DOE Joint Genome Institute

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

    More

    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

    More

    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

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    A panoramic view of a lake reflecting a granite mountain.
    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

    Listen

    A light green shrub with spiny leaves, up close.
    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

    Listen

    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.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    iPHoP image (Simon Roux)
    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

    More

    Abstract image of gold lights and squares against a black backdrop
    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.

    More

    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.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

    More

    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.

    More

    croppe image of the JGI helix sculpture
    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

    Listen

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

    More

    image from gif that shows where in the globe JGI fungal collaborators are located.
    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.

    More

    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.

    More

Our Science
Home › News Releases › Supercharging SIP in the Fungal Hyphosphere

May 31, 2023

Supercharging SIP in the Fungal Hyphosphere

High-throughput stable isotope probing helps ID novel interactions between bacteria and fungi

Stalks or blades of a green plant grow from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.

A speedier way to study microbes has been successfully applied to study the hyphosphere, the area immediately surrounding fungi’s long filaments, or hyphae. [Credit: Video abstract for Nuccio EE et al. in Microbiome.]

The Science

Researchers have successfully automated aspects of a commonly-used process for studying microbial communities, with results published in the November 2022 issue of Microbiome. High-throughput stable isotope probing (SIP) proved to vastly reduce labor and improve results. Applying this method to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

The Impact

Stable isotope probing is a long and laborious process — as well as a key way scientists study microorganisms. Because microorganisms live in complex communities, like within soils or the gut, they are difficult to study individually. Many microorganisms hold clues to processes like biodegradation, with potential applications in industry and biotechnology for the production of clean energy.

Summary

Arbuscular mycorrhizal fungi, the most widespread type of mycorrhizal fungi, live within a plant’s root system. They form mutually beneficial relationships with over 80% of land plants, which means they offer a lot of insights into how plant materials can be broken down for things like biomass and biofuels. However, AMF and the microbial
communities they inhabit are notoriously difficult to study, due to the difficulty replicating the individual compositions of these unique communities.

SIP is an effective way of studying these communities. The process involves “labeling” a given substance by applying a stable isotope to it. The isotopes are incorporated into the DNA of specific microbes who consume the labeled food or water. Later, their DNA can be tested for the isotope, which tells researchers which microorganisms used the labeled substance and which microbes did not.

This is normally an arduous wet lab process. Typically, after incubating microbial communities with labeled food or water, the microbial DNA is manually separated into a few different groups based on its density — DNA containing isotopes is “heavier” than DNA lacking isotopes. This manual collection of DNA is time consuming, tedious and potentially error prone, which limits the size and complexity of research studies that use SIP.

Researchers at Lawrence Livermore National Laboratory and the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, have developed a semi-automated pipeline to apply robotics to the process.

This automation lets researchers study more samples and provides better resolution by splitting the DNA into more density fractions. It also limits the potential for human error that might compromise samples. In addition, high-throughput SIP places samples into standardized microwell plates, allowing them to be processed at a larger scale through downstream DNA purification and sequencing steps. Ultimately, researchers found their updated strategy required one-sixth the labor of the manual process, allowing them to process dozens of samples simultaneously.

Soil microorganisms play a critical role in sequestering carbon and mitigating greenhouse gas emissions, and understanding how to improve soil health can help mitigate the effects of climate change. The team’s study used samples from the area immediately surrounding AMF’s long filaments, or hyphae. This region is called the hyphosphere. By studying its microbial communities, scientists can better understand how the fungi interacts with them.

In this case, scientists identified a wide variety of microbes, including both bacteria and archaea, actively engaging with the fungi — highlighting the hyphosphere as an even more complex and dynamic environment. By further streamlining the process for studying such microbial communities, HT-SIP ramps up the pace at which researchers can extract the bioenergy secrets they hold.

HT-SIP is a capability available to request through the JGI proposal calls.

Contacts

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

PI Contact
Jennifer Pett-Ridge
Lawrence Livermore National Laboratory
pettridge2@llnl.gov

JGI Contact
Rex Malmstrom
Microscale Applications Group Lead
DOE Joint Genome Institute
rrmalmstrom@lbl.gov

Funding

Work at Lawrence Livermore National Laboratory was conducted under the auspices of the U.S. DOE under Contract DE-AC52-07NA27344. The work conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

Publications

Nuccio, E.E. et al. “HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi.” Microbiome, 10, 199 (2022). doi:10.1186/s40168-022-01391-z

Related Links

  • Video: Erin Nuccio at the 2021 JGI Annual Meeting
  • JGI Engagement Webinar: SIP technologies at EMSL and JGI
  • JGI Genome Insider podcast episode: A Powerful Technique to Study Microbes, Now Easier
  • JGI Genome Insider podcast episode: Party in the Rhizosphere

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

More topics:

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

Related Content:

JGI announces 2023 Functional Genomics awardees

Digital index card with JGI logo reads: Community Science Program (FY23) Congratulations to our CSP Functional Genomics recipients! Picture from left to right: (top) Thom Booth, Gabriel Castrillo, Han Li; (bottom) Jorge A. Marchand, Emre Özdemir, Fong Tian Wong

Researching and Solving Real-World Problems with the 2023 JGI-UC Merced Interns

2023 JGI-UC Merced interns (Zhong Wang/Berkeley Lab)

RECAP: Multi-Omic Journeys with 2023 JGI Annual Meeting Keynotes

Bruce Hungate stands at a podium and gesticulates as he discusses microbes.

For the Tiniest Archaea, A Genomic Switch of Friend or Foe

A grey microscopy photo taken at micron-scale. Microbes shown are small, round and slightly spiky in shape.

Doubling Down on Known Protein Families

An illustration of a microscope emitting a beam of light that hits a small, nondescript item.

The JGI announces 2024 awardees for our Community Science Program annual call

A series of headshots: From left to right: [above] Olivia Ahern, Adriana Corales, Hugh Cross, Megan DeMarche, Joanne Emerson, Matthew Hudson, Megan Keller and Julia Kelliher; [below] Vassili Kouvelis, Seppe Kuehn, Tesfaye Mengiste, Egbert Schwartz, Hannah Schulman, Bram Stone and Jana Voriskova
  • 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