Making Feed Safer for Livestock

Inside the leaves, stems, fruits, flowers and roots of most land plants are communities of bacteria, fungi and other microorganisms that form plants’ microbiomes. Just like your gut microbiome, the collection of microbes that live in your intestines, plants have microbial communities that live in and around their tissues. These microbes communicate with the plant and one another, drive plant health outcomes and shape how the plant interacts with its environment.

As a FFAR Fellow and microbiome science and plant pathology PhD student at the Pennsylvania State University, I study microbes called “fungal endophytes” in corn leaves. Endophytes get their name because they live inside (“endo”) the plant (“phyte”).  Endophytes can both benefit and harm the plant. They provide “beneficials”, with the potential to support plant health against disease and environmental stress, and “commensals” with unknown relationships, good or bad, to their plant host. Still, and even more importantly to me as a plant pathologist, these fungi can be parasites with the ability to cause disease and produce dangerous toxins that put human and livestock health at risk if ingested.

So why would I be interested in fungal endophytes of corn leaves? You don’t eat corn leaves at a BBQ, do you? You may not, but livestock, especially in Pennsylvania where I work, eat the leaves along with the rest of the green corn plant, as part of a feed product called silage. Silage is a fermented feed product where the whole plant is chopped and ground down at peak water content, then pressed and stored in an anaerobic (without oxygen) environment. This oxygen-free environment promotes good bacteria that pickle the corn material, allowing farmers to store it for long periods of time so that cows, chickens and other livestock have a continuous food source all year long.

Unfortunately, silage can be contaminated by fungi, affecting its quality and palatability, and potentially poisoning the animals that eat it. Many of these fungi grow as pathogens on corn ears called ear rots, producing fluffy pink, white or green growth, while producing toxic compounds called mycotoxins. These pathogens are often visible on open corn ears in the field. Many of these fungi can also grow in other tissues like leaves, without causing disease and may still produce dangerous mycotoxins.

While we know broadly that fungal endophyte communities can be shaped by factors like climate and seasonality, plant species, tissue type and plant development, little is known about how the agricultural environment shapes foliar fungal endophyte communities in corn. I want to understand how the agricultural environment drives both the communities of all fungi in the leaf and those that can be pathogenic and mycotoxin-producing. I explore how factors like plant development, use of organic vs conventional management, the application of fungicides and drought events shape foliar fungal endophyte communities. Understanding how the agricultural environment drives fungal endophyte communities gives us foundational information on their ecology and contributes to future disease and mycotoxin management.

Currently, mycotoxin management focuses on the reduction of disease in the ears, as this is a visible means of determining risk. Extension educators in Pennsylvania recommend the use of hybrid corn with tolerance to these pathogens. Hybrids with downward turned ears, for example, can reduce opportunities for infection and hybrids with insect resistance reduce insect feeding, thereby limiting opportunities for wound-based pathogen infection. Debris (stover) management in the field can also reduce pathogen inoculum sources, and crop rotation with non-host species (non-grasses) may further reduce inoculum when corn is planted again. My research will support mycotoxin management by helping us understand more about what factors in the agricultural environment drive pathogen presence (increase or decrease) and may help identify additional opportunities during the corn growing season to deploy management strategies.

So far, my work has shown that one of the most economically important ear rot pathogens of corn and a mycotoxin-producer, Fusarium graminearum, can be found in corn leaves all season long, and its presence may not be driven by management practices. We found that F. graminearum is highly abundant in corn leaves from early development to plant death, regardless of management style. This may suggest that current mycotoxin management practices, while focused on the ear, may not protect the leaf nor reduce available inoculum. Further, this work expands on what we know of F. graminearum’s ecology outside the current disease and lifecycle models used for disease and mycotoxin management. Current models focus on inoculum originating in field debris during the plant’s tasseling stage (flowering), while my work points to the consistent presence of inoculum all season long. This begs me to question: where is the inoculum coming from, can we reduce the source and what does the continuous presence of F. graminearum inthe leafmean for mycotoxin contamination?

My PhD work excites me because it connects both applied agricultural questions in food safety with foundational microbial ecology and microbiome science. I have a background in both field ecology, working in natural systems restoration in undergrad and applied plant pathology, working on fungicide resistance in my master’s. Being in a terminal degree program that allows me to call on both sets of past skills while building new skill sets is a deeply rewarding and validating experience.

My PhD work has also required and allowed me to collaborate with extension educators and research teams from across agricultural science. Something that few graduate students get to do. This has both given me access to research sites and resources beyond my program and helped me gain perspective on the agricultural landscape of Pennsylvania. By collaborating, my research has been enriched, its potential impacts expanded and I have built both a stronger sense of personal connection to my work and the place I work.

The FFAR program has been a transformational experience that enriched both my professional and personal development. The Fellowship helped me to better understand my strengths and areas for growth, learn communication, project management, presentation and leadership skills. These skills have been essential for navigating my PhD program, my collaborations mentioned above, home life and preparing for a future career in industry.

The mentorship component of the program has been deeply impactful and is not something I think I would have even thought to seek out without the Fellowship. I have had mentors in industry, non-profit and extension, who have not only shared their experiences and career journeys with me, but also given valuable perspective and advice that I use regularly to overcome challenges in grad school and daily life.

Of all the resources the Fellowship has given me, my cohort has been one of the most valuable. I have had the immense privilege to learn and grow alongside people with diverse agricultural science interests, backgrounds and future careers. I see my cohort as both friends and an established professional network that will travel with me beyond my PhD and into my future career.

I would like to thank my sponsors, Pasa Sustainable Agriculture and the FFAR Fellows program, my advisors, Sharifa G. Crandall and Gretchen A. Kuldau, as well as my mentors and collaborators, for whom my research and this fellowship would not be possible. Thank you for believing in me and my potential, and for seeing the value of my research.