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

News & Publications
Home › News Releases › Characterizing Permafrost Microbes in a Changing Climate

March 4, 2015

Characterizing Permafrost Microbes in a Changing Climate

In the effort to curb climate change by reducing global greenhouse gas (GHG) emissions, thawing permafrost poses a critical challenge. These reservoirs of frozen organic matter embedded in Arctic soils are one of the major (~1.5 billion tons) stores of carbon on Earth. One of the abiding concerns regarding permafrost is that as global temperatures rise, as is projected over the coming centuries, soils may thaw completely. This event has the potential of causing the release of this carbon in the form of the potent greenhouse gases carbon dioxide (CO2) and methane, resulting in the largest contribution of carbon transferred to the atmosphere by a single terrestrial process.

Jenni Hultman prepping permafrost samples

Study first author Jenni Hultman prepping permafrost samples. The team investigated three types of Alaskan soils, ranging from completely thawed to completely frozen. (Janet Jansson, PNNL) Listen to Janet Jansson discuss the project on NPR’s Science Friday at http://bit.ly/SciFri15Jansson.

To help understand the processes that control the conversion of organic matter to CO2 and methane, scientists from the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility managed by the Lawrence Berkeley National Laboratory, reported on the application of multiple molecular technologies collectively referred to as “omics,” to better characterize microbial activities in a paper published online March 4, 2015 in the journal Nature. The team also included members from Berkeley Lab’s Earth Sciences Division, from Pacific Northwest National Laboratory (PNNL) and from the United States Geological Survey. The team sought to determine the composition of microbial communities and their role in degrading permafrost organic carbon and the subsequent production of CO2 and methane.

Microbial ecologist Janet Jansson from PNNL led the team that investigated three types of Alaskan soils, ranging from completely thawed to completely frozen. Metagenomics (MG), or environmental genomics, enabled the researchers to identify the phylogeny—i.e., history of organismal lineages—of the communities’ microbial members, and the functional gene composition. Metatranscriptomics (MT) allowed the team to determine which genes were being expressed. Finally, metaproteomics (MP) provided insights on which proteins were actually produced.

Comparing microbial activities in various soils

The data collected for the permafrost study was impressive. “Together these analyses resulted in a large amount of data including 84.2 Gb [billion nucleotide bases] of MG sequence, 20.4 Gb of MT sequence, and approximately 7,000 proteins, which are among the highest yields obtained for any soil type to date,” the team reported.

frozen peaty soil collapsing into a thermokarst bog

Frozen peaty soil collapsing into a thermokarst bog. For the study, the team studied the microbes in intact permafrost, in the active layer above the frozen soil that seasonally freezes and thaws, and in other soils including the collapsed thermokarst bog that represents the terminal state of thaw. (Mark Waldrop, USGS)

For the study, researchers relied on soil cores collected in Alaska, focusing on their bacteria and archaea. With the DOE JGI mobilizing its panoply of sequencing approaches and data analysis tools, the team studied these microbes in intact permafrost, the active layer above the frozen soil that seasonally freezes and thaws, and in other soils including the collapsed thermokarst bog that represents the terminal state of thaw.

Comparison of the MG, MT and MP data from the three soils provided insight into the linkages between omics data and elemental cycling pathways. In the thermokarst bog they found the highest rates of methane production and identified several microbes involved in this pathway. Additionally, several genes involved in methanogenesis were detected in both the MG and MT data sets and corresponding proteins in the MP data sets. Three draft methanogen genomes were identified, and comparisons with sequenced methane producers suggest these are previously undescribed microbes.

The team found that the active layer had more diverse microbial species than the other soils, and the most active genes were involved in nitrogen, iron and methane cycles. In the permafrost samples, although fewer genes were expressed and fewer proteins were detected, they found that many of the proteins were those that allowed the microbes to tolerate the cold environment, more so than were found in the active layer and bog samples. They also found proteins in permafrost that suggest some of the microbes can move around, and proteins for pathways such as methane oxidation. The latter finding suggests that either the RNA and proteins have been preserved in the frozen environment, or the microbes with these functions are merely dormant in subzero conditions. Alternatively, they may represent physically active microbes in permafrost, thus providing a first insight into microbial survival strategies in permafrost.

Modeling microbial communities in Alaska

The work builds on findings from a previous collaboration between the DOE JGI and Jansson. In that study, which appeared in Nature, November 6, 2011, the draft genome of a novel methanogen was identified through environmental genomics studies that focused on Alaskan soil cores that contained both the active layer, and the permanently frozen soils beneath.

The work done by Jansson and her colleagues is just one of the ecosystem studies being conducted by the Department of Energy in Alaska. Through the Next-Generation Ecosystem Experiments (NGEE Arctic) project in Barrow, Alaska, a consortium of academic institutions and national laboratories is developing a process-driven ecosystem model that will allow researchers to better predict the evolution of Arctic ecosystems in a changing climate. Jansson is currently leading a Community Science Program project at the DOE JGI for sequencing of samples collected for the NGEE Arctic project.

The insights arising from this study are shedding light on microbial processes involved in GHG release, potentially as a consequence of temperature changes. A better understanding of these processes is necessary, the team maintained, for generating more accurate models and thus predictions of the environmental consequences.

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:

You can move, but you can’t hide

Illustration of a magnifying glass identifying viruses and plasmids.

JGI announces second round of 2023 New Investigator awardees

From left to right: [above] Emma Bell, Mallory Choudoir, Sneha Couvillion, Tobin Hammer, Christina Hazard, Rachel Mackelprang, Brook Moyers, Mei, Ran,; [below] Benjamin Peterson, Dacheng Ren, Allison Rober, Neal Scott, Chikae Tatsumi, Vojtech Tlaskal, Fernando Torralbo, Luis Felipe Valdez-Nuñez

A Collaboration to Improve Plant Genome Annotations Across Species

A tiled collage of square photos of different plants - soybeans, and sorghum, for example.

From Berkeley to Binghamton: Tracking Strawberry Evolution

iPHoP: A Matchmaker for Phages and their Hosts

iPHoP image (Simon Roux)

Supercharging SIP in the Fungal Hyphosphere

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.
  • 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