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
    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

    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

    More

    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

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

    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

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

    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

    More

    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

  • 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

    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 › Science Highlights › Building Sphagnum Genomic Resources

June 13, 2018

Building Sphagnum Genomic Resources

Sphagnum fallax (Image courtesy of Jonathan Shaw, Duke University)

Sphagnum fallax (Image courtesy of Jonathan Shaw, Duke University)

Sphagnome data would enable researchers’ insights on their potential carbon cycling impact.

The Science

Enabled by the JGI’s Community Science Program (CSP), researchers are developing a number of resources to build up Sphagnum as a plant model system focused on carbon cycling studies, rather than for food or fuel applications.

The Impact

Sphagnum’s impact on global carbon cycling and climate is estimated to be larger than any other single plant genus. Peatlands accumulate partially decomposed matter, and researchers estimate that they hold about 25 percent of the world’s soil carbon. In high latitudes, sphagnum can also act as a protective layer insulating permafrost from the warming regional temperatures. For this reason, the U.S. Department of Energy is overseeing the SPRUCE (Spruce and Peatland Responses Under Changing Environments) project, assessing how northern peatland ecosystems respond to increases in temperature and elevated concentrations of atmospheric carbon dioxide.

Summary

Sphagnum (peat moss) is an unassuming plant, but it thrives in nutrient-poor, acidic and waterlogged environments, occupying every continent except Antarctica. Researchers estimate a quarter of the world’s terrestrial carbon is stored in peatlands, which make up nearly 3 percent of the earth’s land surface. In the New Phytologist, researchers led by David Weston of Oak Ridge National Laboratory make the case for sphagnum as “an unparalleled model system for ecological and evolutionary genomics.” Understanding the nature and genetic basis of functional traits in sphagnum growth and decomposition is critical to predicting the ecosystem response to climate change. Through the CSP, researchers are aiming to have two high quality reference genomes for peat-forming species that occupy different microhabitats – Sphagnum fallax and S. magellanicum. The draft genome for S. fallax is already available on the JGI plant portal Phytozome, and the S. magellanicum genome is currently being assembled. These resources would provide the research community with the ability to address questions such as sphagnum’s associations with methane oxidizing bacteria, nutrient uptake, and its productivity and decomposition rates.

Peatlands, like other wetlands, can act as a carbon sink or carbon source. Sulfur cycling is a carbon flux regulator since sulfate-reducing microbes prevent methane production by routing the carbon away from methanogens. In The ISME Journal, a team led by researchers from the University of Konstanz and the University of Vienna reported recovering draft metagenome-assembled genomes for seven novel species of Acidobacteria through an approved CSP proposal. The researchers found that these species encode a sulfate reduction pathway, but also have genes for sulfide oxidation. The findings lead them to speculate that these microbes could use the same pathway for either sulfur reduction or sulfur oxidation. The pathway’s reversibility could be a factor in determining if the peatlands act as a carbon sink or a carbon source.

These research results, building on the availability of genomic information from two distinct environments, strengthen the case for Sphagnum as a versatile model system for studies of carbon cycling in diverse environments. In addition, this work reflects a collaboration between two programs within different Divisions of the Office of Biological and Environmental Research, the Joint Genome Institute supported by the Biological Systems Science Division and the Spruce and Peatland Responses Under Changing Environments (SPRUCE) program of the Terrestrial Ecosystem Science program, supported by the Climate and Environmental Sciences Division.

BER Contacts

Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
daniel.drell@science.doe.gov

Daniel Stover, Ph.D.
Program Manger
Climate and Environmental Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
Daniel.stover@science.doe.gov

PI Contacts

David Weston
Oak Ridge National Laboratory
westondj@ornl.gov

Michael Pester
Leibnitz Institute DSMZ, Germany
Michael.pester@dsmz.de

Funding

The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. For the sphagnome project, germplasm establishment and maintenance is supported by the US DOE, Office of Science, Office of Biological and Environmental Research, Early Career Research Program. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S. Department of Energy under Contract Number DE-AC05-00OR22725. Funding for the peatlands work was also supported by the Austrian Science Fund (FWF, P23117-B17, P25111-B22, P26392-B20, and I1628-B22), the JGI (CSP 605), the German Research Foundation (DFG, PE 2147/1-1), the European Union (FP7-People-2013-CIG, Grant No PCIG14-GA-2013-630188 and Marie Skłodowska-Curie Grant No 660280), and the VILLUM FONDEN (research grant 15510).

Publications

  • Weston DJ et al. The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project. New Phytol. 2018 Jan;217(1):16-25. doi: 10.1111/nph.14860.
  • Hausmann B et al. Peatland Acidobacteria with a dissimilatory sulfur metabolism. ISME J. 2018 Feb 23. doi: 10.1038/s41396-018-0077-1. [Epub ahead of print]

Related Links

    • Sphagnum fallax genome on Phytozome
    • David Weston’s 2013 Genomics of Energy & Environment Meeting talk: http://bit.ly/JGI13UMWeston
    • DOE Office of Science Terrestrial Ecosystem Science program on SPRUCE
    • SPRUCE at ORNL as part of a Scientific Focus Area
    • University of Vienna links to coverage of the ISME J paper
    • JGI Science Highlight: Insights into How Soil Microbes Regulate Carbon & Sulfur Cycling

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)

Filed Under: Science Highlights

More topics:

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

Related Content:

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.

New Research Sheds Light on Diversity in the Deep Sea

A photo taken in the deep sea. Black clouds billow out of hydrothermal vents.

Sequencing Sphagnum Leads to Discovery of Sex Chromosomes

A photo of two sphagnum species: S. divinum (red) and S. angustifolium (green)]

Busting the Unbreakable Lignin

Pictured is a micrograph of Neocallimastix californiae.

Tracing the Evolution of Shiitake Mushrooms

A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.

Soil virus offers insight into maintaining microorganisms

  • 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