Plant Pathology & Plant-Microbe Biology Projects

2024 projects

13. The Orchards are Melting!

Fire blight, a disease caused by the bacterial pathogen Erwinia amylovora, and named for the necrotic “burnt” look it gives to infected trees is considered the most devastating disease of pome fruit. It can destroy entire orchards in a single growing season and costs farmers millions of dollars in the United States each year. Modern fire blight management relies almost exclusively on antibiotic sprays, which are under public scrutiny due to the potential development of antimicrobial resistance in both the pathogen and in off-target bacterial populations. Each year biological control options are developed for fire blight, but they often provide poor control and aren’t optimized for temperate production regions. Summer scholars will have the opportunity to examine alternative management programs, evaluate antimicrobial resistance in E. amylovora, and investigate the distribution and movement of bacterial strains utilizing CRISPR genotyping techniques while honing their lab experience, participating in field work, attending workshops, and meeting with growers and graduate students. Scholars will also have opportunities to visit orchards with actual fire blight outbreaks and learn about modern apple production.

Lab: 50%, Field: 50%

Mentor: Kerik Cox

14. Come to the light!

Apple Scab, powdery mildew, apple blotch, and numerous other emerging fungal diseases limit sustainable production of apples in temperate climates. Fungal pathogen populations are becoming resistant to the safest and most environmentally sustainable fungicides. We’re investigating the potential for using germicidal light to mitigate fungal diseases of apple. Organically approved and pesticide residue free, germicidal light in the form of UV-C may be able to eliminate germinating spores and stop disease.  Scholars will need to suit up, enter apple orchards after dark, and carefully use UV-light arrays with their mentors to assess the potential field use of this new technology. In the lab, scholars will conduct experiments on fungal cultures and sporulating lesions to assess the impacts and determine optimal doses. Scholars will also have opportunities to visit orchards with disease outbreaks and learn about modern apple production.

Lab: 50%, Field: 50%

Mentor: Kerik Cox

15. Does a virus a day keep the apples away?

Several viruses can infect apple trees. Once a tree is infected with a virus, no treatment options exist in the orchard. For this reason, optimized sample collection methodologies and robust diagnostic tools are needed to detect virus infections in apple trees. Using samples collected from infected trees over the course of an entire growing season, you will quantify virus titer across different parts of the trees, track seasonal titer variation, and compare diagnostic assays to identify when, how, and from which part of the tree viruses are most reliably detected. In addition, viruses can be present on the seeds of apple fruits produced by infected trees. Could these viruses be transmitted to the apple seedlings that germinate from these seeds? You will solve this mystery by testing apple seedlings, embryos, and seedcoats for virus infection. You will gain experience with molecular biology techniques including plant nucleic acid isolation, endpoint and quantitative reverse transcription polymerase chain reaction, and data analyses, as well as with greenhouse experiments.

Lab: 90%, Greenhouse: 10%

Mentors: Marc Fuchs, Anna Wunsch

16. NASA Acres at Cornell AgriTech: Predicting fungal disease risk from remote sensing data

Fungi are responsible for >65% of all pathogen-driven biodiversity loss and cause >75% of economically important plant diseases. The Gold Lab at the Cornell AgriTech in collaboration with NASA Acres is developing a scalable remote sensing based framework for fungal disease risk monitoring using grapevine powdery mildew as a case study. This project will be 100% computational with the opportunity to participate in other ongoing Gold Lab field projects for experience.

Computer: 100%

Mentor: Katie Gold 

17. Clearing the path to sustainable disease management: Characterizing genetic resistance to apple scab

Apple production is strongly impacted by the apple scab disease, caused by the Venturia inaequalis fungus. To produce scab-free apples worldwide, over 30 fungicide sprays are needed during scab-conducive seasons, as most commercial apple cultivars are scab-susceptible. Cultivar resistance is the most promising sustainable solution to enhance economic returns due to fruit quality loss because of apple scab lesions. To contribute towards understanding genetics of scab-resistance in apples and towards development of scab-resistant cultivars, you will participate in the functional validation of candidate scab resistance genes from ‘Honeycrisp’ apples. To achieve this, you will participate in cloning candidate resistance genes and perform subsequent transformation into a susceptible apple cultivar. Your work this summer will help characterize a potential major resistance gene and pave the way to a sustainable future in apple production!

Lab: 70%, Greenhouse: 10%, Computer: 20%

Mentors: Awais Khan, Hana Feulner

18. Peeling Back the Layers of the Onion on Stemphylium Leaf Blight

Stemphylium leaf blight (SLB), caused by the fungus Stemphylium vesicarium, is a major foliar disease affecting onions in NY. Multiple sources of inoculum have been proposed including crop residue, infested seeds, volunteers (onions from the previous season that remain in the field), transplants, weeds and other crops. This project will use population genetics and epidemiology to elucidate the contribution of volunteers to SLB epidemics in NY. Using molecular-based population biology tools, we can advance our knowledge on how SLB epidemics are initiated and how the pathogen is dispersed between cropping seasons and among fields. The summer scholar involved in this project will improve their skills in plant disease diagnosis, pathogen isolation and preservation, and nucleic acid extraction. The student will also learn how to use molecular tools such as polymerase chain reaction, molecular markers, fragment analysis, and R studio for population genetic analyses.  

Lab: 60%, Field: 40%

Mentors: Sarah Pethybridge, Natalia Pineros-Guerrero

19. Cultivating Resilience: Strategies to Combat Septoria Leaf Spot in New York's Hemp Industry

In New York, hemp serves as a crucial crop for fiber, grain, and cannabinoids. Septoria leaf spot is a common and devastating fungal disease that significantly impacts hemp yields. Resistant cultivars are the key to tackling this disease! Participants will gain practical skills in hemp cultivation in both greenhouse and field settings, along with techniques such as inoculation and disease rating. Additionally, the program covers Septoria cannabina DNA extraction, providing insights into the genetic diversity of the pathogen population. This research will provide valuable insights for hemp growers and breeders to push for sustainable and disease-free hemp!

Lab: 50%, Field: 50%

Mentors: Chris Smart, Jocelyn Schwartz


20. Pathogen Pioneers: Unraveling the Mystery and Crafting Solutions for Cucurbit Yellow Vine Disease

The cucurbit enemy: Cucurbit Yellow Vine Disease (CYVD) is a disease caused by the bacterium Serratia marcescens, and it is transmitted by the squash bug, a common pest of cucurbits. CYVD was just recently found in NY and there is a lot learn. We will evaluate the preference of the squash bug for different cucurbit species (watermelon, melon, zucchini, pumpkin, cucumber, and squash) and how it affects the amount of CYVD we see in each species. We will also have lab work to do! We will collect samples, isolate the bacterium, and use simple molecular techniques to identify the causal agent, as well as collect squash bugs to determine the presence or absence of Serratia marcescens in their gut.

Lab: 50%, Field: 50%

Mentors: Chris Smart, Kensy Rodriguez-Herrera