Grad Student Johnson Uses Amino Acids to Demystify Salt Marsh Food Webs

Jessica presents her research at the 2016 Gulf of Mexico Oil Spill & Ecosystem Science conference in Tampa, FL. (Photo by Michael Polito)

Jessica presents her research at the 2016 Gulf of Mexico Oil Spill & Ecosystem Science conference in Tampa, FL. (Photo by Michael Polito)

Salt marshes support commercially and culturally important species and are often subject to natural and human-caused stressors. Gaps in our knowledge of salt marsh food webs made management and restoration decisions difficult after the Deepwater Horizon spill. Jessica Johnson helps fill this gap using novel chemical analysis techniques to describe the diets of salt marsh organisms and trace how energy flows through the marsh ecosystem food web. Her work may help inform decision making if a future spill occurs.

Jessica is a masters’ student with the Louisiana State University (LSU) Department of Oceanography and Coastal Sciences and a GoMRI Scholar with the Coastal Waters Consortium II (CWC II).

Her Path

Jessica participated in the Williams-Mystic Maritime Studies program in 2010 while completing a biology undergraduate degree at Tufts University. One of the program’s activities placed her at the Louisiana Universities Marine Consortium to gain experience working with salt marshes and the coastal environment. The Deepwater Horizon oil spill occurred one month after she returned to Connecticut. “The spill had a very strong impact on me because I had just studied coastal issues in the spill area and knew how much it would affect the coastal environment,” said Jessica.

Jessica graduated from Tufts and worked in a Massachusetts genomics laboratory to gain practical research experience before pursuing graduate school. Although her position did not involve marine ecology, she kept herself close to the water through volunteer work for the Charles River Watershed Association and an internship with the New England Aquarium. While she worked, the oil spill was constantly at the back of her mind, and she wondered how that event had changed the coastal community in Louisiana.

Jessica saw an advertisement in 2015 for a graduate research position investigating Deepwater Horizon impacts on coastal salt marsh ecology and knew she had to pursue it. She contacted Dr. Michael Polito at LSU to learn more about the position. He encouraged her to apply for the Oceanography and Coastal Sciences graduate program, and Jessica moved to Louisiana in August 2015 to begin her CWC research.

Her Work

Jessica characterizes flow of energy between producers (such as plants, bacteria, and algae) and consumers (such as crabs and birds) from oiled and unoiled marshes using trophic biomarkers called stable isotopes. Basic analyses can determine stable isotope ratios in an organism’s tissues, which becomes a bulk geochemical signature deriving from all the fats, sugars, and proteins that the organism consumed. However, Jessica uses a compound-specific stable isotope analysis technique, which ecologists have just begun exploring for salt marsh research application, to identify the signatures of individual essential amino acids within an organism’s tissue proteins. She then identifies signatures from the food web base that show up in consumers farther up the food chain and maps how energy flows through the food web.

Jessica explains that the concept behind using stable isotopes for dietary research is “you are what you eat.” Producers can make essential amino acids themselves, but consumers cannot and must ingest them through their diets. This means that the essential amino acids found in consumer tissues ultimately come from the plant or algae source that made them. Because the geochemical signatures of amino acids do not change as they move up the food web, scientists can use this technique to observe how energy flows through a food web and whether a disturbance has altered that food web.

While Jessica can compare the energy flow of food webs in oiled and unoiled salt marshes, the lack of data pre-Deepwater Horizon makes it difficult to describe spill impacts confidently. Instead, her research helps establish a picture of what the marshes currently look like and provides responders with a clearer understanding of the way future spills may spread through and impact marsh ecosystems. “Our finished research will describe the ecology and food web of this system far better than anyone understood prior to the oil spill,” said Jessica. “I think that’s a common theme for GoMRI overall – people filling the knowledge gap they didn’t know existed until the oil spill happened.”

Her Learning

Jessica traces the flow of energy through the marsh ecosystem food web. (Provided by CWC)

Jessica traces the flow of energy through the marsh ecosystem food web. (Provided by CWC)

Jessica’s research experiences taught her that analyzing fieldwork is sometimes more difficult than conducting laboratory experiments. Although the method behind her stable isotope analyses was straightforward, interpreting her results properly and responsibly was more complicated than she anticipated. “You have to be very careful with how you interpret what you measure in the field and make sure you understand what factors are driving the patterns that you see,” explained Jessica. “You have to be very rigorous in your experimental design and the conclusions you make from your research.”

Jessica’s first semester was with CWC, and it included her first experience conducting fieldwork and participating in a group workshop to build a marsh food web model using only existing literature. She initially expected to work only with her advisor on the project, but these early experiences show her how important collaboration is to scientific research. “This is a very unique organization in that we’re all here for the same basic purpose, but we’re also all coming from different places and going different places,” she said. “I was lucky that, in my very first semester, I got to be part of a team and not just work alone.”

Her Future

Jessica will begin a Ph.D. program studying stable isotope ratios in human diets at the University of Alaska Fairbanks next spring. Her research will investigate how the techniques used in her salt marsh research can apply to more clearly and objectively describe the human diet.

She believes that a willingness to take risks is the most important trait for students considering a scientific career. “Approaching a potential advisor can be very scary, especially when you’re young, but scientists want to train people who are enthusiastic and dedicated to the science,” she said. “Don’t be afraid to show your interest, that’s how you get your foot in the door.” She also emphasized that students shouldn’t be discouraged if their risks result in failure. “If you contact someone and they’re not interested, contact ten people – it will happen. Not everyone ends up there the same way, as there are many paths to science.”

Praise for Jessica

Polito was impressed initially with Jessica’s drive, maturity, and level of interest in the project. He was a new professor looking for a student who could take charge and hit the ground running. Jessica exceeded his expectations and took on an ambitious thesis project despite having little experience with isotopes. Two years later, Polito describes her as an expert in stable isotope analysis and says that she often teaches him new things about the technique.

“She really dug into the literature, learned the nitty-gritty details of the methodology, and came out the other end with a strong and exciting thesis that pushes the techniques to their limits,” he said. “This is a really powerful and novel technique, and she’s using it in the salt marsh where it’s really never been done at this level before.” Polito credited the project’s advancement on Jessica and her hard work and talent, “She’s going to have a bright future in sciences, and I’ll be sad to see her go when she graduates.”

The GoMRI community embraces bright and dedicated students like Jessica Johnson and their important contributions. The GoMRI 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 CWC website to learn more about their work.


The Gulf of Mexico Research Initiative (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

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