Department of Biology

The USDA National Institute of Food and Agriculture has awarded Agriculture and Food Research Initiative Predoctoral Fellowships to Alexandra "Allie" Margets and Delaney Miller.

NIFA’s Agriculture and Food Research Initiative helps to develop new scientists and professionals to enter research, education, and/or extension fields within the food and agricultural sciences in the private sector, government, or academia. The initiative's fellowships aim to cultivate future leaders who can solve emerging agricultural challenges of the 21st century.

Margets and Miller are both Ph.D. candidates in the College of Arts and Sciences Department of Biology at Indiana University Bloomington. Margets—who is in her fourth year in IU's Genome, Cell, and Developmental Biology Graduate Program—is a member of Distinguished Professor of Biology Roger Innes's lab.  Miller is in her fifth year working toward her degree in IU’s Evolution, Ecology, and Behavior Graduate Program. She is a member of Associate Professor of Biology Irene Newton's lab.

Marget’s award will provide $180,000 over three years toward her investigation of the molecular mechanisms of soybean cyst nematode effector proteins. Miller, who is studying the genomics of a honey bee defensive symbiont, is identifying symbiont distribution and natural variance in antifungal production. Her fellowship of nearly $120,000 will provide two years of support for her research.

I asked them both about their research interests and specifics about the research supported by the fellowships. We also discussed what led them to an IU Ph.D. program and what their next steps will be.

What are your research interests in general and more specifically?

MARGETS: My overall research interest is in the molecular interactions between pathogens and their plant hosts. Specifically, I am interested in the plant immune system and how pathogens can successfully bypass or suppress its robust responses. Identifying and understanding the intricate components of the plant-pathogen interface motivate my research questions. Furthermore, I am always thinking about how the findings of my research could be applied to developing pathogen resistance strategies that can be used in agriculture. With my current and future research, I hope to gain information that expands our knowledge of plant immunity and use that information to address problems that impact agriculture.

MILLER: I am interested in how microbe-microbe interactions in a community drive larger-scale phenomena such as host health and disease outbreaks. Specifically, I am interested in how insect microbiomes interact with fungal diseases and how they shape the disease ecology and outcome.

Tell me about your research project the fellowship will support.

MARGETS: In agriculture, the soybean cyst nematode (SCN) is the most devastating pathogen of soybean in North America, jeopardizing crop yields each season. There are very few methods that protect soybean from SCN infection and still many unanswered questions in the field as to how this nematode parasitizes its host. Development of durable prevention methods is enabled by a deep understanding of how the pathogen establishes infection. In the case of SCN, the nematode delivers a variety of different proteins into the plant through saliva secretions. Many of these proteins have specific roles that ultimately reprogram the plant’s molecular machinery to create a suitable environment for a successful infection. One of the most interesting to me is how the nematode can bypass/suppress the plant immune system.

My research is focused on understanding how several of the proteins secreted by the nematode during infection influence infection. To accomplish this, I have proposed experiments that will investigate how these nematode proteins influence the plant immune system as well as identify the plant proteins that are targeted by the nematode proteins during infection. Findings from my project will further illustrate the plant-nematode interface on a molecular level as well as provide a foundation for exploring new avenues for developing resistant soybean varieties. This addresses the long-term goal of increasing crop production with fewer chemicals, such as pesticides, that will ultimately reduce environmental costs of agriculture, including its carbon footprint.

MILLER: For thousands of years humans have used bees for pollination of crops and food production. Most major crops in the U.S. are pollinated by honey bees. It is estimated that a third of all food depends on honey bee pollination services. For nearly two decades honey bee populations have been in decline. The causal agents of bee colony losses are complex but include fungal disease. To prevent fungal disease, bees have adopted a variety of defensive strategies, including grooming behaviors and repurposing chemical compounds. I have discovered that honey bees also have co-opted a bacterium, Bombella apis, that protects from fungal disease via the production of an unidentified antifungal. This bacterium is largely found in association with honey bee young (brood) but is also found associated with the queen bee and with shared colony food stores. Within a single colony there can be many different genetic variants of B. apis, called strains, but we do not know how strain variation impacts B. apis-mediated protection from fungal pathogens.

The goal of my USDA-funded project is to 1) determine if different strains produce more antifungal and are subsequently more protective for their host and to 2) map those strains to a particular environment in the colony. Understanding this could not only lead to the discovery of a new antifungal therapy but will also help us understand the ecology and distribution of this important symbiont within the honey bee colony.

What inspired your interest in research and/or your specific research interests?

MARGETS: As a first-generation college student, I had no idea what it meant to “do research.” I was first exposed to the world of research by my genetics professor, Dr. Michelle Barthet at Coastal Carolina University [where Margets earned her B.S. in biochemistry]. I expressed my general interest in plants and biology to Dr. Barthet one day after class after learning her lab was a plant molecular lab. The following summer, I began working in her lab where I fell in love with the scientific process. I was fortunate to remain in her lab for three full years and work on my own project, present at several conferences, and receive the mentorship that put me on track for pursuing a Ph.D. I fell in love with being able to apply what I know to a research setting to address questions that have not yet been explored. I have always loved learning, but I quickly found that there was nothing better than learning something new from an experiment you planned, executed, and analyzed yourself. My current interests were inspired by the complexity of the relationship by plant-pathogen interactions. I think it is so fascinating how it is a constant evolutionary battle between the pathogen and the plant host, and I am constantly seeking ways to “tweeze apart” these interactions on a molecular level.

MILLER: My first exposure to microbiology and disease ecology was working in Dr. Jamie Voyles' lab studying traits underlying the virulence of a devastating fungal pathogen of amphibians, Batrachochytridium dendrobatitus (Bd) [at New Mexico Institute of Mining and Technology where Miller earned her B.S. in biology]. My initial interest in her work was due to her conservation efforts, although I left with a deep appreciation for microbiology. My goal became to understand how large-scale events such as disease outbreaks can hinge on small-scale interactions such as the pairwise interaction of two microbes in a community.

When I was considering going to graduate school, I searched for model systems that were both ecologically important and manipulatable so I could ask more mechanistic questions. That led me to honey bees.

Why did you choose to pursue your PhD at IU Bloomington?

MARGETS: I had learned about the GCDB [Genome, Cell, and Developmental Biology] graduate program through Dr. Scott Michaels. I was at the American Society of Plant Biologists meeting in Orlando, FL, the spring before application season where Dr. Michaels presented in a symposium and visited my poster presentation. After the meeting, I reached out to Dr. Michaels who gave me more information about IU Bloomington and the other plant labs. IU Bloomington quickly became my top choice which was later confirmed during recruitment weekend. I felt at home within the biology community and had great interactions with the faculty and graduate students. There were several labs through which I was eager to rotate as I searched for my thesis lab which gave me confidence that I would find exactly what I needed to thrive. More broadly, I felt that the Bloomington community had everything I needed and more as well as being different from anywhere I had lived before—which kept it exciting.

MILLER: Dr. Irene Newton’s research on the honey bee microbiome is what initially drew me to IU Bloomington. When I interviewed at IU during Graduate Recruitment Weekend, I discovered and appreciated the interactive environment there. I knew that IU Biology’s collaborative nature would allow me to pursue research questions that bridged both the microbiology and the ecology and evolution program.

What are your goals and/or plans once you’ve earned your degree?

MARGETS: I entered my Ph.D. with the goal of pursuing a career in academia as I have always had a love for independent research, mentorship, and teaching; however, I have been enjoying my opportunities to also explore non-academic career paths within my field. It’s extremely important for me to have a career that remains in the field that focuses on plant immunity and plant pathology as well as one that allows me to be involved in outreach. I do plan on pursuing a postdoc position once I finish my studies at IU and hope to remain focused on the molecular plant-pathogen interactions with a specific focus on plant parasitic nematodes. I already have a few labs on my radar for when that time comes!

MILLER: My goal is to pursue a tenure-track position in academia and start my own lab researching the impact of microbiome membership (the presence, absence, and abundance of mutualistic microbes associated with a host) on fungal diseases. Through my research I hope to develop a deeper understanding of the factors which shape fungal disease prevalence, transmission, and outcomes. From this fundamental research we could develop new therapeutic strategies and/or antifungal drugs to address emerging and worsening fungal disease outbreaks.