Fermented foods like kimchi have been an integral part of Korean cuisine for thousands of years. Since ancient times, Korean chefs have used onggi — traditional handmade clay jars — to ferment kimchi. Today, most kimchi is made through mass fermentation in glass, steel, or plastic containers, but it has long been claimed that the highest quality kimchi is fermented in onggi.
Kimchi purists now have scientific validation, thanks to recent research from David Hu, professor in the George W. Woodruff School of Mechanical Engineering and the School of Biological Sciences at Georgia Tech, and Soohwan Kim, a second-year Ph.D. student in Hu’s lab.
In a combined experimental and theoretical study, Hu and Kim measured carbon dioxide levels in onggi during kimchi fermentation and developed a mathematical model to show how the gas was generated and moved through the onggi’s porous walls. By bringing the study of fluid mechanics to bear on an ancient technology, their research highlights the work of artisans and provides the missing link for how the traditional earthenware allows for high quality kimchi.
Their research was published in the Journal of the Royal Society Interface.
“We wanted to find the ‘secret sauce’ for how onggi make kimchi taste so good,” Hu said. “So, we measured how the gases evolved while kimchi fermented inside the onggi — something no one had done before.”
The porous structure of these earthenware vessels mimics the loose soil where lactic acid bacteria — known for their healthy probiotic nature — are found. While previous studies have shown that kimchi fermented in onggi has more lactic acid bacteria, no one knew exactly how the phenomenon is connected to the unique material properties of the container.
First, Kim obtained a traditional, handmade onggi jar from an artisan in his hometown in Jeju, South Korea, a region famous for onggi. Back at Georgia Tech, Hu and Kim first tested the permeability of the onggi by observing how water evaporated through the container over time.
Next, they installed carbon dioxide and pressure sensors into both the onggi and a typical, hermetically sealed glass jar. They prepared their own salted cabbage and placed it in both containers. They then used the sensors to measure and compare the change in carbon dioxide — a signature of fermentation.
Hu and Kim also developed a mathematical model based on the porosity of the onggi. The model allowed them to infer the generation rate of carbon dioxide, since the onggi lets carbon dioxide out gradually.
They concluded that the onggi’s porous walls permitted the carbon dioxide to escape the container, which accelerated the speed of fermentation. The onggi’s porosity also functioned as a “safety valve,” resulting in a slower increase in carbon dioxide levels than the glass jar while blocking the entry of external particles. Their data revealed that the carbon dioxide level in onggi was less than half of that in glass containers.
They also found that the beneficial bacteria in the onggi-made kimchi proliferated 26% more than in the glass counterpart. In the glass jar, the lactic acid bacteria became suffocated by their own carbon dioxide in the closed glass container. It turns out that, because the onggi releases carbon dioxide in small rates, the lactic acid bacteria are happier and reproduce more.
“Onggi were designed without modern knowledge of chemistry, microbiology, or fluid mechanics, but they work remarkably well,” Kim said. “It’s very interesting to get these new insights into ancient technology through the lens of fluid dynamics.”
Onggi’s semiporous nature is unique compared to other forms of earthenware. A clay container that leaks, but only slightly, is not easy to make. Terra cotta containers, for example, quickly leak water.
“It's amazing that, for thousands of years, people have been building these special containers out of dirt, but in many ways, they are very high tech,” Hu said. “We discovered that the right amount of porosity enables kimchi to ferment faster, and these onggi provide that.”
Kim said that some artisans still use ancient methods when making onggi, but their numbers are decreasing. Now, the market is flooded with inauthentic versions of the vessels.
“We hope this study draws attention to this traditional artisan work and inspires energy-efficient methods for fermenting and storing foods,” he said. “Also, the onggi are quite beautiful.”
Citation: Kim Soohwan and Hu David L. Onggi’s permeability to carbon dioxide accelerates kimchi fermentation. J. R. Soc. Interface. 2023.
DOI: https://doi.org/10.1098/rsif.2023.0034
This material was supported by the Woodruff Faculty fellowship and the NSF Physics of Living Systems student network.
Event Details
For the past 10 years, there’s only been one place in Atlanta where you can touch a brain, see a science fashion show, watch scientists give improv performances, and more — and that’s at the Atlanta Science Festival.
And during that time, the faculty and students of STEMcomm have become a festival staple.
STEMcomm, which stands for Science, Technology, Engineering, and Math (STEM) communication, is a course in Georgia Tech’s Vertically Integrated Projects (VIP) program. Established in 2016 by three faculty in the College of Sciences, the course uses science communication to create outreach events for the Atlanta Science Festival — and popular-science content to share on social media and online publications.
“I feel like there is a gulf in the world between people who do science and the general public,” says Jennifer Leavey, a principal academic professional in the School of Biological Sciences, the College’s assistant dean for Faculty Mentoring, and one of the founders of the course. “There is very little crosstalk there.”
The goal of STEMcomm is to bridge that gap and connect with an at-times overlooked audience: adults.
“When it comes to science, I think in general, there’s not a lot of new learning once you get beyond school-age. Teachers do a great job of engaging children with science, but for adults, I mean, there's not a lot there,” Leavey added. “I think there’s a real space for people with science knowledge to help bring that conversation more into the mainstream.”
Visit the College of Sciences website to hear how the faculty and students of STEMcomm are bringing science to Atlanta.
For the past 10 years, there’s only been one place in Atlanta where you can touch a brain, see a science fashion show, watch scientists give improv performances, and more — and that’s at the Atlanta Science Festival.
And during that time, the faculty and students of STEMcomm have become a festival staple.
STEMcomm, which stands for Science, Technology, Engineering, and Math (STEM) communication, is a course in Georgia Tech’s Vertically Integrated Projects (VIP) program. Established in 2016 by three faculty in the College of Sciences, the course uses science communication to create outreach events for the Atlanta Science Festival — and popular-science content to share on social media and online publications.
“I feel like there is a gulf in the world between people who do science and the general public,” says Jennifer Leavey, a principal academic professional in the School of Biological Sciences, the College’s assistant dean for Faculty Mentoring, and one of the founders of the course. “There is very little crosstalk there.”
The goal of STEMcomm is to bridge that gap and connect with an at-times overlooked audience: adults.
“When it comes to science, I think in general, there’s not a lot of new learning once you get beyond school-age. Teachers do a great job of engaging children with science, but for adults, I mean, there's not a lot there,” Leavey added. “I think there’s a real space for people with science knowledge to help bring that conversation more into the mainstream.”
Visit the College of Sciences website to hear how the faculty and students of STEMcomm are bringing science to Atlanta.
John Wallingford, PhD
University of Texas at Austin
Body Sculpting: How the embryo constructs itself
The fascinating thing about embryos is that they construct themselves. Indeed, it is the behavior of the individual cells within that directs dictates the construction of our tissues and organs, and defects in these behaviors are a key cause of human birth defects, which kill more than twice as many children as pediatric cancer. Thus, understanding the cell biology of developing embryos is a crucial challenge in biology. For the last two decades, our lab has used in vivo imaging, biomechanics, and proteomics to understand the collective cell behaviors that elongate the body axis in vertebrate embryos. In this talk, I’ll discuss our recent work illuminating the nexus between tissue-specific developmental signaling systems that govern cell movements and the ubiquitous cell biological machinery that executes them. The talk will focus on the interplay of Planar Cell Polarity signaling, actomyosin contraction, and cadherin-based cell-cell adhesion.
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Justin Meyer, PhD
University of California, San Diego
Coevolution between phage and bacteria drives the evolution of key innovations, new species, and biological complexity
Coevolution is predicted to be a creative force in the evolution of life, possibly contributing to the evolution of phenomena such as diversity, novelty, and complexity. One key mechanism by which coevolution promotes the emergence of these phenomena is by causing fitness landscapes to fluctuate, inducing continual evolutionary change, and causing exploration of new adaptations. For this talk, I will discuss several experimental studies on bacteria and phages that demonstrate the role coevolution plays in driving the evolution of key innovations, speciation, and the formation of complex ecological networks. The studies include quantification of how fitness landscapes change during coevolution by leveraging high-throughput gene editing-phenotyping technologies.
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There are times when John McDonald, emeritus professor in the School of Biological Sciences and founding director of Georgia Tech’s Integrated Cancer Research Center, is asked to share his special insight into cancer.
“Over the years, I’ve gotten calls from non-scientist friends and others who have been diagnosed with cancer, and they call me to get more details on what’s going on, and what options are available,” said McDonald, also a former chief scientific officer with the Atlanta-based Ovarian Cancer Institute.
That’s the primary motivation why McDonald wrote A Patient's Guide to Cancer: Understanding the Causes and Treatments of a Complex Disease, which was published by Raven Press LLC (Atlanta) and is now available at Amazon or Barnes and Noble in paperback and ebook editions. The book describes in non-technical language the processes that cause cancer, and details on how recent advances and experimental treatments are offering hope for patients and their families.
A book for the proactive patient
McDonald said he couldn’t go into detail for every type of cancer, but provides a generally applicable background for the disease. For those who want more information, he provides links to other resources, including videos, that provide more detail on specific types of cancer. “There’s not much out there in one place for patients who want to understand the underlying causes of cancer, and the spectrum of therapies currently available,” he said.
McDonald, who was honored in January by the Georgia Center for Oncology Research and Education (CORE) as one of “Today’s Innovators,” also didn’t want A Patient’s Guide to Cancer to be a lengthy book, and it checks in at only 86 pages.
McDonald believes that when patients talk to their physicians about cancer treatments, they should ideally have a basic understanding of the underlying cause of their cancer, as well as a general awareness of the range of therapies currently available, and what may be coming down the road in the future.
“My book is specifically designed to provide newly diagnosed cancer patients who are not scientists with this kind of background information, empowering them to play a more informed role in the selection of appropriate treatments for their disease”.
The current experimental treatment landscape; McDonald’s 2023 research goals
McDonald’s own cancer research has led to two related startup companies, co-founded with School of Biological Sciences colleagues.
McDonald is working with postdoctoral researcher Nick Housley on using nanoparticles to deliver powerful drugs to cancer cells while sparing healthy tissue. The other company, founded in collaboration with Jeffrey Skolnick, Regents' Professor, Mary and Maisie Gibson Chair & Georgia Research Alliance Eminent Scholar in Computational Systems Biology, uses machine learning to create personalized diagnostic tools for ovarian cancer.
He and his lab team are also preparing to submit a research paper that builds off their 2021 study on gene network interactions that could provide new chemotherapy targets for breast cancer. That paper focuses on the three major subtypes of breast cancer. McDonald and his colleagues will also soon submit another study detailing genetic changes that happen with the onset and progression of ovarian cancer.
When it comes to current experimental treatments, McDonald says he’s especially excited about the potential of cancer immunotherapy, which uses the body’s own immune system to fight cancer cells. But he writes in A Patient’s Guide to Cancer that because these drugs are also delivered systemically, healthy tissues can also be affected, potentially leading to autoimmunity or the self-destruction of our normal cells.
“In the future, I believe many of the negative side-effects currently associated with the system-wide delivery of cancer drugs will be averted by the use of nanoparticles designed to target therapies specifically to tumors”.
There are times when John McDonald, emeritus professor in the School of Biological Sciences and founding director of Georgia Tech’s Integrated Cancer Research Center, is asked to share his special insight into cancer.
“Over the years, I’ve gotten calls from non-scientist friends and others who have been diagnosed with cancer, and they call me to get more details on what’s going on, and what options are available,” said McDonald, also a former chief scientific officer with the Atlanta-based Ovarian Cancer Institute.
That’s the primary motivation why McDonald wrote A Patient's Guide to Cancer: Understanding the Causes and Treatments of a Complex Disease, which was published by Raven Press LLC (Atlanta) and is now available at Amazon or Barnes and Noble in paperback and ebook editions. The book describes in non-technical language the processes that cause cancer, and details on how recent advances and experimental treatments are offering hope for patients and their families.
A book for the proactive patient
McDonald said he couldn’t go into detail for every type of cancer, but provides a generally applicable background for the disease. For those who want more information, he provides links to other resources, including videos, that provide more detail on specific types of cancer. “There’s not much out there in one place for patients who want to understand the underlying causes of cancer, and the spectrum of therapies currently available,” he said.
McDonald, who was honored in January by the Georgia Center for Oncology Research and Education (CORE) as one of “Today’s Innovators,” also didn’t want A Patient’s Guide to Cancer to be a lengthy book, and it checks in at only 86 pages.
McDonald believes that when patients talk to their physicians about cancer treatments, they should ideally have a basic understanding of the underlying cause of their cancer, as well as a general awareness of the range of therapies currently available, and what may be coming down the road in the future.
“My book is specifically designed to provide newly diagnosed cancer patients who are not scientists with this kind of background information, empowering them to play a more informed role in the selection of appropriate treatments for their disease”.
The current experimental treatment landscape; McDonald’s 2023 research goals
McDonald’s own cancer research has led to two related startup companies, co-founded with School of Biological Sciences colleagues.
McDonald is working with postdoctoral researcher Nick Housley on using nanoparticles to deliver powerful drugs to cancer cells while sparing healthy tissue. The other company, founded in collaboration with Jeffrey Skolnick, Regents' Professor, Mary and Maisie Gibson Chair & Georgia Research Alliance Eminent Scholar in Computational Systems Biology, uses machine learning to create personalized diagnostic tools for ovarian cancer.
He and his lab team are also preparing to submit a research paper that builds off their 2021 study on gene network interactions that could provide new chemotherapy targets for breast cancer. That paper focuses on the three major subtypes of breast cancer. McDonald and his colleagues will also soon submit another study detailing genetic changes that happen with the onset and progression of ovarian cancer.
When it comes to current experimental treatments, McDonald says he’s especially excited about the potential of cancer immunotherapy, which uses the body’s own immune system to fight cancer cells. But he writes in A Patient’s Guide to Cancer that because these drugs are also delivered systemically, healthy tissues can also be affected, potentially leading to autoimmunity or the self-destruction of our normal cells.
“In the future, I believe many of the negative side-effects currently associated with the system-wide delivery of cancer drugs will be averted by the use of nanoparticles designed to target therapies specifically to tumors”.
If you’re an avid gardener, you may have considered peat moss — decomposed Sphagnum moss that helps retain moisture in soil — to enhance your home soil mixture. And while the potting medium can help plants thrive, it’s also a key component of peatlands: wetlands characterized by a thick layer of water-saturated, carbon-rich peat beneath living Sphagnum moss, trees, and other plant life.
These ecosystems cover just 3% of Earth’s land area, but “peatlands store over one-third of all soil carbon on the planet,” explains Joel Kostka, professor and associate chair of Research in the School of Biological Sciences at Georgia Tech.
This carbon storage is supported in large part by microbes. Two microbial processes in particular — nitrogen fixation and methane oxidation — strike a delicate balance, working together to give Sphagnum mosses access to critical nutrients in nutrient-depleted peatlands.
The coupling of these two processes is often referred to as the “missing link” of nutrient cycling in peatlands. Yet, how these processes will respond to changing climates along northern latitudes is unclear.
“There are tropical peatlands — but the majority of peatlands are in northern environments.” notes Caitlin Petro, a research scientist who works with Kostka in Biological Sciences at Tech. “And those are going to be hit harder by climate change.”
Kostka and Petro recently led a collaborative study to investigate how this critical type of ecosystem (and the “missing link” of microbial processes that support it) may react to the increased temperature and carbon dioxide levels predicted to come with climate change. The team, which also includes researchers from the Oak Ridge National Laboratory (ORNL), Florida State University, and the University of Tennessee, Knoxville, just published their work in the scientific journal Global Change Biology.
By testing the effects of increasing temperature and carbon dioxide on the growth of Sphagnum moss, its associated microbiome, and overall ecosystem health, Kostka and Petro say computational models will be better equipped to predict the effects of climate change.
“Down the road,” Kostka added, “we hope the results can be used by environmental managers and governments to adaptively manage or geoengineer peatlands to thrive in a warmer world.”
Raising the heat
To see how northern peatlands will react to climate change, the team, which also included School of Earth and Atmospheric Sciences Associate Professor Jennifer Glass, turned to the ORNL Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment — a unique field lab in northern Minnesota where the team warms peat bogs and experimentally changes the amount of carbon dioxide in the atmosphere.
Starting in 2016, the team exposed different parts of SPRUCE’s experimental peatlands to a gradient of higher temperatures ranging from an increase of 0°C to 9°C, capturing the Intergovernmental Panel on Climate Change models’ predicted 4°C to 6°C increase in northern regions by 2100.
The moss’s reaction was significant. Although nearly 100% of the bog’s surface was covered in moss at the beginning of the experiment, moss coverage dropped with each increase in temperature, plummeting to less than 15% in the warmest conditions.
Critically, the two microbial processes that had previously been consistently linked fell out of sync at higher temperatures.
“Peatlands are extremely nutrient-poor and microbial nitrogen fixation represents a major nitrogen input to the ecosystem,” Kostka explained. Fixing nitrogen is the process of turning atmospheric nitrogen into an organic compound that the moss can use for photosynthesis, while methane oxidation allows the moss to use methane released from decomposing peat as energy. “Methane oxidation acts to fuel nitrogen fixation while scavenging a really important greenhouse gas before it is released to the atmosphere. This study shows that these two processes, which are catalyzed by the Sphagnum microbiome, become disconnected as the moss dies.”
“These processes occurring together are really important for the community,” Petro explained. Yet many microbes that are able to both fix nitrogen and oxidize methane were absent in the mosses collected from higher temperature enclosures. And while elevated carbon dioxide levels appeared to offset some of the changes in nitrogen cycling caused by warming, the decoupling of these processes remained.
“These treatments are altering a fairly well-defined and consistent plant microbiome that we find in many different environments, and that has this consistent function,” Petro explained. “It's like a complete functional shift in the community.”
Though it’s not clear which of these changes — the moss dying or the altered microbial activity — is driving the other, it is clear that with warmer temperatures and higher carbon dioxide levels comes a cascade of unpredictable outcomes for peat bogs.
“In addition to the direct effects of climate warming on ecosystem function,” Petro adds, “it will also introduce all of these off-shooting effects that will impact peatlands in ways that we didn't predict before.”
This work was supported by the National Science Foundation (DEB grant no. 1754756). The SPRUCE project is supported by the U.S. Department of Energy's Office of Science, Biological, and Environmental Research (DOE BER) and the USDA Forest Service.
DOI: https://doi.org/10.1111/gcb.16651
Citation: Petro, C., et al. Climate drivers alter nitrogen availability in surface peat and decouple N2 fixation from CH4 oxidation in the Sphagnum moss microbiome. Global Change Biology. (2023).
Aerial Photo: Hanson, P.J., M.B. Krassovski, and L.A. Hook. 2020. SPRUCE S1 Bog and SPRUCE Experiment Aerial Photographs. Oak Ridge National Laboratory, TES SFA, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A. https://doi.org/10.3334/CDIAC/spruce.012 (UAV image number 0050 collected on October 4, 2020).
When you see something buzzing, how do you know if it will sting?
Bees sting occasionally, but in general they are not aggressive — they’re defensive, and tend to only sting when they feel threatened.
“It’s mostly wasps that sting — they’re predators, they’re carnivores, and they’re more aggressive,” said Jennifer Leavey, assistant dean for faculty mentoring in the College of Sciences and principal academic professional in the School of Biological Sciences.
Leavey also serves as director for Georgia Tech’s Urban Honey Bee Project. She offers a few tips on how to identify the myriad arthropoda around campus and shares knowledge about each.
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