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 › Science Highlights › Examining a predominant Deepwater Horizon microbe

August 7, 2014

Examining a predominant Deepwater Horizon microbe

Single-cell genomics unravels a microbial species’ role in breaking down hydrocarbons.

The Science:

Researchers sequenced and analyzed a single cell of Colwellia bacteria to understand why these microbes were predominant in the Gulf of Mexico after the Deepwater Horizon oil spill.

oil plume simulation ANL LLNL

Simulation of oil plume equilibrating at mid-depth of the ocean domain. (Tamay Ozgokmen, University of Miami; Paul Fischer and Aleks Obabko, Argonne National Laboratory; and Hank Childs, Lawrence Livermore National Laboratory via Flickr CC BY-NC-SA 2.0)

The Impact:

Understanding the characteristics of the Colwellia bacteria furthers the researchers understanding of the particular roles microbes played in degrading the oil plume during the Deepwater Horizon oil spill.

Summary

In response to the oil spill from the Deepwater Horizon oil rig in the Gulf of Mexico four years ago, various microbial communities helped disperse the hydrocarbons. At the time, researchers from Lawrence Berkeley National Laboratory (Berkeley Lab) collected samples at the site, and with assistance from researchers at the U.S. Department of Energy Joint Genome Institute (DOE JGI), they studied the microbial community’s expressed functional information or metatranscriptome, and also isolated single cells to identify the predominant microbial members in the deep ocean oil plume.

Olivia Mason of Florida State University, formerly a postdoctoral fellow with Berkeley Lab microbiologist Janet Jansson, has continued exploring the microbial communities that responded to the Deepwater Horizon oil spill. In a Frontiers in Microbiology paper published July 8, 2014, she re-teams with Jansson and DOE JGI researchers, to examine Colwellia bacteria, which was the second group to become predominant in the Gulf of Mexico microbial community surrounding the oil plume. (The first was Oceanospirillales, which degraded certain non-gaseous hydrocarbons. Colwellia then degraded the gaseous and simple aromatic hydrocarbons.) “Few detailed descriptions of the cellular physiology of the indigenous microbes that responded to the hydrocarbon inputs have been presented,” the researchers wrote in explaining the focus of their work.

For the study, the genome of a single cell of Colwellia bacteria collected from 1,200 meters below sea level was amplified, sequenced, assembled, and analyzed. This single amplified genome (SAG) was then compared against that of a cultured Colwellia strain isolated from the Arctic, and other Colwellia strains found in the oil plume. One of the questions researchers wanted to answer through the analyses was how the Colwellia bacteria in the Gulf of Mexico were able to break down polycyclic aromatic hydrocarbons such as benzene and propane when the cultured strain had shown no indication of being able to degrade hydrocarbons at all. They found part of their answer in the fact that the Colwellia SAG contains genes that are involved in degrading volatile organic compounds such as benzene, toluene, ethylbenzene, and xylenes.

Contact

Janet Jansson
Lawrence Berkeley National Laboratory
jrjansson@lbl.gov

Funding

  • U.S. Department of Energy Office of Science; University of California at Berkeley, Energy Biosciences Institute (EBI).

Publication

Mason OU et al. Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill. Front. Microbiol. 2014 July 07;(5):332. doi: 10.3389/fmicb.2014.00332

Related Links

  • http://jgi.doe.gov/news_12_06_21/

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:

You can move, but you can’t hide

Illustration of a magnifying glass identifying viruses and plasmids.

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.

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.
  • 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