DOE Joint Genome Institute

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

    Algae growing in a bioreactor. (Dennis Schroeder, NREL)
    Refining the Process of Identifying Algae Biotechnology Candidates
    Researchers combined expertise at the National Labs to screen, characterize, sequence and then analyze the genomes and multi-omics datasets for algae that can be used for large-scale production of biofuels and bioproducts.

    More

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

    Ian Rambo, graduate student at UT-Austin, was a DOE Graduate Student Research Fellow at the JGI
    Virus-Microbe Interactions of Mud Island Mangroves
    Through the DOE Office of Science Graduate Student Research (SCGSR) program, Ian Rambo worked on part of his dissertation at the JGI. The chapter focuses on how viruses influence carbon cycling in coastal mangroves.

    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
    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

    Integrating JGI Capabilities for Exploring Earth’s Secondary Metabolome
    Natural Prodcast podcast: Nigel Mouncey
    JGI Director Nigel Mouncey has a vision to build out an integrative genomics approach to looking at the interactions of organisms and environments. He also sees secondary metabolism analysis and research as a driver for novel technologies that can serve all JGI users.

    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:

JGI at 25: Solving the Mystery of the Missing Oil

A surface slick in the Gulf of Mexico, taken ~1.5 km from the Deepwater Horizon wellhead (Olivia Mason, LBNL).

JGI at 25: The Human Genome Project, or the JGI’s Origin Story

JGI contributions detailed in DOE Human Genome Project poster

JGI at 25: A Single Cell, Myriad Microbial Discoveries

Artistic rendering of a microbial genome layered over a dark forest. (Composition by Zosia Rostomian/Berkeley Lab)

Calculating the Costs of Multiple Switchgrass Gene Copies

: Documented occurrences of different switchgrass cytotypes (4X in blue and 8X in orange) throughout the United States. One of the early interests in exploring 8X switchgrass was because the noticeable occurrence of 8X in 4X distribution gaps. (Joseph Napier)

The Power of One, Amplified

One of the pools at Dewar Creek hot springs in British Columbia, Canada. (Allyson Brady)

JGI at 25: Roots of a Mutualist Relationship

Laccaria bicolor
  • 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

© 1997-2022 The Regents of the University of California