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 › Blog › Yellowstone Hot Springs: A Hotbed of Microbial Life

September 15, 2013

Yellowstone Hot Springs: A Hotbed of Microbial Life

[Note: This article originally appeared in the Autumn 2013 issue of the JGI Primer.]

Life on Earth finds a way to survive almost anywhere there is a source of energy to support it. In Yellowstone National Park (YNP), this phenomenon is in the extreme by microorganisms that thrive in harsh, acidic hot springs found unsuitable for the rest of Earth’s inhabitants.

Niki Parenteau (left) and Beverly Pierson (right) sample red-layer phototrophic mats at Fairy Geyser, August 2007 (Image courtesy of Bill Inskeep)

Niki Parenteau (left) and Beverly Pierson (right) sample red-layer phototrophic mats at
Fairy Geyser, August 2007 (Image courtesy of Bill Inskeep)

A team of researchers including DOE JGI scientists set out to investigate how these habitats support microbial life, and to correlate the microbial inhabitants with geochemical variables across different springs in YNP. From the Department of Energy’s perspective, the microbes at Yellowstone are of interest to biofuels researchers because they are thermophilic, meaning they thrive in high-temperature environments. Some of these thermophilic bacteria have been found to contain enzymes that break down biomass into sugars that can be deployed in the industrial-scale production of biofuels.

“The idea was to get a comprehensive overview of microbial communities in Yellowstone National Park,” said DOE JGI Metagenome Program head Susannah Tringe, an author on a series of papers on Yellowstone microbial communities that appeared in Frontiers in Microbial Physiology and Metabolism between May 15, 2013 and June 3, 2013. “Many springs have been studied by independent lab groups, but there had been no coordinated attempt to compare them.”

William Inskeep, a professor at Montana State University and long-time DOE JGI collaborator who has dedicated a great portion of his life’s research to studying YNP, initiated the project to get in-depth looks at the three separate types of communities collected from 20 separate sites within the park. Through the DOE JGI’s Community Sequencing Program (CSP), Inskeep and his collaborators were able to complete a large-scale project in which he and a team of scientists provided samples of phototrophic (light energy dependent), chemotrophic (chemical energy dependent), and streamer-like (biofilm-forming) community DNA for metagenome sequencing.

The working theory was that certain ecological and geochemical factors contribute to the niche specialization of microbes in YNP. The fruits of the team’s labors are now becoming available to the public, allowing insights into microbial community structure and function in geothermal habitats of YNP.

“These high-temperature systems provide model environments in terms of dissecting community structure,” Inskeep said. For this reason, each of the three community types was the focus of a separate paper, with their own respective findings, in addition to an overview paper summarizing the complete project.

One of the studies focused on different types of phototrophic microbial mats that either produce oxygen (oxygenic) or not (anoxygenic). Through shotgun sequencing of several mat types, researchers were not only able to classify many of the organisms present, but also link them to processes like fermentation, carbon fixation, and photosynthesis. These processes help determine why life is sustainable in these microbial mats. The interactions that occur among members of the community are also critical to the function and survival of these organisms. The second type of community studied was the streamer-like microbial mats found in fast- flowing channels within YNP. These communities varied in metabolic and geological traits, with research pointing out that streamer communities are found across a broad pH range and under high and low levels of oxygen. However, because of the way these communities are distributed, the genes associated with energy production show that these microbes have adapted to special niches within YNP.

The third type of community analyzed during the project was Archaea-dominated microbial communities within a pH range of 2.5 to 6.4. Through Sanger sequencing, researchers were able to determine that Archaea were dominant populations in all environments sampled. Several biological processes like electron transport and energy conservation differed among sample sites, and were consistent with the ecological and geochemical traits of each community. Results obtained from archaeal-dominated communities yielded results consistent with the project’s initial hypothesis that ecological and geochemical characteristics (e.g., pH, oxygen versus sulfide) allow these communities to thrive. The project demonstrated that many local ecological factors including temperature, pH, and the sampled depth in uence the types of organisms observed.

Once DNA was isolated from all the sites, researchers were able to analyze the metagenomes to identify the types of microorganisms present. However, many of the organisms whose genomes were sampled have not been cultivated or sequenced. In fact, each data set contained genome sequences from organisms that could not be classified past the level of “Bacteria.” However, the cumulative results of the three studies produced a wide array of information in terms of reconstructing the microbial structure of these environments.

“We were able to find at least ten to fifteen major populations with good assembly,” Inskeep said. “This project was the first major attempt to look at this many separate communities in this environment.” Characterizing the community compositions at these sites is critical for the next steps of linking composition to activities and potentially following them over time.

From top to bottom: Natsuko Hamamura, Rich Macur, Dustin Morse and Mark Kozubal sample streamer communities at Calcite Spring area, August 2007. (Image courtesy of Bill Inskeep)

From top to bottom: Natsuko Hamamura, Rich Macur, Dustin Morse and Mark Kozubal sample streamer communities at Calcite Spring area, August 2007. (Image courtesy of Bill Inskeep)

It is likely that these organisms would not be able to survive independently in these environments, noted the researchers, but the fact that there are not nearly as many distinct populations of organisms present as there are in soil or in water makes it easier for scientists to differentiate between the behaviors of these organisms in their natural habitat, as opposed to a study conducted in a laboratory. By studying these organisms in their natural habitats, researchers can gain insight as to how certain archaea and bacteria thrive through interdependence.

“Research is still ongoing,” Tringe said. “There has been a lot of work with gene expression that can be related to genome data, so we can look at relative gene expression in these communities.”

This study was aimed primarily at analyzing how microbes function in the context of a relatively simple community. Looking ahead, most of the work will focus on these extreme microbes to gain knowledge of what they can do based on the study of their genomes. Now that researchers have accomplished a comprehensive study of microbial communities in a narrowly defined environment, they are more confident that it can be done in more complex communities like lakes, oceans, and even soils and permafrost.

As for the near future, Inskeep knows that there is still much work to be done in YNP. He realized in the beginning of the genomic era that there was a clear scientfic need to sequence thermophilic communities; if not just for the advancement of biofuels, then for the sheer knowledge of how these communities operate. His projects with hot springs provided an excellent base for continued research within the park, but his work continues in identifying new microbial populations found in YNP.

“This was a great foundational study, but we’re just scratching the surface,” he said. “We didn’t have enough coverage to reveal the whole community structure, so our work continues.”

 

Charles Ucciferri was a DOE JGI Summer 2013 Public Affairs intern. He is studying journalism at San Diego State University.

 

REFERENCES:

  • Inskeep WP et al. doi: 10.3389/fmicb.2013.00067 http://bit.ly/JGI13-Yellowstone1
  • Klatt CG et al. doi: 10.3389/fmicb.2013.00106 http://bit.ly/JGI13-Yellowstone2
  • Takacs-Vesbach C et al. doi: 10.3389/ fmicb.2013.00084 http://bit.ly/JGI13-Yellowstone3
  • Inskeep WP et al. doi: 10.3389/fmicb.2013.00095 http://bit.ly/JGI13-Yellowstone4

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: Blog

More topics:

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

Related Content:

JGI at 25: Mapping Switchgrass Traits with Common Gardens

Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)

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

JGI at 25: Expanding Metagenomics to Capture Viral Diversity

Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)

JGI at 25: Cow rumen and the early days of metagenomics

  • 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