DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Science Highlights
    • Scientists
    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.

    More

    (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.

    More

    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.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    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.

    More

    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.

    More

    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.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    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.”

    More

    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.

    More

    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.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    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.

    Read more

    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.

    More

    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.

    More

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    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.

    More

    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.

    More

    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.

    More

News & Publications
Home › News Releases › Adaptable Button Mushroom Serves Up Biomass-Degrading Genes Critical to Managing the Planet’s Carbon Stores

October 8, 2012

Adaptable Button Mushroom Serves Up Biomass-Degrading Genes Critical to Managing the Planet’s Carbon Stores

The button mushroom occupies a prominent place in our diet and in the grocery store where it boasts a tasty multibillion-dollar niche, while in nature, Agaricus bisporus is known to decay leaf matter on the forest floor. Now, owing to an international collaboration of two-dozen institutions led by the French National Institute for Agricultural Research (INRA) and the U.S. Department of Energy Joint Genome Institute (DOE JGI), the full repertoire of A. bisporus genes has been determined. In particular, new work shows how its genes are actually deployed not only in leaf decay but also wood decay and in the development of fruiting bodies (the above ground part of the mushroom harvested for food). The work also suggests how such processes have major implications for forest carbon management. The analysis of the inner workings of the world’s most cultivated mushroom was published online the week of October 8 in the journal, the Proceedings of the National Academy of Sciences (PNAS).

Photo: Button mushrooms (A. bisporus) are the world's most cultivated mushrooms. (Fred Stevens, MykoWeb.com)

Photo: Button mushrooms (A. bisporus) are the world’s most cultivated mushrooms. (Fred Stevens, MykoWeb.com)

“Our hypothesis was that metabolic strategies and niche adaptations of Agaricus might not be present in the white-rot and brown-rot wood-decomposing fungi,” said senior author Francis Martin, Head of the ‘ARBRE’ Lab of Excellence at INRA, Nancy, France.

“Compared to genomes of these fungi, that we previously characterized, the Agaricus genome surprisingly has shown many similarities in gene composition,” added Igor Grigoriev, the study’s senior co-author and leader of the DOE JGI Fungal Program, “At the same time, our data also supported the view that Agaricus fits neither brown-rot nor white-rot classifications and that its adaptation to growing in a leaf-litter humic-rich environment is not typical of classic wood degrading fungi.”

OLYMPUS DIGITAL CAMERA

Photo: Close-up of A. bisporus mycelia (Bam Herman, Swansea University, UK)

The ancient Romans used the word “humus” to designate soil and compost, the complex natural interaction of organic compounds from plant cell wall residues. Humus contributes the chemicals that drive the decomposition process through substances like humic acid that serve as a complement to fertilizer, adding organic matter to deficient soils and contributing to overall plant health to foster root vitality and stimulate the growth of beneficial microbial communities in the soil.

Agaricus is the ideal mushroom to study for adaptation and growth in humic-rich environments, noted Grigoriev and his co-authors. They surveyed the genomes and the transcriptomes—the subset of genes expressed under particular conditions— of two A. bisporus lines, a commercial strain and related wild variety. This analysis of Agaricus turned up several families of well-known sugar-degrading enzymes similar to the repertoire found in wood-decaying fungi. However, the enzymes in Agaricus such as heme-thiolate peroxidases and etherases predominate in the presence of humus-rich soil habitats, suggesting a higher ability to metabolize complex mixtures of derivatives of lignin and other polymers.

Photo: A cross section of A. bisporus cultivation showing colonized compost and production.  (Anton Sonnenberg, Wageningen University, Netherlands)

Photo: A cross section of A. bisporus cultivation showing colonized compost and production.
(Anton Sonnenberg, Wageningen University, Netherlands)

“The ability to use proteins prevalent in soil confers an advantage to Agaricus over other fungal scavengers,” said Martin. “To our knowledge, Agaricus had not been shown in nature to decompose wood,” said Martin. “Yet, we now see how Agaricus has adapted to growing in this ecological niche. Our understanding of the carbon cycling role of Agaricus in ecosystems is a prerequisite to modeling and optimizing carbon management for sustainable forests.”

Unlike brown-rot and white-rot fungi, A. bisporus is a very poor competitor on fresh non-degraded plant wastes like wood but competes well on partially decomposed litter on forest floors and grassland soils rich in humic substrates. The comparative analysis also revealed a dozen other genes that are dialed up during mushroom formation. “Key master switches may be manipulated to control fruiting body formation—the mechanisms triggering the complex cascade that leads from undifferentiated mycelia, the mass of branching, thread-like fingers, to the button mushrooms most commonly consumed” said Martin.

“Comparative genomics of fungi just got more interesting because the contributions of Emmanuelle Morin at INRA and the 42 co-authors, many of them at the JGI, that led to analysis of the Agaricus genome,” said John Taylor, Professor of Plant and Microbial Biology at the University of California, Berkeley and member of the DOE JGI Fungal Advisory Committee. “The most exciting discovery may be the expansion of these heme-thiolate peroxidases, the versatile catalysts that have an important industrial applications and seemingly allow Agaricus to live in humus, the lignin-rich residue of plants that pervade compost.” Such industrial applications include the breakdown of lignin-derived compounds in novel biorefineries to obtain novel high value chemicals.

Taylor further considered the implications of the findings as applied to climate trends. “If the peroxidases do degrade humus, there could be serious effects on the sequestration of soil carbon as soil warms.”

Martin pointed out that additional value will be accrued by making the gene map of Agaricus publically available: for identifying pathogen resistance traits and for highlighting wild germplasm collections benefiting the multi-billion dollar industry producing the button mushroom. “The genome sequence will expedite mushroom breeding for improved agronomic characteristics,” he said.

The DOE JGI is among leading worldwide contributors of fungal genomes to the public databases, having sequenced over 150 fungal genomes, providing a vital computational infrastructure for such large-scale comparative analyses. The Agaricus genome, originally proposed by Mike Challen, while at the University of Warwick, now at the Wellcome Trust Centre for Human Genetics, University of Oxford, UK., was sequenced under the auspices of the DOE JGI’s Community Sequencing Program (CSP), supported by DOE’s Office of Science. The CSP (http://www.jgi.doe.gov/CSP/overview.html) was launched in 2004 to provide the scientific community at large with access to unparalleled capabilities in massive-throughput sequencing, computational analysis and other genomic resources for projects of relevance to DOE missions in alternative energy production, global carbon cycling, and biogeochemistry. Sequencing projects are chosen based on scientific merit—judged through independent peer review.

Share this:

  • Click to share on Facebook (Opens in new window)
  • Click to share on LinkedIn (Opens in new window)
  • Click to share on Pinterest (Opens in new window)
  • Click to share on Twitter (Opens in new window)
  • Click to print (Opens in new window)

The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. JGI provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @jgi on Twitter.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Filed Under: News Releases

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles

Related Content:

Introducing New Members of the JGI User Executive Committee

incoming 2023 UEC members

JGI Contributes Nine to 2022 Highly Cited Researchers List

Nine headshots, one for each researcher, laid out beside a purple ribbon reading, "Home to Highly Cited Researchers 2022 Clarivate"

JGI announces first round of 2023 New Investigator awardees

Digital ID card with 10 headshots reads: Congratulations to our 2023 New Investigator recipients!

JGI at 25: Following Fungi that Pry Apart Plant Polymers

A brown goat with white horns looks at green hay

Exploring Possibilities: 2022 JGI-UC Merced Interns

2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)

JGI at 25: Using team science to build communities around data

  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2023 The Regents of the University of California