DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Science Programs
    • Science Highlights
    • Scientists
    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

    More

    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

    More

    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

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

    More

    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

    More

    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

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    Abstract image of gold lights and squares against a black backdrop
    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

    More

    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

    More

    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

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

    More

    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

    More

    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

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

    More

    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

    More

    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

    More

News & Publications
Home › Podcasts › Genome Insider S2 Episode 2: Cracking the Secrets of the Diatom’s Shell

March 9, 2021

Genome Insider S2 Episode 2: Cracking the Secrets of the Diatom’s Shell

Diatoms, a group of tiny algae, are also known as “living opals” because of the strange, beautiful properties of their silica shells. But what genes are responsible for such mesmerizing exteriors? Setsuko Wakao and Kris Niyogi, biologists at both UC Berkeley and Lawrence Berkeley National Laboratory, aim to find out.

The Joint Genome Institute presents the Genome Insider podcast.

Listen on Apple Podcasts Get the RSS Feed

Transcript of the episode

ALISON: Hey! I’m Alison Takemura, and this is Genome Insider, a podcast of the US Department of Energy Joint Genome Institute, or JGI. In soils, waterways, and the ocean, there is an exquisite group of microscopic organisms. They’re called diatoms.

Diatoms. (Randolph Femmer, USGS Library of Images From Life, CC BY-NC 2.0)

Diatoms. (Randolph Femmer, USGS Library of Images From Life, CC BY-NC 2.0)

SETSUKO: There are many, many different species. And what’s really amazing about them is that they’re very beautiful. They’re very beautiful in terms of the larger shape of the cell but also when you look at them under the microscope, they have very intricate patterns at the micro- and nanoscale.

ALISON: That’s Setsuko Wakao, a research scientist at UC Berkeley and Lawrence Berkeley National Lab. 

And Setsuko is studying diatoms. Diatoms make, or biomineralize, hard, silica shells. And these shells  give them some unique shapes — like stars, triangles, and pinwheels, bean pods, orange slices, and saucers. I know. Weird right?

Also, did you know that it was a Victorian hobby to arrange diatoms into pleasing symmetrical patterns? I didn’t! 

But even stranger than what people do with them is that the shells of these unusual organisms have nanoscale patterns. And the patterns create colors. Their shells’ nanostructure affects the behavior of photons. You’re actually already probably familiar with this effect. It’s the same thing you see in peacock feathers and butterfly wings. They’re so beautifully vibrant, not because of pigments, but because of physical structures invisible to the naked eye. Same thing with diatoms. Their shells’ funky interactions with light have earned diatoms the nicknames “jewels of the sea” and “living opals.”

Diatoms arranged in a symmetric pattern, like the Victorians used to do back in the day. (W.M. Grant)

Diatoms arranged in a symmetric pattern, like the Victorians used to do back in the day. (W.M. Grant)

But diatoms are more than just their good looks. They’re self-sufficient. They make food from sunlight using photosynthesis. And in the ocean, diatoms have been wildly successful; they make up about half of the ocean’s photosynthesizing microbial community: the phytoplankton. It’s a wonderfully evocative name: “phyto” means plant, and “plankton” means wanderer. 

As diatoms wander, they have a huge effect on our planet. They account for 20 percent of the carbon fixed globally every year. They transform carbon dioxide into biomass that they can incorporate into their bodies.

And then when they die, their shells are heavy enough that they can cause them to sink to their watery graves. In death, diatoms take some of the carbon that they’ve fixed with them. And it becomes locked away.  

KRIS: And so this is a, an important mechanism for sequestering carbon in the deep ocean over geological time, those algae that grew millions of years ago, can be turned into oil reserves. And so essentially, what we’re doing now by burning those oil reserves is releasing carbon dioxide that was fixed by phytoplankton many millions of years ago, all at once.

ALISON: That’s Kris Niyogi, a plant and microbial biologist, and like Setsuko, also affiliated with UC Berkeley and Lawrence Berkeley National Lab. Setsuko is a member of Kris’ lab. 

The light green swirls in the sea are phytoplankton, visible from space. This bloom occurred off the coast of western Iceland. (NASA Goddard Space Flight Center, CC BY 2.0)

The light green swirls in the sea are phytoplankton, visible from space. This bloom occurred off the coast of western Iceland. (NASA Goddard Space Flight Center, CC BY 2.0)

Kris and Setsuko are interested in better understanding this process where diatoms sink and sequester carbon. It’s part of a phenomenon called the “biological carbon pump” — think of it as diatom deaths and their heavy silica shells “pumping” or moving carbon from one place to another.

KRIS: I’m really interested in what sort of the, the underlying fundamental mechanisms are. This is something that’s really important for the biological carbon pump, and we need to understand how they do this silica biomineralization to fully understand how that process works. 

ALISON: So, diatoms affect the Earth’s carbon cycle. But …

SETSUKO: As important as it is, diatoms themselves and the biosynthesis of these silica cell walls are still not understood completely in terms of what genes are involved. 

ALISON: And so, Setsuko and Kris are investigating how diatoms make their shells.

The answers could influence the design and manufacture of new materials, as well as give us insight into a natural process of sequestering carbon.

But first, let’s get to know diatoms a little better. 

ALISON: Can you describe what a diatom might look like? 

SETSUKO: They’re almost like a mesh of silica patterns.

Setsuko Wakao, a research scientist at UC Berkeley and Lawrence Berkeley National Lab. (Queena Xu)

Setsuko Wakao, a research scientist at UC Berkeley and Lawrence Berkeley National Lab. (Queena Xu)

ALISON: I tried to imagine what that might look like, and thought: maybe chainmail? Eh, no.

SETSUKO: Well, it’s not really like a chain— links of chains. Because it’s more like if you have some kind of contiguous surface, and you started poking holes in a very regular pattern, so [there isn’t this kind of,] it’s still two dimensional. But the pores are formed in very regular ways that makes it look like a mesh.

ALISON: It’s kind of like a tea strainer. Scientists think that diatoms are so abundant, in part, because their silica cell walls are made with the element silicon (Si) instead of carbon.

SETSUKO: So if you’re not using carbon that you fixed, but rather a different element, you’re being a little bit more efficient in terms of your energy, because you can use that carbon that you fixed for some other parts of the cell. The other advantage that is commonly discussed is that by having a silica cell wall, it’s very hard to be digested.

Kris Niyogi, plant and microbial biologist at UC Berkeley and Berkeley Lab’s Biosciences Area Molecular Biophysics and Integrated Bioimaging Division. (Peter Barreras)

Kris Niyogi, plant and microbial biologist at UC Berkeley and Lawrence Berkeley National Lab. (Peter Barreras)

So when you think about the marine environment, where there are predators that eat up all these phytoplankton, maybe it allowed them to survive better. And there are other points like their optical properties and how that might help capture more light.

ALISON: But that’s still kind of iffy. What’s clear is these shells have a powerful influence on their lives. So, how do they make them? Right now, a little is known. It seems like there’s a protein template that the silica structure gets built upon. But Setsuko and Kris aim to dig deeper — to figure out what genes are involved. 

So they’re coming at the problem, cleverly, from the side. They’re analyzing not only diatoms, but a related group of microalgae called synurophytes. Their name means a plant with a tail. They have flagella, which look like little tails.

SETSUKO: So these are algae that grow in freshwater. They also make silica cell walls but in very different forms. 

ALISON: Unlike diatoms, with their perforated mesh shells, synurophytes make scales. And they overlap, just like on the body of a fish.

A synurophyte, Synura petersenii, with its silica scales. False-colored. (Drew Lindow, CC BY-SA 3.0)

A synurophyte, Synura petersenii, with its silica scales. False-colored. (Drew Lindow, CC BY-SA 3.0)

SETSUKO: They become completely covered in these scales.

ALISON: And these scales are actually quite big relative to the synurophyte’s body. To me they look like a ball wrapped in leaves. Anyway, Setsuko and Kris think synurophytes and their genes could give them clues to how diatoms make their hard shells.

SETSUKO: If we sequence the genomes of these synurophytes, we might find common genes that will tell us about the important processes in silica cell wall biosynthesis by comparing it with diatoms. 

ALISON: So, Setsuko and Kris are working on sequencing synurophyte genomes with JGI. And, in the meantime, they’re poring over already sequenced diatom genomes. JGI actually sequenced the very first diatom genome from the species Thalassiosira pseudonana. And since then, JGI has sequenced four more diatoms. And it recently committed to sequence an additional one hundred diatom genomes. Setsuko and Kris will be able to use all of that data.  

But comparing just genome sequences is a static enterprise. In other words, it’s limited. Setsuko and Kris also want to investigate  genomes dynamically. So, they plan to figure out which genes synurophytes express when they make their silica scales. Because they don’t make them all the time. 

SETSUKO: What’s unique about synurophytes, is that they’re not completely dependent on silica as diatoms are. 

ALISON: Diatoms can’t grow without silica, because they can’t grow without their cell walls.

SETSUKO: So, diatoms, if you remove silica completely, they can’t grow. Which makes it difficult for us as an experimental system, because we would like to compare when you don’t have silica versus when you have a lot of silica, but you cannot do this with diatoms. 

ALISON: So, Setsuko and Kris are looking to the synurophyte cousins for answers. Synurophytes do grow without silica. They’re perfectly OK being unprotected, naked cells. And that flexibility gives scientists an opportunity.

SETSUKO: You can compare the genes that are expressed when it doesn’t make any scales, versus when you dump an amount of silica on it. And now it’s producing this multiple layers of scales. 

ALISON: Setsuko and Kris aim to find what genes get switched on when synurophytes go into these scale-making mode. Those genes are likely to be important for building the silica (SiO2) cell wall. So, the team will then look for those genes in diatoms. 

SETSUKO: And the last part is to test whether disrupting those genes actually lead to the loss or alteration of silica cell walls.

ALISON: That’s how the team will make sure they’ve found the right genes. They’ll use a technique that’s growing in popularity: CRISPR interference, or CRISPRi. It blocks the expression of genes using small CRISPR guide RNA sequences that target the genes of interest. And the JGI is making the DNA templates for those guide RNA sequences. 

SETSUKO: So, we’re taking advantage of the DNA synthesis capacity of JGI to make CRISPRi guide RNAs to test all these candidate genes. 

ALISON: In other words, Setsuko and Kris will see whether blocking the expression of these genes in a model diatom actually changes its cell wall. The approach is like having workers at a construction site. Let’s say, some of them are building a brick wall. But you don’t know who. You do have a list of people, though. So you do an experiment. You prevent one worker at a time from going to the job site. And then you see whose absences affect the wall the most. Is it not being built well or even at all anymore? That’s basically what Kris and Setsuko are going to try to do with the diatom genes.

And they hope that all of these efforts — analyzing synurophyte genomes, depriving them of silica, and blocking the expression of interesting genes — will help illuminate how diatoms build their silica shells.

Zooming in on a marine diatom, Detonula pumila, you can see the mesh-like nanoscale patterning on its shell surface. (Health Sciences and Nutrition, CSIRO)

Zooming in on a marine diatom, Detonula pumila, you can see the mesh-like nanoscale patterning on its shell surface. (Health Sciences and Nutrition, CSIRO)

One potential result of this knowledge? It could help researchers develop new biomaterials. These biomaterials could be based on a diatom shell’s nanoscale patterns. 

SETSUKO: So, all these very regular and small patterns lead to certain optical properties. 

ALISON: And those properties could be useful for biomedical or electronic applications, for example. The advantages of a biomaterial?

SETSUKO: A biomaterial is very reliable. I mean, biology can do things easily, as compared to chemical processes.

ALISON: Those processes require hard work in the lab. Diatoms, by contrast, just need sunlight, water, and a few trace nutrients to build a nanomaterial.

But that’s not all that could come from better understanding how diatoms biomineralize their cell walls. Even though it’s a tiny, molecular process, it could also help us fight climate change.

KRIS: I think it’s far in the future. But understanding how biomineralization works could lead to new ideas for, for carbon sequestration.

ALISON: Setsuko says that one example of how not to do it is to add silica into the ocean, in the hope of making more diatoms grow and sink. That could have unanticipated, and undesirable, side effects. Ocean ecology is complex. And adding silica might change the rate of diatom sinking. We could end up sequestering less carbon, which is the opposite of what we want. So, Setsuko and Kris hope that better understanding diatoms will give humans better ideas in the future.

Together, diatoms and their evolutionary cousins, the synurophytes, might show us the way. If some come out of their shells.

ALISON: This episode was directed and produced by me, Alison Takemura, with editorial and technical assistance from Massie Ballon and David Gilbert.

Genome Insider is a production of the Joint Genome Institute, a user facility of the US Department of Energy Office of Science. JGI is located at Lawrence Berkeley National Lab in beautiful Berkeley, California. 

A huge thanks to Kris Niyogi and Setsuko Wakao from UC Berkeley and Lawrence Berkeley National Lab’s Biosciences Area’s Molecular Biophysics and Integrated Bioimaging Division for sharing their research and the startling beauty of diatoms. Setsuko is the principal investigator on this project, as part of JGI’s New Investigator program.

If you enjoyed Genome Insider and want to help others find us, leave us a review on Apple Podcasts, Google Podcasts, or wherever you get your podcasts. If you have a question or want to give us feedback, Tweet us @JGI, or record a voice memo and email us at JGI dash comms at L-B-L.gov. That’s jgi dash c-o-m-m-s at l-b-l dot g-o-v.

And because we’re a user facility, if you’re interested in partnering with us, we want to hear from you! We have projects in genome sequencing, synthesis, transcriptomics, metabolomics, and natural products in plants, fungi, algae, and microorganisms. If you want to collaborate, let us know!

Find out more at jgi.doe.gov forward slash user dash programs. 

And if you’re interested in hearing about cutting-edge research in secondary metabolites, also known as natural products, then check out JGI’s other podcast, Natural Prodcast. It’s hosted by Dan Udwary and me. That’s it for now. See ya next time!

Additional information related to the episode

  • Community Science Program proposal: Sequencing 100 Diatom genomes
  • JGI News Release: Tracking Antartic Adaptations in Diatoms
  • JGI News Release: First diatom genome sequenced
  • Algal genomics resource, Phycocosm
  • JGI’s Fungal & Algal Program
  • The JGI Strategic Plan, noting an algal focus, is available here
  • Our contact info:
    • Twitter: @JGI
    • Email: jgi-comms at lbl dot gov

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)
Genome Insider is available on Apple Podcasts, Google Play, Spotify, iHeart Radio, and TuneIn Radio - Subscribe today! Natural Prodcast is available on Apple Podcasts, Google Play, and Spotify - Subscribe today!

Filed Under: Podcasts Tagged With: genome insider

More topics:

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

Related Content:

JGIota: A biofuel breakthrough in anaerobic fungi with Michelle O’Malley and Tom Lankiewicz

A Genome Insider Logo Image

JGIota: Sequencing Shiitakes with David Hibbett

A Genome Insider Logo Image

Natural Prodcast Episode 19 – Bill Fenical

Natural Prodcast Episode 18 – A CSP Primer

Natural Prodcast podcast logo

Genome Insider S3 Episode 5: Work With the JGI! Tips for a Winning CSP Proposal

A Genome Insider Logo Image

JGIota: Looking back at how our cow rumen study drives higher learning

A Genome Insider Logo Image
  • 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