Seadragon Aquarium Project Helps Texas A&M Graduate Students Gain Real-World Research Skills

Story by Megan Bennett, VMBS Marketing & Communications

Learning how to conduct research can be a difficult process, especially for students interested in a complex field like metagenomics. In a unique graduate-level course at the Texas A&M College of Veterinary Medicine & Biomedical Sciences (VMBS), however, graduate students are not only learning the ins and outs of research but are also using that experience to make a real-world impact.

Each spring semester, graduate students enrolled in the Metagenomics Sequencing Informatics (VLCS 606) class — taught by Dr. Lee Pinnell, a research assistant professor with the VMBS’  Veterinary Education, Research, & Outreach program in Canyon — learn how to process huge quantities of complex data, turning individual “pieces” of data into a complete story with applicable research findings. 

“The general concept for the class was based on one that my Ph.D. supervisor taught in which he gave the class real data to process, not mock data,” Pinnell said. “Using a data set that’s good enough to get published is really important because it lets students see their work making a real impact.”

For the seven students enrolled in spring 2024, the data also led them to a discovery they did not expect — one that could have a major impact on how aquarists around the world manage saltwater tanks. 

Their project, which studied the microbial community in a saltwater weedy seadragon exhibit at Chicago’s Shedd Aquarium, was recently published in the journal Animals.

“One reason I developed the class the way I did was to try to ensure students don’t spend time doing a bunch of things that aren’t going to be useful for their actual research,” Pinnell said. “The processes and techniques we use are widely translatable and can be applied to almost anything they end up doing. Microbes are everywhere and they play an important role in a lot of different research disciplines.”

Diving Into The Data

Metagenomics is the study of microbial communities using DNA extracted from environmental samples.

Pinnell and his students were granted access to certain data sets collected through Shedd’s Aquarium Microbiome Project — a research initiative aimed at understanding the microbiome’s role in animal and ecosystem health within a controlled aquarium ecosystem — because Pinnell had previously worked as a postdoctoral scientist at Shedd. 


The newly commissioned saltwater habitat studied by Pinnell’s class

The spring 2024 class project examined how the microbiome in a saltwater aquarium develops in a newly commissioned habitat and how it responds when other animals are introduced.

“Before you can put fish in a new habitat, you have to kickstart the microbial community so that it can break down — or oxidize — ammonia and keep it to a level that’s not toxic, a process called nitrification,” Pinnell said. “People running aquariums do it all the time, even if they may not fully understand what’s going on at the microbial level — they know it’s working, but they don’t really know why.”

Two of the major microbial players in this process are ammonia-oxidizing bacteria and archaea, two distinct types of microbes that can perform a similar role. Aquarium scientists have long believed that bacteria are the main drivers of nitrification, but the data analyzed in Pinnell’s class shows that archaea played a bigger role.

“In this saltwater system, the archaea were overwhelmingly dominant compared to the bacteria. We didn’t expect that,” he said. “The importance of this is that if you’re starting a home aquarium, you typically buy little containers of bacteria to kickstart the microbial community, but based on what we found, archaea might actually be more important, at least for this kind of saltwater system.”

Pinnell plans to continue the collaboration with Shedd as long as new data is available, providing students with new, interesting topics to study each year. In spring 2025, for example, the class studied how microbes in Shedd’s penguin exhibit were impacted by the aquarium’s disinfection techniques.

Success Stories

Aquariums are just one of many places where microbes have a big impact. Microbial communities can span anything from viruses causing infectious diseases to bacteria that clean up oil spills, making metagenomics a diverse field that can impact people, animals, and the environment. 

The concepts and techniques covered in Pinnell’s class provide a foundation for students to use no matter what direction their studies and careers take them.

“The interpretation of the results is, in this case, aquarium-specific, but the process itself is widely applicable,” Pinnell said. “I come from a marine biology background, and while I don’t really work in that area very much anymore, I still use the same techniques. Hopefully, the students can take what they’ve done in class and easily apply it to their other research questions.”

Tiana Sanders, a second-year Ph.D. student and veterinary parasitology resident, found a lot of value in the class and how it helped prepare her for her future career. She also appreciated the hands-on experience she got working with advanced computing resources provided by Texas A&M High Performance Research Computing.

“Dr. Pinnell’s class has been instrumental in shaping both my current and future research endeavors,” Sanders said. “The hands-on experience has become essential for my own data analysis workflow. The skills and knowledge I gained have directly contributed to my growth as a researcher and will continue to support my academic and professional pursuits.”

Likewise, Ilana Mosley, a fourth-year biomedical sciences Ph.D. student interested in infectious diseases, is already applying the skills she learned in Pinnell’s class to her graduate research work.

“Even though the class was focused on microbiome analysis, those same sorts of techniques can be applied to a lot of other things,” Mosley said. “For example, my lab is interested in using those same next-gen sequencing approaches to characterize mosquito communities and other vectors that could potentially spread diseases.”

Both Sanders and Mosley also enjoyed experiencing the process of assembling a paper and seeing it published.

“Microbiome analysis is very data-heavy and uses a lot of methods,” Mosley said. “Getting the experience of putting that together in a concise way was great, and I’ve been able to apply it to my own work already.”

This story by Megan Bennett originally appeared on VMBS News.