Scripps Student Spotlight: James Riddell

Recent graduate of marine biology undergrad program helps identify viruses using bioinformatics tools from hydrothermal vents

James Riddell recently finished his undergraduate education at Scripps Institution of Oceanography at the University of California San Diego, where he received his Bachelor’s of Science in marine biology with a minor in data science. In light of the COVID-19 pandemic, Riddell had been remotely learning from his hometown of Ann Arbor, Mich. until this past spring, when he was able to join the lab of Scripps marine biologist Lisa Ziegler in person.  


explorations now: Why did you choose to attend Scripps?

James Riddell: Scripps seemed like the perfect place to explore the possibilities of a marine science research career, with its wide range of faculty who are happy to mentor undergraduates. All of this was possible while also having access to UC San Diego’s other amazing undergraduate-focused departments, such as the Halıcıoğlu Data Science Institute—the university’s data science department.


en: What are you researching at Scripps?

JR: In the Ziegler Lab, I’m identifying viruses from deep-sea hydrothermal vents using a variety of bioinformatics tools. Hydrothermal vents are unique deep-sea environments that are characterized by extreme temperatures and high hydrostatic pressure, and are able to harbor uniquely adapted microbial communities.

Microbes are fundamentally constrained by viruses, which can account for twenty to forty percent of bacterial mortality each day, reprogram host metabolism during infection, and mediate horizontal gene transfer in their hosts. Despite the crucial role viruses play in microbial processes, only eight bacteriophages (viruses that can infect bacteria) have been fully characterized so far from hydrothermal vent samples. By identifying more viruses from hydrothermal vents, we are able to figure out who is there and what they are doing, as well as understand how viruses are continuing to replicate, infect, and influence the microbial communities of these extreme environments.


Selfie on research vessel
Sampling for microbes aboard the Inland Seas in Lake Michigan.

en: How did you become interested in science and your field of study?

JR: I have always liked thinking about the rules of our universe, and continue to have a deep desire to understand why things happen the way they do and how they are changing. I developed a love for marine science after participating in the National Ocean Sciences Bowl competitions as a high school student, and wanted to pursue an undergraduate degree in marine biology. During college, I became fascinated with a computer’s power to characterize entire microbial communities from environmental DNA samples. I also became more involved in the climate movement, drawn towards researching how anthropogenic climate change would affect the microbial communities that largely control the cycling of greenhouse gases and essential nutrients. Currently, I’m interested in exploring how phage therapy, the treatment of bacterial infections through use of viruses, can be used to restore disrupted microbiomes in humans, soils, lakes, oceans, and other animals.


en: What’s life like as a Scripps student? Describe a typical day.

JR: On a typical day I would attend lectures at UC San Diego, then catch the bus down to Scripps. I would spend a few hours in the lab, then head to my classes at Scripps. In the afternoons, I would study pretty much every day in either my apartment, Geisel Library, or the Eckart Building. After making dinner, I would go watch the sunset at the Torrey Pines Gliderport, then attend meetings for the Green New Deal at UC San Diego, dance workshops, or on-campus concerts. 

In my last quarter at UC San Diego, I made an effort to enjoy Scripps as much as possible. I would wake up at the crack of dawn, grab my wetsuit, and catch the first bus to Scripps. Then I would get my surfboard from the lab and surf by Scripps Pier until I was completely winded (which is usually only forty minutes). I would then head back home, take a nice warm shower, and have a filling breakfast before hopping on my computer and debugging whichever coding scripts errored out the night before. In between working, I would attend classes online and go to the gym. In the evenings, I would spend time with my friends and cross things off my San Diego bucket list.


en: What’s the most exciting thing about your work (in the field or in the lab)?

JR: The most exciting thing is performing exploratory data analysis after mining a dataset for viruses. You never quite know what you’re going to get, and it’s fun to sort through and look at the distributions of viruses and what they are doing in an ecosystem. You can even pick out specific viruses and look at what proteins they are likely transcribing! It’s also exciting to compare the taxonomic and functional diversity of viruses across ecosystems and figure out why they are different or similar.


en: Are there any role models or mentors who have helped you along the way?

JR: By far my biggest role model has been Morgan Lindback, a PhD candidate at the University of Michigan. Over the summers, I am a research assistant in microbial ecologist Melissa Duhaime’s lab at University of Michigan, and Morgan has been mentoring me for the past three years. In addition to all of the science, Morgan has taught me how to do research in a sustainable way that reflects my values.


en: What are some of the challenges you face as a student?

JR: It has been very challenging dealing with the pandemic, family health crises, collapse of the biosphere, the climate crisis, the rise of misinformation, and senseless killings of minorities and children. It often feels like nothing I’m doing matters. It’s become extremely important for me to make enough time to eat, sleep, and exercise regularly so that I have enough energy to help others. It has also been healing to surround myself with people who care about similar issues and work towards a more equitable and sustainable future with organizations.


en: What are your plans post-Scripps?

JR: Now that I’ve completed my undergraduate education at UC San Diego and Scripps, I will be pursuing a PhD in microbiology at the Ohio State University this upcoming fall.

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