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 › Monitoring Inter-Organism Interactions Within Ecosystems

September 24, 2021

Monitoring Inter-Organism Interactions Within Ecosystems

Latest portfolio of approved proposals highlight biodiversity and how ecosystems are adapting to stresses.

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)

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)

A total of 17 proposals have been approved through the annual Community Science Program (CSP) call of the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab).

They were selected through peer review from 41 full proposals out of 50 letters of intent submitted. 

Many of the proposals focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts. Andrew Nelson of the Boyce Thompson Institute at Cornell University seeks to understand and enhance the rubber biosynthesis pathway in guayale, a drought tolerant shrub. Melissa Roth of the University of California, Berkeley aims to redesign and engineer algae by identifying the algal regulators that could boost lipid production.

Eight of the approved proposals are led by researchers, including Nelson and Roth, who have not been a principal investigator on a previously approved JGI proposal. Among them:

Using plots at the Harvard Forest long-term warming experiment, Kristen DeAngelis of the University of Massachusetts Amherst and colleagues are studying how chronic warming is altering how microbes interact with their environment, potentially accelerating soil carbon loss. Orange ribbons mark the heated plots and blue ribbons mark the control plots. (Mallory Choudoir)

Using plots at the Harvard Forest long-term warming experiment, Kristen DeAngelis of the University of Massachusetts Amherst and colleagues are studying how chronic warming is altering how microbes interact with their environment, potentially accelerating soil carbon loss. Orange ribbons mark the heated plots and blue ribbons mark the control plots. (Mallory Choudoir)

  • Ryan Gawryluk at the University of Victoria in Canada is interested in predatory algae known as Rhodelphis.
  • Ederson Jesus of Embrapa, Brazil’s public agricultural research corporation, is focused on microbial interactions on the Amazon forest floor. 
  • Alicia Purcell of Northern Arizona University is studying microbial metabolism in the Antarctic Peninsula.

Additionally, the proposal from Viola Krukenberg at Montana State University successfully evolved from a white paper approved through JGI’s CSP New Investigator call to a full-scale submission. She aims to look at the microbial methane cycle in terrestrial geothermal environments.

 

 

 

In their approved proposal, Zander Myburg of the University of Pretoria and colleagues aim to unlock the genomic diversity within the eucalypts, a group of fast-growing tree species that are a sustainable source of carbon and energy rich biomass globally. Eucalypts are widely grown as feedstocks for lignocellulosic and other biorefinery products. The work builds off a previous international collaboration that produced the reference genome sequence for Eucalyptus grandis. (Courtesy of Zander Myburg)

In their approved proposal, Zander Myburg of the University of Pretoria and colleagues aim to unlock the genomic diversity within the eucalypts, a group of fast-growing tree species that are widely grown as feedstocks for lignocellulosic and other biorefinery products. The work builds off a previous international collaboration that produced the reference genome sequence for Eucalyptus grandis. (Courtesy of Zander Myburg)

Accessing recently burned soils in California and Colorado, Mike Wilkins of Colorado State University and colleagues aim to understand how soil microbiomes in fire-adapted ecosystems respond to low and high severity wildfire. (Courtesy of Mike Wilkins)

Accessing recently burned soils in California and Colorado, Mike Wilkins of Colorado State University and colleagues aim to understand how soil microbiomes in fire-adapted ecosystems respond to low and high severity wildfire. (Courtesy of Mike Wilkins)

The approved proposals start October 1, 2021. The list of approved proposals appears below.

Approved FY2022 Proposals

Name Affiliation Title
Bowen, Jennifer Northeastern University Microbial controls on carbon cycling and storage resulting from salt water intrusion in tidal fresh, brackish, and saline marshes
Colwell, Frederick Oregon State University Defining microbial functional capabilities across high-latitude, glacially impacted, wetland landscapes
de Vries, Ronald Westerdijk Fungal Biodiversity Institute (Netherlands) Mining the unknown part of fungal genomes by combining machine learning with multi-omics and functional characterization
DeAngelis, Kristen University of Massachusetts Amherst Using genomics to understand microbial adaptation to soil warming
Dick, Gregory University of Michigan Metagenomic and metatranscriptomic insights into the role of microbial interactions in the cycling of carbon and nutrients during toxic cyanobacterial blooms
Gawryluk, Ryan University of Victoria (Canada) Adapting ultra-low input long read sequencing methods to predatory algae in a complex culture system
Jesus, Ederson EMBRAPA (Brazil) Unveiling the functional potential of microbial communities of the Amazon forest floor through metagenomics
Krukenberg, Viola Montana State University Exploring the microbial methane cycle in terrestrial geothermal environments
Mengiste, Tesfaye Purdue University Whole genome resequencing of 400 sorghum core subset germplasm collection
Myburg, Alexander University of Pretoria (South Africa) Eucalypt genomic resources for woody biomass production and carbon drawdown
Nelson, Andrew Boyce Thompson Institute (Cornell University) Molecular basis of natural rubber biosynthesis in Parthenium argentatum (Guayule)
Preston, Jill University of Vermont Development of the grass subfamily Pooideae as a powerful comparative genomics model for temperate crop and biofuel development
Purcell, Alicia Northern Arizona University Quantifying the ecophysiology of growing microbes responding to warming along a productivity gradient of the Marr Ice Piedmont Glacier, West Antarctic Peninsula
Read, Betsy Cal State University San Marcos The Haptophyte Genome Project
Roth, Melissa UC Berkeley Deciphering the role of master regulators in carbon flow for enhanced lipid production
Vallon, Olivier Centre National de la Recherche Scientifique (France) A Chlamydomonas pan-genome
Wilkins, Michael Colorado State University Impacts of changing wildfire regimes on soil microbiome succession and function

 

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:

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.

JGI announces final round of 2022 Functional Genomics awardees

Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!

Introducing New Members of the JGI User Executive Committee

incoming 2023 UEC members

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 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"
  • 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