DOE Joint Genome Institute

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

    (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

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

    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

  • 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
    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

    More

    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

News & Publications
Home › News Releases › See and Sort: Developing Novel Techniques to Visualize Uncultured Microbial Cell Activity

June 28, 2016

See and Sort: Developing Novel Techniques to Visualize Uncultured Microbial Cell Activity

New high-throughput and cost-effective approaches provide a better understanding of microbiome functioning

AOM consortia oxidizing methane seen using BONCAT

While typically thought of as solitary life forms, microbes frequently aggregate to form dense cell clusters. This often serves to achieve a common goal that cannot be reached by individual cells acting alone. The depicted cell consortia are composed of archaea and bacteria that, by combining their individual metabolic powers, together achieve oxidation of the greenhouse gas methane in the absence of oxygen. For the first time, these consortia have now been analyzed for their protein synthesis activity under a variety of conditions. In this image, nucleic acids within individual cells are stained in blue. Green color indicates that new proteins have been made. The scale bar equals 10 micrometer, or 1/8th the width of a human hair. (Credit: Roland Hatzenpichler)

Many uncultured microbes play unknown roles in regulating Earth’s biogeochemical processes; everything from regulating plant health to driving nutrient cycles in both terrestrial and marine environments, processes that can impact global climate. While researchers are harnessing multiple approaches to identify these microbes, referred to as “microbial dark matter,” and determine what they’re doing, most techniques don’t allow them to do both at once.

In a study published online June 28, 2016 in the Proceedings of the National Academy of Sciences (PNAS), researchers at the California Institute of Technology (Caltech) and the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, utilized a recently refined technique to identify both individual active cells, and single clusters of active bacteria and archaea within microbial communities. Understanding the true scope of the planet’s microbial diversity is of interest to the DOE in order to learn how they can be harnessed for a wide range of energy and environmental challenges.

“One of the biggest problems in the exploration of microbial dark matter is that so far, it is very complicated to determine when uncultured microbes are metabolically active and what their ecological function in a system is,” said study first author Roland Hatzenpichler, a postdoctoral researcher working in the Caltech lab of microbial ecologist Victoria Orphan. As part of the DOE Biological & Environmental Research (BER) program, Orphan’s lab has been studying the ecology and physiology of uncultured microorganisms catalyzing the anaerobic oxidation of methane in the environment. “When we deal with environmental or host-associated organisms that live within complex communities – typically thousands of species or more co-occur at the same time – it is very hard to determine what an individual species or cell is up to. Historically, this has been accomplished using single cell resolved isotope labeling. This is a comparatively tedious and expensive approach that is, however, very specific and sensitive. However, if we want to better understand microbiome functioning we need new, complementary approaches that are more high-throughput, that can be parallelized, and that are cheap. BONCAT [the new technique] is such a method.”

BONCAT: A High-Throughput Technique to Understand Microbiome Functions

Methane seep site off Hydrate Ridge in Oregon

This video shows the striking difference between the typical ocean seafloor and a methane seep site. As the submersible approaches the bottom of Hydrate Ridge, a seep site off the coast of Oregon, methane gas can be seen venting from below the seafloor. Atop the sediment, where a sample is being taken, a thick microbial mat has formed. Within this sediment, below the mat, clusters of microorganisms harvest energy by converting from methane by converting it into carbon dioxide. This video was taken during a research cruise of R/V Atlantis that was supported by the National Science Foundation (OCE-0825791). (Credit: Victoria J. Orphan, edited by Roland Hatzenpichler)

Short for BioOrthogonal Non-Canonical Amino acid Tagging, BONCAT is a technique developed at Caltech for bioengineering studies, but was adapted by Hatzenpichler and Orphan for use in microbial ecology investigations. BONCAT uses synthetic amino acids to label protein-making cells. These amino acids can then be stained with a fluorescent tag, lighting up active cells in their habitat. For this study, Hatzenpichler and his colleagues used sediment samples collected from deep-sea methane seep sediments off the coasts of Oregon and California for a series of incubation experiments, tracking the slow growth of methane-metabolizing bacterial and archaeal populations. The microbial communities in these sediments include aggregates of methane-oxidizing archaea called ANME (for ANaerobic MEthanotrophs) and sulfate-reducing bacteria (SRB) that live together symbiotically and help to remove some 80 percent of the methane released from ocean sediments.

The Caltech researchers combined BONCAT with fluorescent in situ hybridization (FISH) to analyze active microbes within these simulated environments and identify under which conditions they were active. “Typically, every methane seep site hosts several different groups of archaeal methane-oxidizers,” Hatzenpichler said. “A long-standing hypotheses has been that different members from these groups are differently active at different times. By exploiting the capability to do BONCAT analyses in comparatively high-throughput mode, we found members of all groups of methane-oxidizing archaea were anabolically active during the incubation. Now we can start asking why.”

Applying the BONCAT Technique to Flow Cytometry

DOE JGI researchers then helped develop a process that allowed the team to apply BONCAT to flow cytometry. “It’s the same process as for single cell genomics, but for aggregates of symbiotic bacteria and archaea,” said DOE JGI Microscale Applications Group head Rex Malmstrom of the technique called BONCAT-FACS (BONCAT – Fluorescence-Activated Cell Sorting). “We’re sorting individual aggregates full of cells that are active in a simulated environment and with the cell sorter we can grab active cells to study them. We had to figure out how to adapt the process for the flow cytometer. After the sorting, we performed whole genome amplification on individual aggregates then sequenced the 16S rRNA marker genes to identify cells comprising the aggregate. We’re now doing whole genome sequencing on these samples.” Sequencing could then provide researchers the genetic information explaining why some microbes were active under certain conditions, and why some others were not.

Caltech researchers Victoria Orphan and Roland Hatzenpichler . Image by Stephanie Connon

Caltech geobiologists who spearheaded the research: Victoria J. Orphan and Roland Hatzenpichler. (Credit: Stephanie Connon)

Through BONCAT-FACS, the team found that the methane-oxidizing archaea weren’t interacting with just the known sulfate-reducing bacteria, as had been expected, but were also sometimes associating with members of the less well-studied Verrucomicrobia phylum. These interactions had not been seen previously, and the finding suggests to researchers that methane-oxidizing archaea have a broader range of symbiotic relationships than had been thought. Whether these interactions are beneficial to both cell types or not is currently being addressed.

“JGI’s main power lies in the ability to decipher the genetic code of microorganisms,” noted Hatzenpichler. “By teaming up, we were able to isolate individual cell clusters involved in the degradation of the greenhouse gas methane from our samples, identify the cellular partners involved in this process, and gain insights into their genetic code.” Orphan and her team plan to use the genomic information from the paired methane-oxidizing archaeal and bacterial partners to develop deeper insights into the physiology and mechanisms of interaction and energetic exchange between different methanotrophic consortia coexisting in the environment.

In the fall, Hatzenpichler will be starting his own lab at Montana State University-Bozeman. He will continue to work closely with DOE JGI researchers to uncover the biogeochemical impact and biotechnological potential of uncultured microbes.

The work was supported by the NSF Center for Dark Energy Biosphere Investigations, the Gordon and Betty Moore Foundation, the Austrian Science Fund and the DOE’s Office of Science.

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:

Introducing New Members of the JGI User Executive Committee

incoming 2023 UEC members

JGI Contributes Nine to 2022 Highly Cited Researchers List

Nine headshots, one for each researcher, laid out beside a purple ribbon reading, "Home to Highly Cited Researchers 2022 Clarivate"

JGI announces first round of 2023 New Investigator awardees

Digital ID card with 10 headshots reads: Congratulations to our 2023 New Investigator recipients!

JGI at 25: Following Fungi that Pry Apart Plant Polymers

A brown goat with white horns looks at green hay

Exploring Possibilities: 2022 JGI-UC Merced Interns

2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)

JGI at 25: Using team science to build communities around data

  • 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