For more than a century, faculty in the Department of Entomology and Plant Pathology have been studying and managing plant diseases. Researchers within the Alabama Agricultural Experiment Station have a united goal to address the major issues facing the world’s expanding population. Plant pathologists develop sustainable production methods and pest management strategies for farmers to ensure food security.
Dr. Neha Potnis, an associate professor in the department, continues this legacy as she works to find sustainable solutions to manage endemic bacterial plant diseases.
“It’s not just the pathogen and the host that we need to focus on, but also how climatic variability is affecting the pathogen itself, the defense responses of the plant and the plant microbiome,” Potnis said. Potnis and her team are taking a holistic approach to studying how pathogens adapt to hosts, evade management strategies and manipulate plant microbiomes for their benefit.
The project, funded by a National Science Foundation CAREER award, enables the team to explore the mechanistic basis of pathogen adaptation and identify the genetic factors that allow the pathogen to cause disease in specific hosts. Using classic genetic and molecular biology techniques, the team is investigating this host specificity.
Graduate students Palash Ghosh and Kylie Weis are studying these microbial interactions. Potnis explained the significance of the research being conducted by the graduate students and how it will give the team more insight into microbial behaviors.
“Just like us humans, plants also have their own microbiome that acts as a second layer of their immunity. We are trying to understand how the pathogen mediates interactions with the members of the microbiota. We are interested in figuring out the friends and foes of this pathogen,” Potnis said.
Potnis lab team members, Zoe Little, a research assistant and Deepak Shantharaj, research fellow, are studying what makes up a tomato microbiome and which members of the microbiome are important for the plant. “This work is specifically important as we make our plants resilient to different stressors.” Her team is contributing to a USDA-SAS- funded project focused on this subject.
“As a plant pathologist, we recognize the importance of climatic conditions for the disease to occur. We have a little experimental evidence as to how the variability of plant growth conditions have shaped plant disease outbreaks in the past.”
Potnis recognizes that climatic variability makes it even more challenging to predict disease outcomes. The research team is studying how endemic pathogen Xanthomonas continues to evolve by examining the genetic makeup of the pathogen.
“We are totally underestimating the pathogen diversity that is out there in the fields, and we really need approaches to learn how the pathogen manages to continue to cause disease on plants that are already struggling with adapting to sudden shifts in the temperature, humidity or droughts,” Potnis said. “Thanks to the next-generation sequencing methods, my team has now optimized high-resolution metagenomics protocols to identify the variants of the pathogen that are out there in the fields.”
A multi-faceted project titled “Interaction Between Climatic Variation and Pathogen Diversity Shape Endemic Disease Dynamics in Agricultural Settings” is funded by the Foundation for Food and Agricultural Research New Innovator Award. The Potnis Lab team worked closely with extension agents, growers from Alabama, Georgia, North Carolina and South Carolina, and mathematical modelers — Dr. Roberto Molinari from Auburn University's Department of Mathematics and Statistics, and Dr. Samuel Soubeyrand from INRAE, France. As part of the study, the team carried out a large-scale survey of tomato fields across the four states.
The team analyzed pathogen genetic diversity, the influence of climatic shifts on pathogen diversity, and how their interactions are driving variable disease dynamics in the fields over three growing seasons. The team found that in the Southeastern U.S., multiple pathogen variants — rather than a single genotype — coexist in the fields. Their dynamics are shaped by changes in plant growth conditions. Thus, plant breeders can focus on multiple pathogen variants that show different levels of fitness to adapt to different environments rather than a single variant.
Graduate student Amanpreet Kaur recently investigated changes in pathogen populations recovered from resistant and susceptible pepper plants simultaneously challenged with abiotic stress. This work, now published in Evolutionary Applications, highlights the high genetic variation in the pathogen and suggests that its future behavior is unpredictable.
“We are continuing to monitor the pathogen and are working in collaboration with the modelers to develop reliable methods to predict future disease outbreaks.” Potnis said.
As Potnis continues this valuable research, she explained her short-term and long-term goals that she hopes the research will provide over time. The immediate goal is to reduce overall disease incidence. Her long-standing goal is to reduce the evolutionary potential of the pathogen over time through ongoing research.
“We are learning what the weaknesses of this pathogen are when it interacts with the host and when it interacts with other resident microbiota.” Potnis said. She continues to work with plant geneticists and breeders to develop disease-resistant and climate-resilient plant varieties.
As the team learns how pathogens adapt to plants and different growing conditions, they can understand the durability of disease management practices, especially resistant plant varieties, and how reliably they can predict future disease outbreaks.
Potnis and the research teams within the Department of Entomology and Plant Pathology prove time and time again to be trailblazers in sustainable innovations for agricultural systems.
