Microbiology

Archives for March 2023

Faculty Spotlight – Ben Parker and the Parker Lab

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Faculty Spotlight – Ben Parker and the Parker Lab

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Walking into Ben Parker’s lab, you are greeted by rows upon rows of small plants, each in their own enclosed container with a complex handwritten label. What initially looks like a greenhouse operation changes quickly when you look closely at the plants: each is covered by hundreds of tiny bugs, or pea aphids. 

Parker’s lab utilizes the pea aphid as a model organism to study its life history traits and genetics and uses the findings to further understand larger questions in biology, evolutionary biology, and microbiology. The pea aphid system offers two main advantages: the insects give live birth to genetically identical offspring in just 10 days, and their bodies contain a simple microbial community, allowing Parker and his researchers to easily add or remove microbes in the systems and complete various mechanistic studies. 

Bacteria are one microbe that inhabit aphids. They are vertically transmitted, which means they are passed from parents to offspring, and can form important symbiotic relationships with their hosts. 

“The bacteria Regiella insectcola makes aphids resistant to the fungal pathogen Pandora neoaphidis,” Parker elaborates. “Not all aphids harbor Regiella, but those that do are more resistant to fungal infections.” 

However, the bacteria are not entirely beneficial. 

“One big question we are interested in is how the aphid’s immune system evolves to accommodate these beneficial bacteria in ways that still allow it to fight off bacterial pathogens,” Parker says. 

For example, the lab has been focusing on the phenoloxidase mechanism, which is an enzyme aphids use in melanization (a method insects use to fight pathogenic microbes). Aphids harboring Regiella have reduced gene expression of the phenoloxidase enzyme producing genes. 

The lab theorizes that this occurs because the bacteria are attempting to maximize their abundance, despite compromising the aphid’s ability to fight off other bacteria, but this finding is just a first glimpse into the mechanism. 

“We want to understand that in a broader context,” Parker states. “We want to know what effects that has on interactions with pathogenic bacteria and how those mechanisms are evolving in natural populations.” 

Viral genes are also vertically transmitted between aphid parents and their offspring. One such gene has interesting morphological effects on the host wherein in two genetically identical offspring, one can be winged while the other is wingless.  

This occurrence is an example of a phenotypically plastic traits, or a morphological trait influenced by the environment. In this case, the environmental trait influencing gene expression is plant crowdedness, which aphids have evolved to sense. The viral gene triggers the production of winged offspring by making aphids more sensitive to crowding.

 “When it is too crowded, they produce winged offspring, so they can fly to another plant and start over,” Parker explains. 

Currently, the Parker lab is focusing their studies on the genome and microbiome of the Pandora neoaphidis fungal pathogen. Additionally, they are working to understand aphid immune systems and how different aphid genotypes interact with bacteria. This talented group undoubtedly has a promising future.

-By Taylor Mattioli

Mikucki Awarded for Excellence in Teaching

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Mikucki Awarded for Excellence in Teaching

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Faculty in the College of Arts and Sciences were honored for their research, teaching, creative activities, outreach, and leadership in diversity at the college awards banquet Tuesday, February 28, 2023. Theresa Lee, Herbert Family Dean of the College of Arts and Sciences, and members of her cabinet hosted the annual event at the UT Conference Center.

Jill Mikucki, associate professor of microbiology, received the junior-level Excellence in Teaching award. Mikucki is a one of a few leading Antarctic microbiologists in the world and has been a lynchpin member of the interdisciplinary team exploring this difficult-to-access environment. She brings this remote region to the UT campus through her thoughtful and creative research laboratory and classroom instruction. 

She helps students learn microbiology through the lens of exploration and discovery, engaging them in independent learning, and piquing their curiosity about real-world issues. She gives students insights into life on Earth and other planets through the development of novel and effective curriculum that promotes learning through storytelling. 

In the past several years, she created a graduate level topics course on microbial justice that focuses on the intersection of microbiological research and environmental, social and racial justice, and an undergraduate course on astrobiology that, according to one student, is the “coolest, most thought-provoking course … at UT.”

Elkins (‘95, ‘01) Receives Professional Achievement Award

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Elkins (‘95, ‘01) Receives Professional Achievement Award

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Christopher Elkins (‘95, ‘01) received the Professional Achievement Award, which recognizes alumni who have achieved a high degree of success in their chosen field, a record of notable accomplishments, and a history of outstanding contributions to their discipline and/or creative pursuits. 

Elkins, who received his master’s and PhD in microbiology, is an internationally recognized expert in antibiotic resistance and microbial pathogen detection. He is regularly sought as an expert speaker for national and international scientific conferences and has played instrumental roles as an agency representative for both the FDA and CDC. Elkins has authored, or co‐ authored, more than 65 peer-reviewed scientific publications and five books or book chapters. He has also held leadership roles for the American Society for Microbiology, and served as an editor or on the editorial board of four different scientific journals.

Elkins has made significant contributions to research aimed at identifying and combating microbial pathogens, including SARS‐CoV‐2 (aka COVID‐19). He has successfully led the development and coordination of scientific research and pathogen surveillance programs. In addition to his professional accomplishments, Elkins volunteers his time and talent as an advisory board member to the Department of Microbiology.

“I found that simply taking advantage of every opportunity that was ever afforded to me has never steered me wrong,” Elkins said. “And it aligns with the Volunteer spirit that provides the pedestal that puts me with what I credited as seemingly being at the right place at the right time.”

Walton Receives Gilliam Fellowship

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Walton Receives Gilliam Fellowship

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There are two things PhD candidate Jill Walton is passionate about – microbiology and community outreach – and the work she has done to incorporate the two is impressive, to say the least. 

Walton studies how different members of the roseobacter clade are able to degrade polycyclic aromatic hydrocarbons, which are harmful to the environment and difficult to break down because of how stable they are. 

“My project started by reading a paper that introduces this idea that this family of bacteria (roseobacters) is able to degrade polycyclic aromatic hydrocarbons, or PAHs,” Walton said. “My thinking was that they show some members in some environments can do this, but I want to see if our bacteria that we work with do this.” 

Walton set up a plate-screening assay by spreading a thin, cloudy top agar containing PAHs, then inoculating the bacteria on top. After incubation, she scrapes the bacterial growth off, and if some of the cloudiness in the augur cleared out, that indicates that the bacteria were able to degrade the PAHs. 

“Their genomes didn’t have anything to indicate that they can do this,” Walton said. “They’re missing a lot of the biomarkers for this sort of degradation, so I thought maybe they’re doing this via a novel pathway.” 

She decided to investigate the possibility of a novel pathway by focusing on randomly disrupting the genome and re-running the plate assays of Regalia pomeroyi DSS-3, a member of the Roseobacter clade. She sequenced the genome-disrupted strains that did not degrade the PAHs for this round of assays to figure out which gene was disrupted, and thus involved in PAH degradation. 

“This was my groundwork. From that I went looking for novel degraders in marine ecosystems as a whole, looking for novel degraders using a genetic biomarkers search. I found it seems a lot of marine bacteria are able to degrade PAHs, but don’t have the tell-tale genetic biomarkers for this ability,” Walton said. 

While Walton continues her research on PAH-degrading bacteria, she is also widely involved in community outreach. Beyond her weekly volunteer work at the Sustainable Future Center, she runs the Knoxville Tennessee Environmental Soil and Stream Testing (K-TESST) program, which aims to educate Knoxville residents about local soil and water quality. She also serves on the Student Disability Services advisory board, mentoring students with disabilities through the NSF-funded TAPD-INTO STEM program. 

This past summer, Walton was awarded the HHMI Gilliam Fellowship for advanced study. Fellows and their mentors receive support for three years of research for their dissertation, and an award amount of $53,000 per year. 

“It was nice to have my work be recognized, and to be able to engage in the professional development opportunities that came with the fellowship,” Walton said. 

Jill Walton is an exceptional graduate student, both in the lab and in the community. There is no doubt she will go far in her research and in her community work.

Research in Extreme Environments

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Research in Extreme Environments

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It is easy to feel like you are falling behind or missing out as you go through the process of pursuing an advanced degree. We often find, however, that things fall in place exactly as they are meant to, whether we planned for it or not. That is one of the defining takeaways when learning about how Caleb Schuler came to receive his PhD in microbiology at UT. 

Before starting college at 25, Schuler had an active career in the military as a Navy reserve, simultaneously working at UPS. When he started working towards his Bachelor of Science in Biology, Schuler looked for ways to connect his love for geology and astronomy with biology. 

After doing research in a microbial ecology and astrobiology lab during his undergraduate studies, Schuler decided to apply for graduate school. He attributes his ability to pursue and work on both his bachelors and PhD to his experience in the military. 

“The military background has really helped me,” Schuler said. “The stress that a lot of graduate students go through never seems to impact me that much. It’s still stressful, but it’s the kind I can handle in a way that people who haven’t been deployed don’t really have.” 

Much of Schuler’s research in graduate school involved intensive fieldwork in the lab of Jill Mikucki, associate professor of microbiology. The field work and missions he had to do in the military was important for the challenging environments he would encounter as part of his PhD.       

His dissertation focused on three projects, each of which involved field work in extremely cold, desolate environments. 

The first chapter was a project examining the possible contamination mechanisms that come from using a novel probe for sample acquisition. This was a project he was primed for, with his military background making him the ideal candidate to spearhead the project.       

The second project was originally meant to expand on the melt probe research in the first chapter, but when they got to the field site, found they had arrived a little too late in the season. Instead, he took the opportunity to study the life cycle of snow algae, and how it in turn impacts the communities in that ecosystem. 

The final project in Schuler’s dissertation involved trying to figure out how the phototropic inhabitants of a microbial mat in Antarctica are able to adapt and remain active despite the constant daylight or lack thereof as seasons change throughout the year. Schuler’s PhD work took him from the mountains of Wisconsin and Washington, to the extreme environments of Greenland and Antarctica. 

“Everyone has, in those harsh conditions, their own limits. The most important thing is to understand yourself so you can accomplish tasks,” Schuler said. “That’s something I learned through my experience being a supervisor at UPS and being in the Navy. I really knew I would react in these different environments.” 

Despite not having the most traditional path to his PhD, Schuler’s experiences primed him for it nonetheless. He continues drawing strength from his military experience coming out of graduate school and into the professional realm.

Curiosity and Passion

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Curiosity and Passion

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Pursuit of curiosity is the founding ethos of Lindsey Burcham’s lab at UT, and you can feel that curiosity and passion come through when speaking to her about the work she’s done, and the plans she has for her lab. 

Burcham, assistant professor of microbiology, received her PhD at Mississippi State University, and completed her post-doc work at the University of Colorado-Anschutz Medical Campus. A majority of her research at both these institutions focused on host-pathogen interactions between Streptococcus pneumoniae, Group B Streptococcus and human beings. She joined the Department of Microbiology in August 2022, and her growing lab will study these interactions. 

S. pneumoniae is a commensal bacteria of the nasopharynx, but can become pathogenic when transplanted to other parts of the body. It is the source of many infections such as pneumonia, recurring ear infections in children, and even meningitis. Likewise, Group B Streptococcus is a commensal bacteria of the vaginal lumen, but becomes extremely harmful if it passes through the placenta of pregnant persons leading to ascending infections with a variety of harmful consequences: miscarriage, still-birth, or even meningitis or sepsis in the neonate. 

“This lifestyle switch where these commensal organisms exist asymptomatically, causing no harm, and they get into the right host or space and just wreak havoc. How they evolved to do both things is the basis of my interest,” Burcham said. 

The lab uses immortalized epithelial cell lines isolated from the vaginal lumen, the cervix, and an endothelial line from the human blood-brain barrier to observe S. pneumoniae’s ability to invade and thrive in the cell line. This is especially helpful for examining the changes to gene expression in both the cell line and the bacteria itself. 

Mice are used in the model for examining Group B Strep. The lab directly inoculates the mouse’s vaginal lumen to see how the bacteria travels to the cervix or uterus; they also place the bacteria in the blood and observe its ability to cross into the mouse’s blood-brain barrier. 

Beyond simply examining the bacteria’s efficiency in the mice based on controlling their diet. They find that zinc-deficient mice have weakened immune response and are more susceptible to infection. 

As she builds her lab, Burcham plans to foster an environment of collaboration and curiosity. 

“You can teach anyone the science, but I can’t teach you to be curious.” 

It will be exciting to see Burcham’s lab explore opportunistic human pathogens at UT, with implications on maternal, fetal, and pediatric health.

An Unfamiliar Form of Communication

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An Unfamiliar Form of Communication

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There are definitely more ways to communicate than using words, and human beings are not the only ones who can communicate with each other. 

Doctoral candidate Bridget O’Banion studies the process of chemotaxis between plant root systems and bacteria, an unfamiliar form of inter-species communication. 

“Plants also have bacteria that live inside of them. These bugs help them to ward off pathogens, help them to absorb nutrients from the soil, and help them to retain water.” 

Where humans can move around and leave an environment that’s potentially harmful, plants simply have to remain in place, making them vulnerable to pathogens and other harmful environmental changes. As a result, plants have to adapt by working with the microbes around them. 

“The plant can continually recruit and repel different microbes from the soil based on what it needs. It can send out different signals into the soil to kill or attract different microbes to live inside its tissue.” 

What do the bacteria get out of this relationship? Well, plants can synthesize their own food, primarily in the form of sugars. Microbes feed on a variety of these plant-made carbon sources and thrive in the niche provided to them by the plant. 

For her projects, O’Banion focuses on plant root systems, and how each part releases a different kind of chemical to attract certain microbes. This is called chemotaxis, and it’s how plants and microbes communicate to form that mutually beneficial symbiosis. 

“My favorite part of the process is generally the independence it’s given me. My PI from the get-go let me pick my questions and pursue my own project. Every day when you’re in the lab, you’re seeing something that’s potentially the first thing anyone has ever observed.” 

Independence certainly defines her experience. O’Banion’s process is unique to the average graduate student, since her mentor and other members of her lab changed institutions in 2020, while she remained at UT. Despite the difficulty this poses, O’Banion says that she’s learned to adapt to switching to a more remote collaboration, and has received support from the other professors in the department. 

“There’s no more swiveling my chair around and chatting with the other grad student in my lab. But the department has been super wonderful in making sure I still have a space where I can still do my work and providing me with any support I need.” 

Communication comes in many different forms. Whether it be our face-to-face conversations, or through Zoom collaborations, Bridget O’Banion plans to continue studying plant-microbe interactions, both commensal and pathogenic.

Saving the Planet with Microbes

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Saving the Planet with Microbes

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Kennedi Hambrick is going to be a doctor. Not the clinic-and-patients type, but the saving-the-environment with microbiology type. 

Hailing from Jonesborough, Tennessee, Hambrick first came to UT as an undergraduate student with the goal of one day becoming a medical physician, but ended up discovering her love of working in microbiology research after joining a lab while an undergraduate. 

What is unique about Hambrick is that after completing her bachelor’s degree, she was able to remain at UT to pursue her graduate degree, which is not something many pursuing a PhD get to do. However, she says that staying at UT has helped to make the switch easier. 

“I was actually very thankful to have the opportunity to pursue my PhD at the same institution where I got my bachelor’s degree,” Hambrick said. “The sense of community and support I already had with the microbiology department within UT was great, and it really helped ease my transition.” 

Hambrick is currently in her first year, and joined the lab of Associate Professor Erick Zinser researching the interactions between the cyanobacteria Microcystis aeruginosa and its cyanophage MA-LMM01. M. aeruginosa is naturally found in freshwater lakes. Its NIES-298 strain produces a harmful toxin called microcystin, which can contaminate drinking water, causing health issues for those who drink it. Its cyanophage selectively infects and renders it harmless, helping to offset toxin production. 

“In nature, cyanophages decrease the abundance of cyanobacteria in the environment,” Hambrick said. “We wanted to understand if varying levels of microcystin production had an impact on the infectivity of the cyanophage Ma-LMM01.” 

First, bacteria are incubated at different temperatures. When the host bacteria acclimate to the temperatures, they are infected with their cyanophage. Before and after infection, Hambrick takes toxin samples, cell counts, and DNA samples, which allows for comparisons of host toxin productions at the onset of infection for each temperature. Flow cytometry is used throughout the experiment and infection to account for the quantity of viable host cells in co-culture with the cyanophage. 

Although Hambrick is still early in her graduate studies, it is clear that the work she is doing is laying the groundwork to making a positive impact on the environment. She looks forward to continuing her lab work and hopes to make an impact with her research.

Diverse Applications

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Diverse Applications

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Alex Grossman, who recently earned his PhD in microbiology, had originally started his journey in higher education with the goal of studying ecology. After completing the NSF-funded Research Experience for Undergraduates (REU) program in the UT Department of Microbiology, however, he discovered a passion for microbiology. 

“Ninety to 99% of all the biology on planet Earth is microbiology, and I would say that’s where my passion and fascination come from,” Grossman said. 

It was how he decided to come to UT to pursue his PhD, and brought the experience full-circle when he mentored an REU student during his PhD. 

“I got to be, for someone else, the source of inspiration that I had received myself when I was an REU student” he said. “I enjoyed that opportunity to nurture an interest in science.” 

Grossman completed his PhD work in Professor Heidi Goodrich-Blair’s lab, who also serves as head of the microbiology department. 

“In my first year it certainly was intimidating to have my research mentor be the department head. It was a bit more hands-off, but I really appreciated getting to be more independent,” Grossman said. “Despite how busy she was, she always went out of her way to always be there for the students, myself and others included.” 

Grossman researched microbe-host symbiosis, using nematodes as the experimental system. Nematodes were ideal to work with because of how small and simple a host they are. Ultimately, the work led him to discovering and characterizing a novel gram-negative bacterial secretion system (Type-XI secretion system). 

“The system is a mechanism the bacteria have evolved for secreting protein in the environment, either to survive off the host or to interact with the host by binding host antigens, immune factors, and the like.” 

What is special about this secretion system is that it is found in the microbiome of humans and other organisms as well. It is exciting to think that a bacterial system discovered in nematodes has implications in human medicine, and certainly speaks to the diverse applications of microbiology. 

Grossman explains that beyond the molecular and bench work he gets to do in the lab, he quite enjoys the bioinformatic and coding work he gets to do as a part of the analysis. 

“There’s something exhilarating about this experiment that took weeks of work and now there’s an excel sheet with a gigabyte of random numbers and you need to find the story and the logic in it.” 

Grossman was inspired to pursue microbiology because of how vastly relevant it is to so many different processes of life overall. Looking forward to his post-doc work, he is excited to seek out new biology and systems to study, while deepening his passion for bioinformatics and lab work.

A Gut Feeling

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A Gut Feeling

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Naomi Gilbert started out as an undergraduate student at James Madison University, where she initially found her passion for environmental microbiology. Inspired by her research mentor there, she decided to come to UT for her PhD.

As a part of Professor Steven Wilhelm’s lab, Gilbert was involved in collecting sampling microbes in the open ocean, then using a combination of molecular and computational tools to characterize what microbes are in the ocean, what they do, and how nutrients impact them.

“In undergrad I did some freshwater cyanobacteria work, but Dr. Wilhelm told me about this project that had to do with marine microbiology, and that’s what got me: the prospect of flying to another country and field sampling the open ocean,” said Gilbert, who specialized in examining the phytoplankton, viruses, and bacteria that infect microbes in the ocean to understand how they impact the ocean’s nutrient cycle, and in turn the global carbon cycle.

“Primary productivity is one of the main mechanisms by which the ocean actually takes up carbon dioxide and exports it to the deep ocean,” Gilbert said. “My contribution was showing that there’s certain nutrients limiting the growth of microbes in the southern ocean, which contribute to primary productivity”

When she first started out, what fascinated Gilbert about the work she was getting to do was the computational analysis and integration of travel – also known as field work, which has extensive preparations.

“The travel might be three weeks total, but months before we’re planning the logistics of all of this,” Gilbert said. “It’s time consuming and tedious, but it was nice to have something to look forward to while you were analyzing your data.”

Gilbert began her undergraduate degree with the goal of pursuing medicine, but shifted gears when she discovered her true passion.

“Not restricting yourself is important. If you get that gut feeling that you want to change course to something you’re more passionate about, it’s better to commit sooner rather than later,” Gilbert said.

Environmental microbiology remains a major interest for Gilbert, and she hopes to continue studying it in her postgraduate work. She thoroughly enjoys the computational analyses she gets to do and hopes to move from the field-based research she is used to into the realm of culture-based lab work.