Intern and Postdoc Partner to Discover Dark Ocean Viruses

When one thinks about viruses, what comes to the mind are probably the deadly viruses, like Covid-19, that infect humans. But viruses are everywhere, they infect every form of life, and the vast majority of viruses in the ocean at least are harmless to humans. Unsurprisingly, then, they remain one of the most enigmatic and challenging entities to study in microbiology.

This summer, a Bigelow Laboratory postdoc joined forces with an undergraduate intern to take on that challenge.

Solomon DeMello and Alaina Weinheimer, a postdoctoral fellow in the Single Cell Genomics Center, spent the summer testing new DNA sequencing methods and developing preliminary data on the viral community living in the remote “dark ocean.”

Bigelow Laboratory’s summer interns, funded largely by the National Science Foundation, come from all over the country and spend 10 weeks working with institute scientists on independent, often totally novel, research projects. For many, like DeMello, it’s their first research experience outside of a classroom.

DeMello is originally from Iowa but, in high school, he had the unique opportunity to take a marine science course, working in a small classroom aquarium. It ignited a love of the ocean that inspired him to move almost 1,500 miles to Maine.

While at Southern Maine Community College, DeMello participated in a course called SEA-PHAGES. Hosted by institutions around the world, the program provides hands-on education in microbiology by enabling students to look for new viruses in the environment, teaching how to describe and analyze them, and helping them upload their findings to an international database. Around the same time, he learned about another experiential learning opportunity: Bigelow Laboratory’s summer internship program.

“That project was my first introduction to viruses, but I knew I was interested in the ocean and in bioinformatics,” DeMello said. “So, when I saw that Alaina was looking for an intern for a bioinformatics project about phages, it was a perfect fit.”

The Single Cell Genomics Center is one of the first and most advanced centers for sequencing DNA from individual microbial cells. Weinheimer and colleagues at SCGC have been working on a new tool to increase the quantity and quality of genomes they can construct — of cells, extracellular DNA, and viruses — from a sample of seawater.

Weinheimer’s goal this summer was to scale up and test that new method in a new environment: the deep parts of the ocean, 10,000 feet below the surface far beyond the reach of light.

“We’ve worked on this method with water samples from the surface, where the microbial community is better characterized,” she said. “But, for this project, we wanted to test it with samples from an underexplored environment to get that sanity check that it works and start to tease apart what’s going on down there, especially when it comes to viruses.”

In reality, the researchers needed a sanity check several times throughout the summer.

“The biggest challenge with this work is that we’re looking at this data that is full of novel genomes that no one has sequenced before,” DeMello said. “There’s not a lot of reference data to understand what you’re looking at, and you find a lot of unknown stuff in these samples.”

In fact, they eventually had to overhaul their approach for classifying cellular versus viral DNA — even though that original approach, Weinheimer points out, worked for surface ocean samples, highlighting the importance of testing new methods in lots of different environments.

That said, DeMello says one of the most exciting parts of the project was seeing similarities between the genes they sequenced and the DNA of viruses that have been identified in other, totally different environments, which, he says, provides interesting insight into the evolutionary history of viruses as a whole.

“That’s why this work is so important. Producing more genomes from this environment expands our databases and gives us more information,” Weinheimer said. “Even if we can’t precisely identify everything in our samples, we’ll have genomes so when we sequence something in the future that looks similar, we can say something about its origin.”

DeMello, who is now majoring in biochemistry at University of Southern Maine, says the project solidified his interests and desire to eventually go to graduate school.

“This experience really inspired me to keep working on this, to keep looking for these viruses to help create better reference data,” DeMello said. “It feels a lot more realistic to do that now that I’ve done a true research internship and learned all these new skills.”

For Weinheimer, the experience was equally informative for her long-term career plans.

“This was a great opportunity to learn how to manage a project and move it forward efficiently while also leading another person and helping them grow in their career,” she said. “I also learned so much from Solomon who came in with his own knowledge of phages, which we used to make the project better.”

Weinheimer was one of several postdocs working with undergraduates this summer; others are now mentoring students through the Sea Change Semester program this fall. The institute actually awards the Rodney L. White Fellowship every summer to provide dedicated salary support for a postdoc to bring on an intern and spin up an independent project. Their experiences highlight the important role these researchers play at Bigelow Laboratory as mentors — and the value of the institute’s education programs for their professional development at this critical juncture in their careers.

“Mentoring an intern is a nice preview of what my career could look like if I continued in an academic position, but the skill set in mentoring I’ve built will be valuable in any future position,” Weinheimer said. “It’s just a really meaningful experience overall.”