Answers in the rock pools

Bioinformatics and Honors College student Nasita Islam discovered a way to find bacteriophages in water samples — now she’s teaching her peers her methods of discovery.

A student holding a water sample kit in front of a rock pool along the James River in Richmond, V...
Bioinformatics major Nasita Islam collects a water sample from a rock pool along the James River in Richmond. Islam developed a method to isolate phages from water for a VCU Honors Summer Undergraduate Research Program project. (Tom Kojcscich, University Marketing)

Nasita Islam has made a few acquaintances during her time as a student at Virginia Commonwealth University, but none more interesting than Kyle, Phynn and Beyonphe. One important point, though — they’re microscopic. 

A third-year bioinformatics student in the Center for the Study of Biological Complexity, part of VCU Life Sciences, Islam went from a curious freshman studying bacterial viruses called bacteriophages in the Phage Discovery Lab of associate professor Allison Johnson, Ph.D., to teaching her peers a method she developed using samples from rock pools along the James River in Richmond. 

As a result, Islam has presented her work at conferences and is collaborating with Johnson on a manuscript detailing their discoveries.

Interested in genetics as a high school student but unsure of pursuing a purely medical or biological research path, Islam chose to study bioinformatics as an incoming freshman because of the bridge between computer science and biology. As with other bioinformatics students, the Phage Discovery Lab was the first step of Islam’s new major. “I didn’t know what to expect when I came into the phage lab class. And when Dr. Johnson said, ‘We’re going to be harvesting bacteriophages,’ I was like, whoa, that’s so cool.” 

Since phages outnumber all other living things on the planet, the lab provides students with an opportunity to understand their unique diversity and evolution characteristics. Johnson believes the lab allows students to gain experience in problem solving and persistence. “My perspective is that in this class, I can say that, ‘I don’t know,’ but we can figure out the experiment together that they should do to answer the question that they have,” Johnson said. “It gives them a place where they can fail and fail and fail and then it works.” 

Since 2009, Johnson’s lab has participated in the SEA-PHAGES program, a collection of over 100 higher-learning institutions led by the Howard Hughes Medical Institute's Science Education division with the goal of increasing undergraduate persistence in science through an engaging research and educational experience. VCU is one of 13 institutions in Virginia participating in the program.

While the focus of the lab is to help students learn skills and research that is limited to low-risk microbes, research into phages has the potential to affect lives, Johnson said. “There was a virus that came out of a [SEA-PHAGES] student’s work that was used as part of a phagetherapy treatment for a girl who had an antibiotic resistant bacterial infection. So, the potential impact of the work to improve human health is real, though our research in my class has a more ecology, evolution and diversity of viruses point of view.”

Down in the water

In the standard discovery process used by Johnson’s students, phages are usually isolated and purified through soil samples. However, attempts to find phages in water samples proved elusive. “Our class had been dealing with soil enrichment, so isolating bacteriophages in water was completely foreign to us. … We didn’t know how to approach it,” Islam said.

With guidance from Johnson and James Vonesh, Ph.D., associate professor and assistant director of the VCU Center for Environmental Studies, Islam developed a project as part of the VCU Honors Summer Undergraduate Research Program in 2018 to take samples from the James River rock pools as the basis of developing a method to isolate and catalog water-borne phages. 

A student pouring liquid into a petri dish inside of a laboratory.
Islam working on her Honors Summer Undergraduate Research Program project in Summer 2018. (Photo courtesy of Allison Johnson)

Vonesh and his lab of graduate students served as guides to the rock pools, providing Islam with a contextual background of the unique ecosystem while monitoring which pools were sampled. “We brought them down to the site [and] shared the background of what we’re doing there,” Vonesh said. “Some have lots of sunlight, some have lots of detritus, some don’t get flooded — so there are these cool environmental gradients.”

For Islam, heading to the river wasn’t exactly unchartered territory. “I’ve been to Belle Isle before and I’ve seen the rock pools. … [Vonesh] told us about the ecology of the rock pools, and he showed us mosquito larvae. It was interesting to know the ecology behind the area.” 

Water samples were taken from the rock pools through which bacteria were isolated to use as hosts for bacteriophage discovery. Once the bacteria were purified, Islam returned to Belle Isle to retrieve another water sample to look for phages while working to create a concentrated medium to help increase the probability of phage infection through a nutrient infusion. Finally, with the new water sample filtered and medium created, the combination was plated on a petri dish to see if the bacteria would be killed by phages.

After a few days of trial and error, Islam’s efforts paid off when a phage was discovered. “Every time I see a spot on a plate I get really excited,” she said. By the conclusion of the summer project, Islam was able to identify two host bacteria and several phage samples.

Kyle, Phynn and Beyonphe

After completing her summer project, Islam took the lessons learned and applied them to Johnson’s Phage Discovery I lab course. Working as a teaching assistant, Islam taught freshman students the method she honed as they traveled to the rock pools themselves to sample bacteria and isolate phages. 

“It was my first time having that kind of role — guiding students and stuff,” Islam said. Throughout the semester, she helped steward her peers’ research efforts by acting as a resource and mentor. “It’s not in regards to it being rigorous, but just if they need advice outside of the phage lab in general. It’s nice to have that.”

By the end of the fall 2018 course, the students were able to isolate and purify nine phages from the rock pool samples and some presented on their findings at a regional SEA-PHAGES symposium at James Madison University that November. Islam was able to receive feedback from experts in the field, including from federal agencies such as the Food and Drug Administration. 

A transmission electron microscopy image of a bacteriophage.
Viewed using transmission electron microscopy, Kyle is one of nine identified phages found by Johnson’s Phage Discovery students. (Photo courtesy of Allison Johnson)

Now about those three uniquely named acquaintances, which Islam loves to tell people about. During Johnson’s spring phage lab the following semester, the students were further able to get to know their phages using bioinformatics to annotate the three phage genomes, which were submitted to the National Institute of Health’s GenBank database last summer. In order to submit, though, the names needed to be unique so students took the opportunity to get creative. Thus, Phynn, Kyle and Beyonphe were born. 

“It’s one of the cuter aspects of the SEA-PHAGES program,” Johnson said. “You see the naming go through cycles of pop culture — like, all the ‘Harry Potter’ names are taken, all the ‘Games of Thrones’ names are taken. I think they’re working on Marvel, now … though you’re not supposed to use trademarked names so they modify them in clever ways.” 

“They’ve worked so hard on isolating this phage; it’s like their baby and they give it a name,” Islam said. “It’s part of what makes it engaging to students.” 

Islam’s work culminated last summer with a presentation at the 11th annual HHMI SEA-PHAGES Symposium held in Ashburn, Virginia. However, another presentation during the Rice Rivers Center’s annual research symposium was particularly notable for Johnson.

“She was the only bioinformatics speaker, as well as the only undergraduate speaker, speaking to a room of ecology researchers about the connections we were making with James Vonesh’s work,” Johnson said. “I had tears in my eyes, and I didn’t want to tell her I thought she was the only one because I didn’t want to freak her out.”

“Yeah, she told me at the end,” Islam said, “and I was like, ‘Oh my God!’”

Cross-collaboration

Islam’s research activities were facilitated through interdisciplinary connections made across VCU and within VCU Life Sciences. For Vonesh, the success of this particular project emphasizes the importance of breaking down boundaries between research fields when teaching and cultivating future scientists. “We demarcate these disciplines often by traditional boundaries and areas of emphasis, but in fact, environmental sciences and bioinformatics bleed into each other and some of our students will have interests that are at that intersection.”Between the phage discovery skills learned in the laboratory, and gaining ecosystem-level skills in the rock pools of the James River, Vonesh sees the potential fertile ground for future collaborative efforts.

“I had a grad student friend when I was at the University of Florida who said: ‘James, to be successful in science, you need to be a wizard in the lab and a warrior in the field,’” Vonesh said. “Solving the problems of tomorrow are going to require people who, even if they’re not able to do everything at all of those levels, they’re able to move fluidly and traverse and work across that spectrum.”

From left: Allison Johnson and Nasita Islam behind a rock pool along the James River in Richmond, Virginia.
Allison Johnson, Ph.D., an associate professor in the Center for the Study of Biological Complexity, encourages her Phage Discovery Lab students like Islam to gain experience in problem solving and persistence. (Tom Kojcscich, University Marketing)

With a university the size of VCU, Johnson said, cross-collaboration opportunities such as Islam’s project are a necessity. “It’s great for students to be able to see other things that are happening on campus, but it also allows us to interact in interesting ways,” Johnson said. 

For now, Islam is focused on continuing her bioinformatics research and planning for the next steps, which include an interest in pursuing a graduate degree.

“For the longest time, because it’s a medical campus and all my friends are in the pre-med track, I thought, ‘Oh, maybe I want to do pre-dentistry.’ I think that [last] summer, and going to the conference and meeting people who love bacteriophages ... I think I realized that I wanted to pursue research,” she said. “So I still don’t know what I want to research, but I think it’s definitely going to be bioinformatics related.”

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