His research focuses on harmful algal blooms (HABs) caused by cyanobacteria, or blue-green algae, and how they acquire and share nitrogen, a key nutrient needed by all life. These freshwater HABs can produce toxins that threaten wildlife, drinking water and recreational areas worldwide.

Shannon is studying how cyanobacteria pull nitrogen from the atmosphere and make it available to other algae. Some cyanobacteria can “fix” atmospheric nitrogen, converting it into a form that can be used by living organisms. This process not only fuels their own growth but may also support other algal species in the bloom. Because HABs often consist of several interacting species, understanding how nitrogen moves between them may reveal new insights into how these blooms form and persist in nature.

He is also exploring the role of vitamin B1 and a natural toxin in this nutrient exchange. Vitamin B1, or thiamin, is essential for all microorganisms, including algae. He will test how the availability of thiamin, and a naturally occurring compound that interferes with thiamin use, affects nitrogen transfer between species. This could shed light on hidden chemical interactions that influence the development and toxicity of HABs.

Shannon earned both his bachelor's degree (2020) and master’s (2022) in microbiology from Oregon State. He is now pursuing his Ph.D. as a member of the Colwell Lab in the College of Earth, Ocean and Atmospheric Sciences.

In addition to the DOE award, Shannon was selected as Oregon’s young ambassador for the American Society for Microbiology in 2024.

Ostroverkhova’s research group works on low-cost, organic materials for optoelectronic applications, such as solar cells. Her contribution to the exhibit is part of a collaborative scientific effort with colleagues in OSU’s colleges of Forestry and Engineering. Together, they’re investigating fungi-derived pigments including xylindein, a highly durable pigment, used by artists for hundreds of years, as a promising possibility as a semiconductor material.

Xylindein, a pigment secreted by two types of wood-eating fungi, stains wood a blue-green color, which artists have used for centuries. The pigment is so stable that art made more than 500 years ago still retains the color. It has held up against prolonged exposure to heat, ultraviolet light and electrical stress.

“If something has sat on a church ceiling for 500 years and hasn’t degraded, I want to know why,” she said.

Maude David, associate professor of microbiology, works at the intersection of computer science and microbiome research. She contributed ideas and reflections about artificial intelligence, energy consumption and data ethics. She sees the abstract, immersive nature of the exhibit as a powerful tool for contemplation.

“AI is needed and it’s useful. In fact, I use it for my research. But what is the cost for our children?” she said. “More than 10% of the energy consumption in Oregon is just for data centers.”

Her wish for visitors is simple: stop and think. From pondering data storage’s environmental footprint to engaging with poetic critiques of AI culture, each part of the exhibit encourages personal reflection.

“We are the last generation where some of us grew up without a phone. My daughter’s pretending to make phone calls at three years old,” she said. “AI is difficult to see but technology is in the background of a lot of things we do.”

Microbiome of the deep sea

Beyond her hands-on lab work, David is pioneering artificial intelligence applications in microbiome research. By training machine learning models on massive datasets, her team is discovering how to predict patterns and identify microbial signatures linked to different conditions.

Her AI approach functions similarly to how a person might read thousands of books to develop a deep understanding of a subject before applying that knowledge to something new. Instead of analyzing each microbiome sample from scratch, her team feeds AI models vast amounts of microbial sequencing data, allowing the system to learn and recognize relationships between the different microbes. These models can then be applied to help classify conditions such as inflammatory bowel disease or colorectal cancer with greater accuracy.

“It is awesome, because the model can remember relationships that us humans might not. It’s finding these complex patterns,” David said.

One of the major challenges in microbiome research is the sheer volume of data involved. Each individual has a unique microbiome comprising thousands of different microbial species, each interacting in complex ways. Traditional methods of analyzing these communities can be time-consuming and require extensive resources. AI provides a way to quickly process and interpret large datasets, identifying patterns that can reveal valuable insights.

Her latest National Science Foundation study continues to push the limits of what AI can do. With a $540K grant, David is applying deep learning to analyze oceanic microbial ecosystems, an extension of her expertise in microbiome research.

The deep sea is a crucial, yet poorly understood driver of global biogeochemical cycles, the movement of essential elements like methane and nitrogen. These cycles regulate ecosystem function, influence climate and support life.

“We are looking at microbes in the ocean and researching how we can use AI to discover what role unknown genes play in methane seeps off the coast of Oregon and Washington,” she said.

Methane seep habitats, areas where methane gas escapes from the sea floor, are unique, diverse areas nourished by methane-consuming microbes. However, many of the genes involved in these deep-sea cycles remain unidentified, limiting our understanding of how these ecosystems function and their impact on global biogeochemical processes.

To analyze these complex environments, researchers will develop two AI models designed to decode gene functions. The first model will categorize genes into pathways by studying how they appear together in microbial communities. The second will use generative AI to predict the functions of unknown genes based on protein sequences and text-based data. Together, these models will help scientists identify genes responsible for each of the cycles identified.

The main outcome will be a scalable approach to artificial intelligence that will advance key questions in earth system science. Understanding the genetic mechanisms behind biogeochemical processes is crucial for predicting how ocean ecosystems respond to environmental changes.

The results of this study will include exhibits by artists involved in the research as well as a documentary about how AI can harness big data to help advance the understanding of earth systems.

As science continues to reveal the hidden influence of the microbiome, one thing is clear: critical solutions lie in understanding the powerful role microorganisms play in our bodies and our environment. David’s research has us on the right path to new understandings.

Insecticide resistance in spotted-winged drosophila

Geneticist Alysia Vrailas-Mortimer's project addresses the significant agricultural threat posed by spotted-winged drosophila (SWD), an invasive pest species. The research aims to advance understanding of the genetic basis and evolution of insecticide resistance in these pest populations through experimental work, genetic techniques and mechanistic mathematical modeling. The project involves collaboration with experts from UC Davis and focuses on developing sustainable control methods. Directly connected to the needs of the Oregon agricultural community, this project is a prime example of OSU’s strong community engagement initiatives as a land grant institution. By learning more about the mechanisms of insecticide resistance in spotted-winged drosophila, growers will be better able to plan and prioritize their insecticide applications to mitigate resistance.

Oregon State Collaborators
Alysia Vrailas Mortimer, Biochemistry & Biophysics
Swati Patel, Mathematics
Serhan Mermer, Environmental and Molecular Toxicology (College of Agricultural Sciences)

Analytical Tools to Understand Ecological Communities

Statistician Yuan Jiang’s SciRIS project aims to create novel analytical tools for assessing how organisms in complex ecological communities like microbes and parasites interact and affect each other over time. The research will leverage long-term community datasets from wild vertebrate host populations with improved data techniques that allow these large complex data sets to be analyzed more efficiently and with environmental conditions factored in. In addition to improve our ecological understanding of these communities, Jiang's project seeks to extend the accessibility of these analytical tools to diverse scientific audiences through summer camps, workshops and online tutorials. The project will also involve collaboration with colleagues and students at the Universidad of San Francisco de Quito in Ecuador to build capacity in data analytics.

Oregon State Collaborators
Yuan Jiang, Statistics
Lan Xue, Statistics
Anna Jolles, Integrative Biology
Claire Couch, Fisheries, Wildlife and Conservation Sciences (College of Agricultural Sciences)

Unlocking the potential of seaweed

Algal physiologist James Fox’s project explores the chemical composition and potential applications of Pacific Dulse, a protein-rich seaweed native to the Pacific coastline. The team will create a special growth chamber to cultivate seaweed on land under controlled conditions. This allows researchers to maximize the production of important compounds found in Pacific Dulse, which can be used in nutrition and medicine. The project also emphasizes community outreach and inclusive excellence by engaging diverse student populations and partnering with outreach programs. Additionally, the project will investigate the impact of different processing methods on the nutritional quality of seaweed extracts.

Oregon State Collaborators
James Fox, Microbiology
Myriam Cotten, Biochemistry and Biophysics
Ford Evans, Hatfield Marine Science Center
Evan Forsythe, Integrative Biology
Scott Geddes, Chemistry Program Coordinator OSU-Cascades
Jung Jwon, Department of Food Science & Technology (College of Agricultural Sciences)
Christopher Suffridge, Microbiology

These projects highlight the innovative and impactful research being conducted by the 2025 SciRIS awardees. Each project not only advances scientific knowledge by also emphasizes collaboration, community engagement and inclusive excellence.

From the lab to the field

European foulbrood disease (EFD) targets and kills young larvae before they reach adulthood. After being fed infecting brood food, the larvae turn from pearly white to brown, forming a rubbery scale. The name “foulbrood” refers to the sour, rank and rotting smell that can result from secondary bacterial infections that co-occur.

Beekeepers in Oregon on average pollinate about five different crops in a year. If the colonies are weakened from EFD this means less pollination, worrying blueberry and almond growers.

Oregon grew 158 million pounds of blueberries in 2022, ranking it in the top 10 producing states in the U.S., according to the U.S. Department of Agriculture Statistics Service. Researching how to keep hives safe has become a priority for local scientists.

Transitioning from studying the gut-brain axis in humans to the gut microbiota of honey bees, wasn’t a huge challenge for David. Her main research interest focuses on understanding how microbes can impact our behavior, specifically in Autism Spectrum Disorder and Anxiety.

The human microbiota is highly complex. Honey bees, on the other hand, are the opposite.

“The microbiology part is normal. I’ve done that before. What I love about bees is that you could say the gut microbiota could be considered a lot simpler than the human ones. And that makes it fun because you can study this a little bit more in-depth. It’s an ideal system to study,” David said.

A passionate Ph.D. student roped her into the world of bees and led her to Ramesh Sagili, a professor in the Department of Horticulture and EFD project director.

The agent of EFD is an anaerobic bacteria, meaning it does not grow well when oxygen is present. In humans, these bacteria are most commonly found in the gastrointestinal tract. The research team needed someone who could grow anaerobic bacteria in the lab – something David is familiar with.

“This project is very transdisciplinary. There are people who monitor the bee houses in the field and people like me who are more on the microbiology side of things. There is also an economist on the project,” she said. “I could tell you a lot about the bacteria, I could study this genome well, but I really need the field researchers who collect the data and provide a comprehensive story about the field samplings.”

The four-year project has several components. Researchers will follow honey bee hives as they are transported by commercial beekeepers to pollinate almonds and then blueberries across Washington, Oregon, California and Mississippi. They’ll tag more than 1,500 hives for ongoing observation, which includes checking the frames for signs of foulbrood, estimating colony populations and surveying the microbiota of bees and larvae–the last step is where David comes in.

"As a public land-grant university, we need to build this project and respond to the needs of people in the state.”

Researchers have more questions than answers about European foulbrood disease. How does the disease survive between outbreaks? Does it hibernate in the hive? How does each genetic variation differ? What are the best mitigation strategies?

"Of course, because it’s a bacteria, people try to pour antibiotics to treat it. But, as we all know: one, the bacteria is likely to eventually be resistant and two, it’s not great for everything else around it," David said.

The second and third year of the project will be focused on mitigation strategies. David and her collaborator will be testing a new novel probiotic that has shown promise for tackling EFB in the laboratory. After testing in a controlled environment, they will test the probiotic in the field.

Understanding the genetic variation of the disease is important because pinpointing if a specific strain can better survive winter, develop first, or figuring out which one is the most lethal would help with management.

“Right now, colonies management does not really exist. Our objective is to explain a little bit of everything we are doing to the beekeepers and try to deliver transparent knowledge,” she said.

The team is passionate about connecting with local stakeholders who face an uncertain financial future due to EFB. “It’s important that we keep in touch with the needs of the state. As a public land-grant university, we need to build this project and respond to the needs of people in the state.”

“Medical schools are set up so that you can just call down and have the medium made for you because they were organized for that kind of stuff,” Leong said. It turns out that working in higher education was different. “I remember struggling because I had never made media before. I had to make it myself at Corvallis,” she said.

Media is a substance typically put on Petri dishes to provide nutrients to microorganisms and help them grow. Leong enforced sterile conditions to make the lab a safe and successful environment. But it wasn’t easy.

Four decades ago, research techniques looked very different. “In California, we had Petri dishes and plastic growth chambers that you threw away when you were done. I came to Corvallis and saw they were using glass bottles instead. It was just different,” she said.

Leong challenged her graduate students to make enzymes and other materials from scratch. Everyone learned how to manually analyze samples–a notably more difficult task before the advent of automated gene sequencers.

Leong’s lab used DNA techniques to detect evidence of endogenous retroviruses in fresh placentas soon after women gave birth in the hospital. For Leong, this meant transporting placentas to the lab at 3 or 4 a.m. with her sleeping daughter in her arms.

“If I didn’t have those students and a really supportive Chair, I don’t know if I would have survived,” she said.

The long hours and enthusiasm for virus research did not go unnoticed. From gigantic genomes to viruses with only a limited set of genes, the research opportunities are endless. “You know what I find fascinating about a virus?” Leong said. “You can do all kinds of things with five genes and if you want to use them to begin to understand how the cell works, therein lies a whole wealth of studies you can do.”

Lethal disease leads to uncharted waters

Fast forward to the 1980s, when a sudden virus rocked the Pacific Northwest. Millions of fish suddenly dropped dead in the Columbia River from the Infectious Hematopoietic Necrosis Virus (IHNV), a disease researchers knew little about. Mysteriously enough, the virus only affected steelhead trout and salmon, leaving other fish unharmed.

Every year, salmon and trout frantically traverse the Columbia River, racing upstream and back to their birthplace. There, they spawn offspring that eat and live their busy lives downstream.

This sudden increase in deaths caused a serious problem resulting in millions of dollars in losses annually in the U.S. If these die-offs continued, even non-seafood lovers would notice the impact on the ecosystem.

The Columbia River serves as the largest concentration of hydroelectric power in the U.S., generating 40% of the total hydroelectric generation in 2012. However, there’s a catch—the fish need to succeed.

“The movement of water over those dams along the Columbia River is controlled by the salmon and their return, so the generation of power is an important component,” Leong said.

To preserve the ecosystem, one strategy is to raise more fish to make this journey. In the 1980s, the cost to raise one Chinook salmon capable of surviving the trip was approximately $670. “The cost is a tax on all of us that we pay for in many respects. And it’s a creature that we need to preserve,” she said.

Salmon not returning home has monumental ecological consequences. The entire ecosystem relies on the successful movement of fish back and forth along the river. The river’s health and vitality are sustained by what the salmon consume and their activity, impacting energy usage, food availability, species conservation, and overall ecosystem health.

For Leong, this presented a new avenue for exploration and opportunity. Through this research, she helped discover a new genus of the virus, new treatments, and a recombinant DNA vaccine for salmon.

She didn’t do this alone. Collaborating with John Fryer, the Chairman of Microbiology, she helped found the Center for Salmon Disease Research at Oregon State, where the first work on vaccines for fish took place. At the time, there was no other facility of this type and complexity in the county – specifically the clean water, disease-free conditions, and quarantine capabilities. Finding vaccines and other solutions for fish diseases continues at the center to this day.

After spending more than 25 years at Oregon State, Leong rose through the ranks. When named Distinguished Professor, her jaw dropped and she nearly fell off her seat at the faculty meeting.

She proceeded to serve on Search Committees for University Presidents, assumed roles on National Committees and took on various additional responsibilities.

Leong shared her expertise globally, presenting her work to professionals worldwide, including the European Fish Association in Spain and aquaculture farms in Japan, Norway, China, and Chile. Due to limited resources, some of these farms practiced diverse ways to treat fish diseases.

“Salmon lice is a huge problem, and they couldn’t use some of the anti-lice compounds,” she said. Given that some of the salmon were raised for human consumption, alternative measures were sought. “Sometimes they would bring out a bag of rotting onions from the tank because they were hoping it would keep the lice away. It was the only thing they had at the time.”

A vaccine could change that. Numerous farms sought to develop and use antiviral vaccines for their struggling marine life, which Leong’s work made possible.

Moving forward and across the ocean

After her time at Oregon State, she returned to Hawaii to help take care of her family, including her now 101-year-old mother and 103-year-old father. Departing from Oregon State meant she had to drop her virology research.

She landed a new position as director of the Marine Institute at the University of Hawaii at Manoa. The problem was she is a microbiologist – not a marine biologist.

When she arrived, the lab needed a microbiology background in aquaculture, especially in fish rearing and coral disease research. With 17 other faculty members, Leong led the Hawaii Institute of Marine Biology, including more than 50 graduate students.

Despite being an ocean away, she aimed to maintain her strong Oregon roots. “I used my own funds to bring some of the faculty over. I tried very hard to keep those friendships very strong because I didn’t want to leave them.”

Leong's leadership roles grew including serving as the chairman of the Board of Directors for the Center for Tropical and Subtropical Aquaculture, the president of the National Association of Marine Laboratories, and on the executive secretariat for the National Advisory Committee on Development and Assessment of Climate. When she retired, she thought about stopping science but when her friends kept calling her up to edit new books, she couldn’t resist.

When recalling her wild water adventures, she offers advice for aspiring scientists. “When I was young, I wish I knew to choose subjects and people not because they make you feel good, but because they are doing wonderful things for science and society,” Leong said. “Look to the future and decide what it is that you want, short and long-term, and then make the decision.”

Currently, she enjoys painting, playing piano, growing tomatoes, embarking on boat trips to Indonesia, and engaging in things she didn’t have time for before. Not to mention creating more memories with her husband in a marriage of 57 years and counting.

Even though many years have come and gone, she doesn’t forget the people who supported her through the struggles and the triumphs.

“I grew up as a scientist, teacher, and communicator at Oregon State,” Leong said. “My colleagues have been supportive and the College of Science administration as well as the College of Agricultural Sciences were so helpful as I was struggling as a young professor.”