Grad Student Shin Shines Light on Oil-Degrading Microbes in Sediment

Boryoung Shin works in an anaerobic chamber at the Kostka Lab at Georgia Tech. (Photo credit: Max Kolton)

(Click to enlarge) Boryoung Shin works in an anaerobic chamber at the Kostka Lab at Georgia Tech. (Photo credit: Max Kolton)

Boryoung Shin is breaking new ground in microbiology, uncovering little known facts about an enigmatic and important species in the Gulf of Mexico.

After the Deepwater Horizon incident, certain bacteria rapidly increased and helped degrade the oil. These microbes, who consume naturally-occurring hydrocarbons, rise and fall in number as access to their preferred food supply changes. Boryoung’s research focuses on a subset of this group, the oil-eating bacteria that live deep within seafloor sediment.

A Ph.D. student in Earth and Atmospheric Sciences (EAS) at the Georgia Institute of Technology, Boryoung is a GoMRI scholar with the Deep-C consortium. She shares her journey from South Korea to the depths of the Gulf.

Her Path

When Boryoung was a high school student, she read a magazine article about deep ocean-dwelling creatures that changed her life. She became fixated on the idea of making deep sea ecology her future work. However, geography was a major hurdle as Boryoung had a difficult time locating courses that fit her needs. She explained that marine science programs can be hard to find in Korea: “It’s just not commonly studied.”

Boryoung’s persistence paid off, though, and she found an environmental marine science undergraduate program at the Hanyang University. Luckily, her next favorite subject was English. After obtaining a bachelor’s degree, she searched graduate programs at American universities to pursue her growing passion for microbial ecology. The work of Georgia Tech Professor Joel Kostka on the bacterial populations that consumed oil after the Deepwater Horizon spill impressed Boryoung. In 2012, she enrolled in the EAS Ph.D. program and, under Kostka’s direction, began research on sediment-dwelling microbes.

Her Work

The crew of the RV Weatherbird II collects sediment samples for Boryoung’s projects. Pictured from far left: Arvind Shantharam, Caroline Johansen, Ben LeBelle, Curtis Okolovitch, and Boryoung. (Photo credit: Ian MacDonald)

(Click to enlarge) The crew of the RV Weatherbird II collects sediment samples for Boryoung’s projects. Pictured from far left: Arvind Shantharam, Caroline Johansen, Ben LeBelle, Curtis Okolovitch, and Boryoung. (Photo credit: Ian MacDonald)

Oil-eating microbial communities that live in the water column and top layers of sediment need oxygen to survive. However, microbes that live deeper within Gulf sediments are anaerobic – they can live without oxygen.

Boryoung explained that oil can linger for a long time in sediment, an environment where there is little to no light or oxygen to assist degradation. The microbes she studies are one of the only means of breaking down oil once it has become buried in an anaerobic zone. To learn how these microbes operate, she cultivates Gulf sediment samples collected during a research cruise in June 2014 aboard the RV Weatherbird II. On that expedition, she collected sediment at over 1,000 meters depth for her lab work.

In the lab, she monitors these sediment-dwelling bacteria, a process that requires much patience. Anaerobic bacteria grow incredibly slowly – a year or more can pass before there is measurable activity in her cultures. Boryoung isolates these microbes, enriches them with various nutrients, and observes their community structure response. She analyzes their DNA to determine the succession of microbial groups that follows after oil exposure.

Boryoung laughs, “This process can take so long that I sometimes find myself asking, ‘What am I doing?’ I have to give myself pep talks that this is worth the wait, that it’s valuable science.”

Her results have been worth the wait. Many of these anaerobic microbial groups are not closely related to known hydrocarbon-degrading bacteria. As one of the first scientists to describe these populations, Boryoung has identified unique oil-degrading bacterial communities under sulfate- and iron-reducing conditions. Her long-term goal is to use her results to guide oil spill response efforts and uncover new potential methods for bioremediation.

Her Learning

Boryoung cultivates anaerobic bacteria populations in a Gulf of Mexico sediment sample housed at Georgia Tech. (Photo credit: Boryoung Shin)

(Click to enlarge) Boryoung cultivates anaerobic bacteria populations in a Gulf of Mexico sediment sample housed at Georgia Tech. (Photo credit: Boryoung Shin)

Boryoung’s first research cruise was more difficult than she expected. She did not sleep well and was frustrated with very limited communications on board. But she really enjoyed working with the helpful and friendly crew and research team. Overcoming these obstacles made it that much more rewarding when she successfully completed her mission. Boryoung is greatly looking forward to using her newly-acquired sea skills on an expedition this August.

As much as she enjoys fieldwork, her favorite aspect of research is the science community she has joined. “The people I meet at GoMRI conferences really inspire me,” Boryoung said, referring to the annual Gulf of Mexico Oil Spill and Ecosystem Science conferences. She explained that the researchers she has met are very supportive of one another’s work. Calling it a synergistic relationship, she said, “We help each other, share ideas, and learn from one other.”

Her Future

As Boryoung continues her research with C-IMAGE, she is considering both academic and industry jobs once she completes her Ph.D. An aspect that draws her to academia is the concept of solving problems. She encourages other young people to choose science as a career so that more researchers can work together for the benefit of the Earth and people. She also hopes to continue living in the U.S.

“I want to be a ‘real’ scientist wherever I am,” Boryoung jokes. “Seriously, I like the culture here in the United States and this is where the work is for the most part. I hope I’m privileged enough to stay.”

Praise for Boryoung

Boryoung with her cohorts at the Kostka lab. From far left: Patrick Steck, Will Overholt, Xiaoxu Sun, John C. Gaby, Boryoung Shin, Kaitlin Esson, and Joel Kostka. (Photo courtesy of Deep-C)

(Click to enlarge) Boryoung with her cohorts at the Kostka lab. From far left: Patrick Steck, Will Overholt, Xiaoxu Sun, John C. Gaby, Boryoung Shin, Kaitlin Esson, and Joel Kostka. (Photo courtesy of Deep-C)

Kostka describes Boryoung as a bright and dedicated young researcher, noting the tremendous amount of progress she has made in advancing anaerobic microbiology since she arrived at Georgia Tech. “She has the hardest job of any of my students,” said Kostka. He continued, “Hydrocarbon degrading bacteria grow very slowly under anaerobic conditions, and it usually takes Boryoung about one year to do a single experiment.” He said that Boryoung has isolated some cultures of anaerobic oil-degrading bacteria and is using molecular techniques to understand the processing of oil hydrocarbons in anaerobic sediments. Kostka also commented that aside from her academic capabilities, Boryoung is a pleasure to work with. “She nearly always has a smile on her face and a kind word for her colleagues. Her language skills are amazing, and she has embraced the American culture from the beginning of her tenure in Atlanta.” Kostka sees a bright future in science for Boryoung.

The GoMRI community embraces bright and dedicated students like Boryoung and their important contributions. The Scholars Program recognizes graduate students whose work focuses on GoMRI-funded projects and builds community for the next generation of ocean science professionals.

Visit the Deep-C website to learn more about their work.

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This research was made possible in part by a grant from BP/The Gulf of Mexico Research Initiative (GoMRI) to the Deepsea to Coast Connectivity in the Eastern Gulf of Mexico (DEEP-C) consortium.

The GoMRI is a 10-year independent research program established to study the effect, and the potential associated impact, of hydrocarbon releases on the environment and public health, as well as to develop improved spill mitigation, oil detection, characterization and remediation technologies. An independent and academic 20-member Research Board makes the funding and research direction decisions to ensure the intellectual quality, effectiveness and academic independence of the GoMRI research. All research data, findings and publications will be made publicly available. The program was established through a $500 million financial commitment from BP. For more information, visit http://gulfresearchinitiative.org/.

© Copyright 2010- 2017 Gulf of Mexico Research Initiative (GoMRI) – All Rights Reserved. Redistribution is encouraged with acknowledgement to the Gulf of Mexico Research Initiative (GoMRI). Please credit images and/or videos as done in each article. Questions? Contact web-content editor Nilde “Maggie” Dannreuther, Northern Gulf Institute, Mississippi State University (maggied@ngi.msstate.edu).