Department of Microbiology

Wilhelm Receives John H. Martin Award for Research

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Wilhelm Receives John H. Martin Award for Research

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The Association for the Sciences of Limnology and Oceanography (ASLO) presents the John H. Martin Award to one paper each year that has led to fundamental shifts in research focus and interpretation of a large body of previous observations.

The 2021 John H. Martin Award is for “Viruses and nutrient cycles in the sea,” by Steven Wilhelm (University of Tennessee) and Curtis Suttle (University of British Columbia). The award will be presented at the 2021 ASLO Aquatic Sciences Virtual Meeting in June.

Wilhelm and Suttle’s foundational 1999 paper originated the concept of the ‘viral shunt,’ the phenomenon in which viral infection of marine microbes redirects flow of organic matter away from higher trophic levels and through the microbial loop. Drawing on early estimates of viral production in the water column, Wilhelm and Suttle shined a light on the considerable role viruses play in ocean biogeochemical cycles at a time when much of the research was focused on describing viral diversity and distribution. Their calculations showed that a staggering 25% of all photosynthetically fixed carbon, and associated nutrients, in the ocean may be recycled through the viral shunt.

Additionally, Wilhelm and Suttle made some of the first estimates of the total carbon stored in the viral pool and made eye-opening comparisons to the carbon stored in other types of marine organisms (including whales). Today, the concept of the viral shunt continues to influence our understanding of ocean ecosystem functioning and nutrient cycles. With >1000 citations, and more than 300 in the last five years, the legacy of “Viruses and nutrient cycles in the sea” and the viral shunt concept is still strongly felt in the field today.

“Every so often a novel concept is described which truly transforms a scientific field for decades,” says ASLO President Roxane Maranger. “Wilhelm and Suttle’s conception of the ‘viral shunt’ as a major pathway of oceanic carbon and nutrient flow in their 1999 paper is a stunning example of such a transformation.”

Full Citation: Wilhelm, S.W. and C.A. Suttle. 1999. Viruses and nutrient cycles in the sea, BioScience 49(10): 781-788. doi.org/10.2307/1313569.

ASLO is an international aquatic science society that was founded in 1948. For more than 60 years, it has been the leading professional organization for researchers and educators in the field of aquatic science. The purpose of ASLO is to foster a diverse, international scientific community that creates, integrates and communicates knowledge across the full spectrum of aquatic sciences, advances public awareness and education about aquatic resources and research, and promotes scientific stewardship of aquatic resources for the public interest. Its products and activities are directed toward these ends. With more than 3,800 members worldwide, the society has earned an outstanding reputation and is best known for its journals, interdisciplinary meetings, and special symposia. For more information about ASLO, please visit our website at www.ASLO.org.  

Mind the Gap

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Mind the Gap

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Message from the Department Head
In our Spring 2022 newsletter we are proud to share with you some highlights of the exciting and important research being conducted in the Department of Microbiology here at the University of Tennessee, Knoxville. A distinguishing characteristic of academic scientists is their passion for integrating discovery with education. Scientists stand at the edge of knowledge, pushing outward toward information and ideas that can and do change the world for the better.

Throughout my career I have been inspired by the students with whom I have interacted, who are learning where that edge is, where to push, and how to be comfortable with not knowing all the answers. Often, undergraduate researchers are just beginning to realize that there even is an edge, and as educators we are metaphorically holding up signs that say “mind the gap.” Graduate student researchers know there is a gap, and have decided to commit themselves to exploring what lies within it. This is a brave decision that causes them to diverge from their peers who are starting or continuing their jobs in the ‘real world.’ For many, becoming a graduate student means daily struggles: trying to make the experiments work, trying to explain to friends and family why the results were devastating or exciting, trying to explain to a mentor why the experiment was done that way in the first place, and trying to balance the many obligations that come with being a scientist, student, educator, and a human being.

In my view, one of the greatest privileges of being a faculty member at an institution like ours is watching graduate students grow in their confidence as they realize that they are the world’s expert in the length of the gap they have chosen to study, and as they hone and expand on their ability to communicate old and new scientific ideas to anyone and everyone.

Graduate students are the linchpins of academic research. They are at the frontline of the gap, spending hours at the bench, computer, and field to wrangle large amounts of data and small amounts of liquid into something interpretable for the world. They are at the frontline of our ‘mind the gap’ campaign, helping convey in the classroom and instructional labs the results and importance of scientific discovery to hundreds of undergraduates, most of whom will not share their enthusiasm. They are at the frontline of our self-awareness and image as a department, reminding us of our obligations, both scientific and nonscientific to all members of society; reminding us often of why we are pursuing new knowledge.

Here in the department, as we start the spring semester of 2022, we have just finished interviewing students for the incoming graduate class of fall 2022. The first-year students are entering their second semester and have made the important decision of joining a lab, which will define the general area of the gap they will be exploring. The second-year students are developing and defending their project goals and approaches as they take their preliminary exam or defend their thesis. And the continuing dissertators are running ahead of their mentors, calling back as they transform the unknown into the known.  

As you read through the newsletter and gain a glimpse into the stories of some of our graduate students and faculty, I hope you will share my gratitude and awe for their choice to dedicate themselves to scientific inquiry. This choice, though difficult, makes all the difference to making sure the rest of us have solid ground beneath us. 

Heidi Goodrich-Blair
David and Sandra White Professor and Head of Microbiology

Jill Walton – Graduate Student Spotlight

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Jill Walton – Graduate Student Spotlight

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Marie Curie once wrote “One never notices what has been done; one can only see what remains to be done.” While speaking with doctoral researcher Jill Walton, it’s clear she is the embodiment of Curie’s words. As she excitedly tells me about her studies, volunteer work, and outreach dreams, I see her vision for a more intentional use of research, academia, and scholarship to benefit not only scientific knowledge, but also humanity. 

Walton studies the roseobacter clade of marine bacteria in Alison Buchan’s lab. Roseobacter has a unique ability to degrade stable benzene rings, making it a promising candidate for the natural removal of polycyclic aromatic hydrocarbons (PAHs), which are anthropogenic pollutants composed of 2 to 6 fused benzene rings. 

Both roseobacter and PAHs — which come from oil spills, industrial discharge, wastewater, and runoff — are largely abundant in coastal environments. This mutual presence, along with roseobacter’s degradation ability, present a promising situation. 

“Roseobacter and the pollutants are there. They show the ability to degrade smaller compounds, so can they degrade more complex, structurally similar compounds?” Walton summarizes. 

Her overarching goal is to create an effective solution for PAH removal in degraded coastal environments. 

“I’m looking at roseobacter’s ability in a lab environment to degrade these pollutants to see if we can harness its ability to bioremediate these areas,” she explains. “If we know how to stimulate them, we can use what is already there instead of adding nonnative solutions.” 

Little is known about the intricacies of roseobacter’s degradation ability; however, these hurdles do not phase Walton. 

“We just need to put all the pieces together and build the story,” she enthusiastically states. 

Walton’s passion for research and solution-oriented mindset extends outside of the lab as well, resulting in an extensive list of extracurricular involvement. She regularly volunteers at the Sustainable Future Center, serves as the Microbiology Department’s Graduate Students Association Outreach and Engagement chair, and lends her voice to the Student Disability Services (SDS) Student Advisory Board. 

But her engagement does not stop here. Walton is a participant in the Community Engagement Academy offered through UT’s Diversity and Engagement Department where she applies her love for research to outreach initiatives. 

“We have been learning about engaged scholarship,” she explains. “We are focusing on engagement that not only benefits the community, but also our professional interests.” 

Her goal is to utilize her connection with the Sustainable Future Center to implement a community soil and water testing initiative. Walton hopes to provide free testing kits and educational workshops for community members. 

“I don’t want there to be any barriers to participation,” she elaborates. “I am really excited about it! I think it has a lot of potential to be great and an initiative other people will continue when I am no longer here.” 

Walton undoubtedly has a bright future ahead of her. Her passion for scientific discovery and her unrelinquished kindness make her invaluable to both academia and her community.

-By Taylor Mattioli

Buchan Elected Fellow in the American Academy of Microbiology

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Buchan Elected Fellow in the American Academy of Microbiology

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Alison Buchan, Carolyn W. Fite Professor and associate head of microbiology at the University of Tennessee, Knoxville, was recently elected as a 2022 Fellow in the American Academy of Microbiology. This is an honor that recognizes service, leadership, and creative achievement in the field of  microbiology.  

The fellow selection process is based on several factors, such as scientific and innovative achievements. This year, only 65 professors from across the world received the honor.

“I am humbled and honored to join the ranks of the American Academy of Microbiologists,” Buchan said. ”I am grateful to my many past and current mentors, supporters, and also the many talented and inspiring undergraduate and graduate students that I have had the unique privilege to work with over the years.”

Buchan’s expertise in her discipline has a broad scope. She is a microbial ecologist who studies the interactions bacteria have with one another and more recently she is studying the viruses that infect them. She is also trained as a microbiologist (MSc) and a marine scientist (PhD). The multidisciplinary research Buchan has accomplished at UT has given her the opportunity to collaborate with several other scientists such as chemists, geochemists, and modelers.  

“Science is most definitely a team effort and I am so fortunate to have had the opportunity to work with fabulous students, faculty and research staff here at UT.”

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

Bikash Bogati – Graduate Student Spotlight

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Bikash Bogati – Graduate Student Spotlight

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Hailing from Nepal, Bikash Bogati has traveled far to pursue his doctoral degree at the University of Tennessee. In Nepal, he obtained his undergraduate degree in medical microbiology and worked in a diagnostic microbiology lab. He now works with Elizabeth Fozo, associate professor of microbiology, studying how bacteria survive different stress conditions. 

Specifically, he focuses on enterohemorrhagic E. coli, or EHEC, which is a food-borne pathogen. EHEC produces the Shiga toxin, which causes damage to the intestinal wall and severe illness in humans. 

“I’m looking into a gene segment that codes for a type I toxin protein, called ZorO, to see how it helps the bacteria to survive in different stress conditions,” Bogati said.   

Not much is known about this small protein or its specific function; however, when ZorO is artificially overproduced, cell growth stasis and death ensue. 

“My dissertation work mostly focuses on what we overproduce as toxic [in the lab] might be helpful for the bacteria,” Bogati explains. “This protein can help the bacteria survive antibiotics that we have been testing in the lab.” 

Understanding this system is important, as antibiotic resistance is a growing concern. 

“It is really challenging to have antibiotics synthesized compared to how fast the bacteria are gaining resistance,” Bogati elaborates. 

During his time at UT, Bogati has contributed to more than just the understanding of E. coli. In 2018, he was inspired to seek community service opportunities when he was asked, “what would you do if you had an extra hour in your day?”  

“I said that I would do something for others, because whatever time I have, I’m using on myself,” he smiles. He now volunteers with Volunteer Assisted Transportation, which connects volunteer drivers to individuals in need of transportation. 

The organization has had a large impact on Bogati’s view of America, and he has learned much from those he drives. 

“As an international student, we are used to the school life, and we don’t have much interaction with people outside of school,” he laughs. “I started getting to know their lives. I now realize our lives are all pretty similar.” 

His eyes shine as he talks about the veterans, teachers, and other passengers he has connected with. “We can learn so much from their lives and experiences.” 

After he obtains his PhD, Bogati will continue to study infectious diseases and antibiotic resistance as a post-doctoral researcher at Emory University. He is eager to continue volunteering as well.

-By Taylor Mattioli

Andy Wagner – Graduate Student Spotlight

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Andy Wagner – Graduate Student Spotlight

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Chances are, many have heard of the fungal pathogen Candida albicans without realizing it. The pathogen causes many diseases, including yeast infections, which cause significant issues for women worldwide, and thrush, which is a mouth yeast infection that is common in babies and AIDS sufferers. 

Andy Wagner, a doctoral researcher in Todd Reynolds’s lab, focuses his work on this pesky pathogen. Wagner explains that while yeast infections may be uncomfortable, they are generally mild and easily treated; however, Candida albicans can occasionally cause bloodstream infections. Although rare, these infections have a mortality rate of about 30-50 percent, and they can be especially problematic for people with compromised immune systems. 

Wagner’s work specifically focuses on the idea that microbiologists can alter how the disease is recognized by the patient’s immune system to create a more favorable outcome for the patient. To make these alterations, Wagner focuses on Candida albicans’ cell wall, which is composed of three main layers: a basal layer composed of chitin, a middle layer composed of beta glucans, and an outer protein coat. 

 “The host’s immune system recognizes the beta glucans layer of this cell wall,” Wagner explains. “The outer protein coat serves as a barrier that prevents it from being recognized by the host immune system.” 

Inducing the cell to expose its beta glucans layer is no easy task. 

“There are signal transduction pathways that sense an outside change and will transmit the signal into the fungus to make it change its structural organization,” Wagner explains. “We found that if we can disrupt these signal transduction pathways, we can get the fungus to inappropriately expose the beta glucans layer.” 

Essentially, by altering the signaling pathways, Wagner alters how the cell wall is made. Currently, he is seeing overproduction of the basal layer and underproduction of the outer protein layer. 

“The basal layer is definitely being affected, which prevents the cell wall from being put together correctly,” Wager states. That, in turn, is making the recognizable basal layer more visible to the host’s immune receptors. This process is aptly termed “unmasking.” 

Wagner’s results are promising. “If we infect mice with these mutant fungus cells, we find they are able to recognize and clear the infection and survive longer,” he smiles. 

In the future, Wagner wants to continue working on disease-causing fungi, and he is hopeful that unmasking can be applied to other fungi as well.