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

Our Science
Home › Science Highlights › Feeding at the biofuel trough

February 14, 2014

Feeding at the biofuel trough

Researchers are using “experimental evolution” to develop bacteria that are more efficient at decomposing biomass.

The Science:

Clostridium phytofermentans is a soil-dwelling bacterium that helps decompose leaf litter. Researchers grew successive generations of bacteria on different woody material that make up plant cell walls (cellulose, cellobiose and xylan) and found that the bacteria adapted and became more efficient over generations. Genetic analysis found that mutations were in regions of DNA that coded for or regulated genes that were involved with carbohydrate (simple sugars) use or transport.

The Impact:

This is the first experiment to use an “experimental evolution” approach with a microbe that feeds on cellulose, following generations of bacteria as they adapt to different living environments. The findings suggest that it may be possible to find key genes and mutations that can be used in pinpointing genes that can be used to efficiently break down biomass feedstock, the raw material of biofuels.

The bacteria in this study, Clostridium phytofermentans, were isolated near the Quabbin Reservoir in Massachusetts. The bacteria live in the soil and help break down leaf litter on the forest floor. (Image by Philip Halling via Wikimedia Commons)

The bacteria in this study, Clostridium phytofermentans, were isolated near the Quabbin Reservoir in Massachusetts. The bacteria live in the soil and help break down leaf litter on the forest floor. (Image by Philip Halling via Wikimedia Commons)

Summary

Breaking down cellulose and other woody plant materials is one of the biggest challenges of producing efficient and sustainable biofuels. Biofuel developers depend on fungi and bacteria that are adept at breaking down these materials. Researchers from the University of Massachusetts, Amherst grew one of these bacteria, C. phytofermentans, in the lab on several different woody plant materials (xylan, cellobiose and cellulose) and studied the genes of subsequent generations as they adapted to their new nutrient-rich environment. They published their results in a paper published January 22, 2014 in the journal, PLOS ONE.

Cellulose and other woody plant materials are constructed from long chains of glucose units that can have anywhere from hundreds to thousands of glucose units. They’re a kind of carbohydrate, though humans have a hard time digesting cellulose and similar materials.

C. phytofermentans has more than 100 glycoside hydrolases, compounds for breaking down complex sugars and woody substances and about 50 different molecular transport system dedicated to moving them across cell membranes. So it’s an ideal organism to study genetic and molecular adaptations for carbohydrate metabolism. C. phytofermentans’s genome was sequenced as part of a DOE JGI Community Sequencing Project, which also partially supported this study.

After letting bacteria grow for many generations, the research team sequenced entire populations of adapted bacteria, which gave them a more complete picture of genetic adaptations. All the mutations the researchers identified were in the regions that coded or regulated a specific kind of transporter called CUT1, which are involved in transporting oligosaccharides, relatively small carbohydrate molecules. One series of mutations seemed to help the bacteria move glycoside hydrolases out of the cell faster. The adapted bacteria had several diverse mutations, hinting that there are many ways to efficiently feed off of woody materials – and many molecular pathways that can be tweaked to break down woody materials more efficiently.

The researchers suggest that further study of the mutations they identified is a good next step and that eventually, some of these mutations might someday be useful for breaking down biomass into useable renewable energy sources.

Contact

Jeffrey Blanchard
University of Massachusetts, Amherst
jeffb@bio.umass.edu

Publication

Mukherjee S, Thompson LK, Godin S, Schackwitz W, Lipzen A, et al. (2014) Population Level Analysis of Evolved Mutations Underlying Improvements in Plant Hemicellulose and Cellulose Fermentation byClostridium phytofermentans. PLoS ONE 9(1): e86731. doi:10.1371/journal.pone.0086731

Funding

Department of Energy, Office of Science
The Isenberg School of Management at the University of Massachusetts Amherst
The National Science Foundation
The Howard Hughes Medical Institute Award
Qteros Inc.

Related Links

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0086731

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:

Soil virus offers insight into maintaining microorganisms

Silver age of GOLD introduces new features

Abstract image of gold lights and squares against a black backdrop

Virus Discoveries that Keep Getting Bigger

And illustration of a giant virus in purple and blue tones.

Model fern reveals insight into DNA thievery in ferns

A green fern against a black backdrop

Understanding Wildfire Recovery, Starting in Soil

A photograph of the forest floor, covered in pine needles, with burned trees in the background.

Extracting the Secrets of Secondary Metabolites

A graphic flowchart showing how CRAGE and CRISPR work together
  • 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