 2016

Refining the origins of wood-rotting mechanisms

Calocera viscosa by abejorro34, Flickr CC BY-NC 2.0Genome sequences of early-diverging fungi help track origins of white rot fungi. The Science Researchers utilized draft genome sequences of 10 white rot and brown rot fungi representing early-diverging groups to help refine the timeline that dates the enzymatic origins of lignocellulose decomposition. The Impact Fungi are natural degraders of plant material and contain enzymes… [Read More]
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