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

Our Science
Home › Science Highlights › Bacteria and Fungi Divvy Up the Work in Forest Floor

April 30, 2021

Bacteria and Fungi Divvy Up the Work in Forest Floor

Bacterial enzymes play second fiddle to those from fungi when it comes to breaking down tough plant fibers.

The study site in the coniferous forest located in the Bohemian Forest National Park, Czech Republic. (Petr Baldrian)

The study site in the coniferous forest, located in Bohemian Forest National Park, Czech Republic. (Petr Baldrian)

The Science

Walk in a temperate forest filled with Norway spruce trees, and microbial activity teems beneath your feet. Both bacteria and fungi have genes that can break down plant fibers. But are they both actually doing the job? By analyzing the enzymes present in the complex organic matrix of the forest floor, a team of researchers have found that there is a striking division of labor between the two groups. Fungi are much more active in degrading plant matter, and bacteria are more active in fixing and metabolizing nitrogen, a key ecosystem nutrient.

The Impact

This study is the first to dig into a forest floor ecosystem to discover what carbon- and nitrogen-metabolizing enzymes are abundant, and to which microbes they belong. This study provides further insights into the microbial involvement in carbon and nitrogen cycling and forest floor ecosystem processes. Pinpointing the processes happening on and in forest soil also better enriches models of global carbon and nitrogen cycling, both on the ground and what escapes to the atmosphere in the form of greenhouse gases (e.g., carbon dioxide, methane, and nitrous oxide).

Summary

Roots of forest trees colonized by symbiotic ectomycorrhizal fungi that provide nutrients to their plant host. (Tijana Martinovic)

Roots of forest trees colonized by symbiotic ectomycorrhizal fungi that provide nutrients to their plant host. (Tijana Martinovic)

To do this work, the international scientific team led by Petr Baldrian of the Czech Academy of Sciences first needed to build a detailed database on the denizens in the soil. While large protein databases, like UniProt, exist, are not specific enough for a microbial community like that from a temperate coniferous forest floor — which Baldrian’s team was investigating.

So, to be able to identify proteins, the team compiled DNA sequences (metagenomes) and messenger RNA sequences (transcriptomes) from their soil samples. This gene expression dataset was particularly important for characterizing fungal genes, because, unlike bacteria, they often carry interrupting sequences, called introns. Introns are like having extra words squished into a sentence. The transcriptomes edit out these distractions. Combining genome and transcriptome information allowed the team to have a much more comprehensive picture of microbial genes in the soil and to which type of microbe they belonged.

The team worked with the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory, to create the database. JGI provided metagenome and metatranscriptome sequences, as well as individual reference fungal genome sequences assembled as part of its 1000 Fungal Genomes Project.

To map microbial activity, Baldrian’s team distinguished four specific habitats within the forest floor: the leaf litter on top of the soil, the roots of the trees, the rhizosphere soil (soil under direct influence of the roots), and the remaining soil (further from the roots). The team collected samples from these habitats.

The proteins in the samples were then isolated and sequenced by scientists at the Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science user facility at Pacific Northwest National Laboratory. Analyzing the collection of proteins (the proteome) and referencing the database, Baldrian’s team was able to identify enzymes in the soil and who made them.

Based on data reported in the April issue of Soil Biology and Biochemistry, the team found that fungi are playing a bigger role in soil decomposition processes than expected. The transcriptome data had suggested about a 50/50 split between fungal and bacterial enzymes. Yet, they found proteomic data told a different story: fungal enzymes actually outnumbered bacterial enzymes 3-to-1. Additionally, the fungal enzymes the team found suggest that fungi are breaking down plant fibers, like cellulose and lignin. Bacteria, on the other hand, appear to be ignoring these difficult potential foodstuffs.

The team’s findings also illustrate what’s happening on a spatial scale. Breaking down plant matter by fungi is happening much more in the leaf litter and soil near the roots. But the deeper down and away from the roots one goes, the more bacteria show up.

The data underscore what was already suspected: these microbial groups play different roles in a healthy, forest soil ecosystem. Bacteria are playing an important role that fungi can’t fulfill by fixing nitrogen and using it as an energy source. No fungi are known to be able to do this.

JGI and EMSL’s contributions were enabled by the Facilities Integrating Collaborations for User Science (FICUS) initiative, which allows researchers to integrate the expertise and capabilities of more than one DOE Office of Science National User Facility, with the stroke of a single proposal.

Contacts:

BER Contact
Ramana Madupu, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
Ramana.Madupu@science.doe.gov

BER Contact
Paul Bayer, Ph.D.
Program Manager
Earth and Environmental Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
paul.bayer@science.doe.gov

PI Contact
Petr Baldrian, Ph.D.
Institute of Microbiology, The Czech Academy of Sciences
baldrian@biomed.cas.cz

Funding:

This work was supported by the Czech Science Foundation (18- 25706S and 20-02022Y), by the Ministry of Education, Youth and Sports of the Czech Republic (LTT17022). A portion of this research was per- formed under the Facilities Integrating Collaborations for User Science (FICUS; #49499) program and used resources at the DOE Joint Genome Institute and the Environmental Molecular Sciences Laboratory (grid.436923.9), which are DOE Office of Science User Facilities. Both facilities are sponsored by the Office of Biological and Environmental Research and operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL).

Publication:

  • Starke R et al. “Niche differentiation of bacteria and fungi in carbon and nitrogen cycling of different habitats in a temperate coniferous forest: A metaproteomic approach.” Soil Biology and Biochemistry. 155,108170 (2021). doi: 10.1016/j.soilbio.2021.108170

Related Links:

  • Facilities Integrating Collaborations for User Science (FICUS) program
  • Petr Baldrian’s project proposal is part of the 2016 FICUS collaborative science portfolio
  • JGI Fungal & Algal Program
  • About JGI’s Genomic Encyclopedia of Fungi project
  • EMSL’s Integrated Research Pathway (IRP): Biomolecular Pathways
  • EMSL’s Instruments & Resources
  • Advanced two-dimensional protein separation technique developed by EMSL scientists

 

Byline: Alison F. Takemura

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, Science Highlights Tagged With: 2022-progress-sci-highlight

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