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 › Decoding Virus-Host Interactions in the Oxygen-Starved Ocean

September 15, 2014

Decoding Virus-Host Interactions in the Oxygen-Starved Ocean

screencap of Hallam vid

Steven Hallam’s team at the University of British Columbia collecting water samples from Saanich Inlet over the course of a single day. From the samples, SUP05 bacterial cells were sequenced and analyzed to understand how their interactions with viruses influences their ecology and potentially affects the biogeochemistry of the ocean. (Courtesy of Hallam lab)

For multicellular life—plants and animals—to thrive in the oceans, there must be enough dissolved oxygen in the water. In certain coastal areas, extreme oxygen-starvation produces “dead zones” that decimate marine fisheries and destroy food web structure. As dissolved oxygen levels decline, energy is increasingly diverted away from multicellular life into microbial community metabolism resulting in impacts on the ecology and biogeochemistry of the ocean.

Over the past 50 years, oxygen minimum zones (OMZs) have expanded due to climate change and increased waste run-off from farms and cities. There are currently more than 500 OMZs worldwide, encompassing roughly eight percent of ocean volume that is considered oxygen-starved. Microbial community metabolism in these oxygen-starved waters directly impacts nutrient and energy conversion processes, including the production and consumption of the greenhouse gases carbon dioxide, methane, and nitrous oxide. Knowing how microbial interactions change in response to OMZ expansion is crucial to understanding the organizing principles underlying coupled nutrient and biogeochemical cycling in the ocean and the balance of greenhouse gases in the atmosphere.

Collaborating with the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, Steven Hallam’s lab at the University of British Columbia has been studying a microbial community dominated by SUP05, an currently uncultivated group of microorganisms, related to gill symbionts of deep-sea clams and mussels that thrive in the most oxygen-starved regions of the water column. In a recent study published online August 29, 2014 in the journal eLife, Hallam teamed up with another DOE JGI collaborator, Matt Sullivan of the University of Arizona, to investigate marine viruses infecting SUP05 to better understand how viral infection influences SUP05 ecology and metabolic potential.

“This study represents the first of its kind, exploiting the unique strength of single-cell genomics to explore virus-host dynamics, including viral co-infections, in a completely cultivation-independent manner,” noted Tanja Woyke, head of the DOE JGI Microbial Program and co-author of this study. “The resulting data provide a very robust foundation for future experimental work,” she added. Woyke is also excited about the expansion of this work into dark matter branches of the microbial tree of life.

In work supported by a Gordon and Betty Moore Foundation Investigator Award, postdoctoral researcher Simon Roux led an effort to develop a novel method to identify viral sequences in microbial datasets, an approach that combines single-cell genomics with viral and microbial metagenomic sequencing to explore virus-host interaction dynamics over space and time. A principal conclusion of this study is that viruses appear to be much more important to marine microbial ecology below sunlit surface waters than earlier suspected.

The Hallam lab studies the SUP05-dominated community in Saanich Inlet, a seasonally anoxic (oxygen deficient) fjord on the coast of Vancouver Island, British Columbia, Canada that is a natural laboratory for studying OMZs. Recent studies in Saanich Inlet estimated that SUP05 bacteria could be responsible for as much as five percent of global primary productivity, making them key players in ocean carbon cycling.

“Whenever you sequence a genome from an isolate or single-cell, you’re potentially sequencing infecting viral genomes at the same time, and for a long time those viral sequences have been ignored given the focus on cellular genomes,” Hallam said.  “Through the single-cell genomics approach, we’re able to define lineage-specific infections in natural populations of uncultivated microorganisms opening an unprecedented window on microbial and viral evolution and ecology.” The Hallam Lab single-cell sequencing efforts were supported by grants from the Tula Foundation, the G. Unger Vetlesen Foundation and the Ambrose Monell Foundation.

Map of Saanich Inlet with water depths noted

Map of Saanich Inlet with water depths denoted in color. (Courtesy of Hallam lab)

In the study, the team collected several thousand individual bacterial cells from three depths spanning the Saanich Inlet oxygen gradient (at 100, 150 and 185 meters). Nearly 130 SUP05 single amplified genomes (SAGs) were recovered from this collection by the Bigelow Laboratory for Ocean Sciences and sequenced at the Genome Sciences Centre in Vancouver British Columbia. The sequences were then assembled, quality checked and annotated at the DOE JGI. Forty-two of the sequenced SUP05 SAGs were found to contain a total of 69 viruses representing five new genera. These viral sequences provided new reference genomes and enabled a number of eco-evolutionary inquiries including lineage-specific viral infection and mortality estimates, biogeography and accessory metabolic gene potential. For example, using the new viral genomes as “hooks,” Roux and colleagues queried 186 viral and microbial metagenomic datasets, many of which were generated through DOE JGI Community Science Program (CSP), to demonstrate that while SUP05 viruses were locally restricted to OMZs they persisted in the environment over several years, with some viruses evolving over that time interval.

“At this point, there’s a lot of microbial community sequence data out there, but it’s a lot harder to get the viral sequence data,” said Sullivan. “What we’ve done is leverage the microbial datasets being generated for microbial ecology and automate the process to be able to see the viruses in that data. Here, the results surprised us as it appears that while viruses in sunlit surface ocean waters kill about a third of cells and keep organic carbon available for smaller cells, the same appears to be true in OMZs – even hundreds or thousands of meters below the ocean’s surface. Further, the nature of the data mean that we can, for the first time, look at a single group’s viral mortality, not just community-wide numbers. This is critical for specifically examining virus-host interaction dynamics, and reveals that viruses are playing a big role in OMZ biogeochemistry.”

SUP05 breathes nitrate and exhales nitrous oxide. This respiratory process is coupled to carbon dioxide fixation and the removal of toxic hydrogen sulfide. The presence of SUP05 in non-sulfidic oxygen minimum zones prompted the description of a cryptic sulfur cycle linking the metabolic activities of SUP05 with other microorganisms involved in nitrogen and sulfur cycling. “What we’re ultimately interested in understanding is how different microbial groups interact to drive carbon, nitrogen and sulfur cycling in OMZs,” said Hallam. “SUP05 is a hub for metabolic coupling in OMZs. By studying viruses that infect SUP05, we’re beginning to recognize that viruses can alter the network properties of microbial communities with resulting feedback on nutrient and energy conversion processes, including the production and consumption of climate active gases. That’s where one interesting twist to the story can be found. Given that a third of SUP05 cells may be infected at any given time, to what extent is carbon fixation and energy metabolism modulated by viral lysis or reprogramming?”

David Research Boat for Hallam lab

For the Hallam lab, the research vessel MSV John Strickland provides an ideal sampling platform in the still waters of Saanich Inlet. (Courtesy of Hallam lab)

While the team is still trying to figure out how much carbon SUP05 is fixing, and how much of the greenhouse gas nitrous oxide the bacteria are releasing, Hallam pointed out that the work has provided tools allowing researchers to look at these interactions in a way that could lead to better ecosystem models. Sullivan noted that another research direction is to “go global and go dark,” scaling up the datasets they’re looking at to explore both viral and microbial dark matter.

Both Hallam and Sullivan credit their collaborations with the DOE JGI, particularly through the CSP, for both the opportunity and the capability to study virus-host interactions in OMZs. “These CSP opportunities are critical for building community resources. For example, when researchers isolate a new virus and want to know whether it exists in the world and where, it helps to compare its genome to available viral metagenomic datasets. Right now, at least half of these came out of two of our CSP projects to form the ‘Pacific Ocean Virome’ dataset,” Sullivan said. “For viromics, at the moment this is the only systematically and quantitatively prepared dataset available, so the results provide a strong basis for making ecological inferences. This scale of data is critical, and such CSP deliverables are fundamental for the viral ecology community or anyone who wants to contextualize their favorite new virus.”

Hallam noted that through the CSP program, his lab has been able to generate 340 human genome equivalents of time-resolved microbial metagenome, and metatranscriptome data from OMZs. “That’s the largest data set in existence specifically focused on OMZs,” Hallam said. “The resulting open access archive promotes integrated science. When we wrote those initial CSP proposals, we didn’t envision this kind of synthesis. However having the archive in place gives us the benefit of hindsight as new scientific questions come into focus.”

Hallam also said that the data their labs have generated through the CSP has enabled them to conduct collaborative projects with the Environmental Molecular Sciences Laboratory, a DOE Office of Science user facility at Pacific Northwest National Laboratory. “Genomic and transcriptomic data generated in one national lab is empowering hypothesis-driven research in another focused on proteomic and metabolomic information. These collaborations between people, projects and platforms is opening the floodgates for systems biology in natural and engineered ecosystems in new and unexpected ways.”

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