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 › Game On: High School Students Drive Everglades Metagenomics Study

August 30, 2019

Game On: High School Students Drive Everglades Metagenomics Study

In late June, Kathleen Lail, a member of JGI’s Sample Management Group, attended a conference in Florida to discuss a JGI pilot project involving soil sampling in the Florida Everglades to help train the next generation of scientists. She shares her thoughts about the experience below.

Group shot from the 2019 AESS conference with students from Boca Raton HS

Boca Raton Community High School students (in alphabetical order): Deniz Caglayan, Claire Hagan, Ralph Jeanty, Alexander Klimczak, Sydney Levy, Angel Millard-Bruzos, David Prentice, Richard Roehm, Mulan Yin, with teacher Jonathan Benskin (second from left) presented at the E4 community-building workshop. Also present: David Blockstein (center), one of the Association for Environmental Studies and Sciences (AESS) founders and workshop session leader; and Kathleen Lail (leftmost) of the JGI.

In the summer of 2018, Jonathan Benskin was preparing to teach a second year A-Level Advanced International Certificate of Education (AICE) Biology class at Florida’s Boca Raton Community High School. The course had a defined set of objectives, and started with an image of a spoonful of dirt with the question: Do you want to find out what is in this soil?

Jonathan had been reaching out to many researchers with the hope of getting support for a research project for his class of 18 juniors.  He got turned down consistently, with one of his favorite answers being, “It would take a team of Ph.D.’s over a year to do a project at this capacity.”

Jonathan’s thought to himself was, “Game on.”

Part of the Boca Raton Community High School presentation

Part of the Boca Raton Community High School presentation

Then Jonathan’s email request reached Emiley Eloe-Fadrosh, the Metagenome Program Head at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility. She took special interest in it because she credits her high school teacher with inspiring her to get into science and wanted to pay it forward.

Defining a Diverse Research Topic

After a video conference interview between the class and the JGI, the students found out that their project was approved and was being funded under the JGI Director’s Science Program. The class did not know at the time that the project had already received enthusiastic support from the JGI Director, Nigel Mouncey.

Jonathan credits his intrinsically motivated students with fully defining the project, but it also took a very motivated teacher willing to work and learn in a discipline without the expertise, along with the students.  The project provided the students the freedom to define the specifics. It took the coming together of many unlikely pieces across the United States to enable the class to perform research that would have been difficult, if not impossible, without such a serendipitous partnership.

Boca Raton HS students in the field site. (Courtesy of Jon Benskin)

Boca Raton HS students in the field. (Courtesy of Jon Benskin)

The class decided to do an environmental microbial community (metagenomic) soil study in an untouched region of the Everglades, the Loxahatchee National Wildlife Preserve. They chose this location because much is unknown about the diversity of organisms (taxonomy) and particularly those in processing (metabolizing) methane within the Florida Everglades ecosystem.

There are no roads or real human traffic through this remote part of the Everglades. The students had to come up with an extraction procedure for the soil and acquire the permits to do so. They used images from Google maps to plan their route, and had to adapt when they noticed while collecting the samples on canoes just how much change had occurred in this region since the images used to map their routes had been taken.

Sifting through 16 Trillion Bases of DNA

Taking into consideration some complicated environmental challenges for collecting these soil samples, the students made coring devices, then planned and collected from 4 sites with 5 replicates. They extracted the DNA from the soil with Qiagen DNeasy PowerSoil Kits and sent the samples to the JGI for sequencing.  While JGI processed, sequenced, and analyzed the soil samples, the JGI offered 7 seminars to the class throughout the project life cycle. During regular web conferences, various JGI subject matter experts walked the class through the workflow and all the process steps of sequencing and analyzing the DNA samples. The class was also able to receive training for the JGI’s Integrated Microbial Genomes & Microbiomes (IMG/M) portal for their sample analysis.

Boca Raton HS students sifting soil samples. (Courtesy of Jon Benskin)

Boca Raton HS students sifting soil samples. (Courtesy of Jon Benskin)

The class had to sift through over 55 billion genes and 16 trillion DNA bases of data, to figure out what to study and compare for the project.  At the same time, in order to analyze and compare their soil, the class partnered with Texas A&M researchers to assist them with soil sample analysis for nitrogen and carbon concentrations along with water content.

The class had to work collaboratively and creatively to come up with a sense of what to focus on. With so much data and a lack of experience, this added a layer of complexity to the project for figuring out how to bring this project together. The class understood that much is unknown about the taxonomic diversity and methane metabolism within the Florida Everglades. They decided to look at the predominant taxa and the abundance of genes involved in environmentally significant metabolic pathways related to methane production, nitrogen fixation, and dissimilatory sulfite reduction.

Presenting the Results

Boca Raton HS students working with their samples. (Courtesy of Jon Benskin)

Boca Raton HS students working with their samples. (Courtesy of Jon Benskin)

The Boca Raton A-Level AICE Biology Class was invited to present the results of their efforts during the Energy, Earth and Environmental Education (E4) community-building workshop at the 2019 Association for Environmental Studies and Sciences (AESS) Conference in Orlando, Florida.  The JGI was also invited to participate in the workshop and speak about this special partnership with Boca Raton Community High School.

On June 26, 2019, the students gave a team presentation on how they defined, prepared, and carried out their research and analysis for this project. They had learned many statistical tests for raw data and how to use some bioinformatics tools for analysis to help them focus on what to pull out from the enormous data set on the IMG portal. The class discovered Actinobacteria, Acidobacteria, and Proteobacteria to be the most common phyla of bacteria sequenced from the metagenomic soil samples from the four sites tested.  They found Euryarchaeota to be the most common phylum of Archaea.  Alpha/Beta diversity tests showed significant congruity between three sites. There was slight congruity between all the sites.  Shotgun metagenomic analysis discovered the presence of integral biomarkers: mcrA, nifH, and dsrB.  Lastly, for this project the students calculated the correlations between the integral biomarkers and abiotic factors for water content, nitrogen concentration, and organic carbon concentration.

From Field Studies to Publication

Part of the Boca Raton Community High School presentation

Part of the Boca Raton Community High School presentation

Together as a class, the students learned about how to write a scientific paper. They wrote, edited, and rewrote a microbiome announcement that has been submitted to the journal Environmental Microbiome with significant scientific observations for this Everglades area. Their paper is currently under peer review. Although the class is over and the students are preparing for their senior year, they will have to come back together as the paper goes through additional review and revisions.  It was incredibly exciting and inspiring to see what these students accomplished in such a little amount of time and with minimal direction.

During the presentation, students were asked what they would do differently if they did the project again. Some mentioned that they might sample the west side because it was close to where there was agricultural run-off. They were wondering how that might compare with the east side, and if the run-off might have affected the results. Another idea was to study the different methane-producing bacteria and even how some of the bacteria could be competing with each other.  One student thought that there could be an undiscovered gene that was sequenced in the project to breakdown methane and noted how awesome it would be to discover that gene from this untouched Everglade region.

Boca Raton Community High School teacher Jonathan Benskin

“The JGI has gone over-and-above throughout this research project,” said Jonathan. “Students now have a deeper understanding of both the research process and metagenomics while legitimately contributing to the body of scientific knowledge that can be accessed by the rest of the community. These high school students now feel more empowered and equipped for their future research endeavors.”

The students were able to do professional-level research with hands-on experience for soil collection, processing, and DNA extraction. As a team, they learned and showed invaluable leadership, teamwork, and dedication. This was a first of its kind project, but it is a great model of how the JGI can partner and help train the next generation of scientists.

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:

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 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)
  • 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