A whole world in an apple: Meet Dr. Susan Whitehead, assistant professor of Biological Science at Virginia Tech

How did you first get interested in science and microbiome research? 

My love of science began with a love of playing in the woods and creeks where I grew up in Central Virginia. In college, I chose biology as a major because it got me outside for field courses—identifying plants, hunting mushrooms, watching birds. Then my junior year I spent the whole year studying abroad, first in Madagascar and next in Costa Rica. I fell in love with the science of ecology that year, and I knew I wanted to spend my life studying biodiversity and the complex interactions we see in nature. In graduate school, my dissertation research focused on plant-animal interactions, but I started to gain an appreciation for the microbiome from my colleagues. It was an exciting time—metagenomic sequencing was just emerging and our understanding of the diversity of life was undergoing a revolution. During one of my grad student summers, I was fortunate the have the opportunity to work with Rob Knight and Noah Fierer, two amazing scientists at the forefront of microbiome research, on a project looking at how microbiomes are shared among families and their pets. At the same time, I started to think a lot more about the plant microbiome and its potential interaction with all of the ecological processes I was studying, and I knew I wanted to expand my research to include microbial ecology. 

Can you tell us a little about your project?

Our project will describe microbial communities that live on apples and explore their potential to help us produce safer, healthier fruit. Many of the health benefits of apples come from phytochemicals—hundreds of different naturally produced chemicals in apples can protect against cancer, stimulate the immune system, reduce inflammation, and boost production of detoxifying enzymes. But the apple does not produce these compounds for our benefit. Phytochemicals evolved to help defend plants against their own enemies—fungal pathogens, bacterial diseases, and insect herbivores. Unfortunately, the phytochemical content of our domesticated fruit is substantially lower than that of its wild ancestors. Part of this is due to a long history of breeding, but we think that another big reason might be that our crops today are grown in relatively sterile environments. They are almost entirely devoid of the natural interactions with insects and microbes that would stimulate phytochemical production. We will assess relationships among the apple microbiome, the production of phytochemicals, and the susceptibility of apples to major pests. We hope that these results can eventually be used to develop new microbial inoculation treatments that can stimulate phytochemical production. It’s a win-win; we get fruit with a boost in health benefits that is simultaneously better protected against pests and will require fewer pesticides to grow. 

What will be a typical day for you in the lab?

The thing I love most about my job is that there really is no typical day! During my field season I might spend all day in an apple orchard, talking with growers, collecting fruits, and measuring pathogen and insect damage. I also spend a lot of time in the lab, grinding plant samples, doing extractions, and running phytochemical analyses. When we are not in the midst of data collection, time is spent analyzing data, reading, writing grant proposals and preparing publications. As a new professor, I also balance this with teaching courses in Ecology. It’s never boring! The best days are the days I get to spend working with collaborators or students who are as excited about biology as I am.    

What do you find most interesting about your project? What is the most interesting or surprising result you have found? 

The most amazing thing to me about plants is their incredible ability to respond to their environment. An exposure to a pathogen can cause massive reprogramming of the genome and a rapid phytochemical change. One of the most interesting results I have found was during my post-doc. We treated apple trees with an elicitor that stimulates their innate defense response to damage and found that damage levels were nearly half what they were compared to our controls. This was comparable to the level of control we got with some pesticide treatments! This was amazing to me and gave me a lot of hope that a better understanding of plant ecology can truly make a difference in increasing the sustainability of agriculture. 

What kind of microbiome research do you perform and how does it impact health and disease or the environment? Where do you see this heading in the next five years?

My research explores the microbiome of plants and its impacts on phytochemistry and pest resistance. The importance of this research area for sustainable agriculture is immense. Researchers are only just starting to explore the relationship of the microbiome to plant productivity, pest resistance, and food quality. In the next five years, I believe we will start to see a larger movement toward actually managing the microbiome to our benefit. Extending our management practices beyond the plant to include the microbiome has the potential to completely transform agriculture. With new microbially-based management practices, we will be able to produce more high-quality food with fewer pesticides and detrimental impacts to the environment. 

What are the major challenges you face in your research with regards to sample collection, nucleic acid isolation and data analysis?

One of the biggest challenges we face is with data analysis. As an ecologist, my goal is to uncover natural variation in traits or interactions across lots of individuals. We are examining the microbiome as well as the metabolome across multiple fruits, multiple plants, and multiple orchards, so we end up with two massive datasets that must be integrated and processed in a way that allows us to find meaningful patterns. This is a monumental task, but fortunately there are new bioinformatics tools emerging all the time. 

Which MO BIO or QIAGEN products do you use/have you used in the past and what did you like about the products?

I have mostly used the PowerSoil DNA extraction kits (DNeasy PowerSoil Pro Kit, DNeasy PowerSoil Pro QIAcube HT Kit). I love these kits because it makes the whole process so easy—everything you need is there. Before I did my first DNA extractions as a graduate student, I had the impression that it was going to be something that would take me a lot of time to learn how to do. But the kit makes it so simple and convenient. I also love the bead beater tubes and homogenizers; these kinds of tools make sample prep so fast and easy!