2026 projects

16. Viruses to the rescue: phages to control bacterial diseases in controlled environment agriculture

Bacterial diseases are problematic to crops grown in controlled environment agriculture (CEA). They are notoriously difficult to manage and the number of effective control measures are limited. Bacteriophages, the viruses of bacteria, are the natural predators of bacteria. Preliminary tests demonstrate their applicability as an effective and organic control strategy for disease. In this project, you will isolate, characterize, and evaluate the efficacy of bacteriophages to control disease in CEA. Through targeted experiments, you will assess different application strategies of phage-based products in the lab and the greenhouse. 

Lab: 70%, Field: 30%

Mentors: Dominique Holtappels, Renee Smith, Benjamin Davis

17. Precision Disease Management 

As fungicide resistance continues to rise and concerns about chemical overuse grow, optimizing when and how much pesticide to apply has become critical for sustainable farming. This project aims to develop a smart, sensor-driven plant phenology and disease risk modelling by integrating data from ground-based cameras, drone imagery, and satellite observations. 

Tools & Technologies: Python, Ground cameras & field sensor, Drone imagery, Satellite imagery, Image analysis and Computer vision techniques

Fieldwork & Hands-On Training: 60% 
(Collecting ground images, setting up sensors, and documenting plant growth across field sites)

Data & Lab Analysis: 30% 
(Pre-processing imagery, conducting image-based growth modeling, and using computer vision to generate biological insights)

Professional Development: 10% 
(Technical writing, presenting results, and participating in research team meetings and knowledge-building workshops)

Mentors: Manushi Trivedi, Shivranjani Baruah, Katie Gold

18. Precision Virus Detection & Management in California Vineyards

Grapevine Leafroll-Associated Virus (GLRaV) threatens grapevine cultivation across California, causing vine death and reducing fruit quality, causing long-term economic losses. Early detection and spatial mapping of infections are critical for guiding timely roguing, vector management, and replanting decisions. This project integrates disease scouting data, field management metadata, and satellite remote sensing to build a scalable, data-driven framework for detecting GLRaV symptoms, mapping infection hotspots and disease spread, and supporting precision disease management in commercial vineyards.

Tools & Technologies: Python, R, Satellite imagery, GIS & spatial analysis, Image processing & machine learning 

Fieldwork & Hands-On Training: 20% 
(Collecting ground images, setting up sensors, and documenting plant growth across field sites)

Data & Lab Analysis: 70% 
(Pre-processing and cleaning satellite imagery, mapping vine death over time, training machine learning models to detect virus, and generating spatial infection maps for decision support)

Professional Development: 10% (Scientific writing, preparing presentations and participating in research meetings, extension events)

Mentors: Shivranjani Baruah, Manushi Trivedi, Katie Gold

19. Sweet Success or Fungal Failure! Exploring Muskmelon Cultivars for Foliar Disease Resilience

Muskmelon production in New York faces significant challenges from foliar diseases like powdery mildew, downy mildew, and Alternaria leaf spot. These diseases can cause mid-season defoliation, increasing the risk of yield loss through sunscald and reduced fruit quality. Evaluating cultivar susceptibility to these diseases helps growers select varieties that maintain productivity, reduce pesticide reliance, and support sustainable farming practices. However, up-to-date field data on cultivar performance under New York’s changing climate is limited, leaving small-scale growers, who produce most of the state’s muskmelons, without reliable information to manage these costly diseases.

This project will assess insect populations, disease incidence and severity, and other characteristics (like taste!) in a trial of eight to ten muskmelon cultivars. The summer scholar will gain hands-on experience setting up and monitoring field trials, collecting data on plant health and disease progression, and identifying biotic and abiotic stresses. Together, we will analyze data using R, generate graphs, and interpret results to create extension materials for growers and stakeholders. This project provides valuable training in applied plant pathology, sustainable agriculture, and data analysis, offering practical skills for understanding and addressing agricultural challenges in real-world settings.

Field: 60%, Lab: 40%

Mentors: Sarah Pethybridge, Kaitlin Diggins

20. Bugs, bacteria, & viruses. Oh my!

An essential step of a virus infection cycle is transmission by hemipteran insect vectors. Transmission efficiency can be affected by endosymbiotic bacteria that live within insect vectors; little is known about the microbial communities within vectors of grapevine viruses such as mealybugs and treehoppers. This summer, you will work to characterize these endosymbionts. Work will comprise insect colony rearing, dissection, nucleic acid isolation, PCR, qPCR and sequencing.

Lab: 80%, Growth Chamber: 20%

Mentors: Elliot McGinnity Schneider, Marc Fuchs

21. Clearing the path to sustainable disease management: Mapping genetic resistance to apple scab

Apple scab, caused by the fungus Venturia inaequalis, significantly impacts apple production worldwide. Frequent fungicide applications are often required during scab-conducive seasons to produce scab-free apples, as most commercial cultivars are susceptible. Developing scab-resistant apple cultivars offers a sustainable solution to improve fruit quality and reduce economic losses.

This summer, you will contribute to advancing scab resistance research by mapping potential quantitative trait loci (QTLs) in two apple accessions identified as resistant during field evaluations. Your work will include phenotyping bi-parental mapping populations to assess resistance in both progeny and parents, as well as using genetic data to connect genotype to phenotype. Your work this summer will help identify new genetic resistance to apple scab and pave the way to a sustainable future in apple production!

Lab: 10%, Greenhouse: 40%, Computer: 50%

Mentors: Awais Khan, Hana Feulner 

22. Overcoming a vegetable villain: Managing one of the most destructive pathogens of vegetables

A formidable member of the infamous “plant destroyer” genus, Phytophthora capsici threatens a wide range of vegetable crops including pepper, eggplant, tomato, and squash. In this project, scholars will explore whether individual P. capsici isolates show preference for particular vegetable hosts, generating novel insight into these host-pathogen relationships. Furthermore, while fungicides remain a cornerstone of integrated pest management, resistance to these treatments is alarmingly common in P. capsici populations. Sensitivity to commonly used chemistries will be evaluated in a diverse collection of P. capsici isolates, and candidate loci associated with fungicide resistance will be mapped through genetic analyses. Through hands-on laboratory and greenhouse experiments, scholars will gain experience in bioinformatics, microbial culturing, plant inoculations, and data analysis, all while helping improve disease management recommendations for New York vegetable growers.

Lab: 50%, Greenhouse: 50%

Mentors: Emma Nelson, Chris Smart

23. Cold Case: How Hemp Downy Mildew Sticks Around from Year to Year 

How does hemp downy mildew stick around from year to year, and can it jump to other crops? In this project, you'll investigate whether the pathogen’s overwintering spores are actually viable using plasmolysis assays, fluorescence-based viability stains, and microscopy. You’ll also help test a set of crop species, like hops and cucurbits, to see if they can serve as alternative hosts. Along the way, you'll gain hands-on experience with fluorescence microscopy, maintaining a plant pathogen, inoculating hemp plants, and rating disease symptoms. 

Lab: 80%, Greenhouse: 10%, Data Analysis: 10%

Mentors: Chris Smart, Taylere Herrmann

24. Don't eat the mold

Blue mold of apple, caused by the necrotrophic fungus Penicillium expansum, is a major post-harvest disease worldwide. Specifically in apple, losses are estimated around $4.5 million annually. P. expansum undergoes rapid asexual life cycles, produces the mycotoxin patulin, and has a highly plastic genome which contributes to the pathogens’ ability to mutate. Together, these factors contribute to its “high risk” classification as a postharvest pathogen and thus enable rapid onset of resistance to commonly used fungicides. 

Efforts in the Cox lab aim to understand the development of fungicide resistance and how to effectively manage this devastating disease in real time. Aside from the practical importance of optimizing yield, the broader impact of this research is to reduce blue mold incidence and in turn enhance food safety by reducing the secondary metabolite produced by P. expansum, patulin a potent and toxic mycotoxin. Patulin is heavily regulated in processed apple products, particularly products marketed towards children which are most susceptible to this toxin. Moreover, by optimizing fungicide applications there would be fewer more impactful inputs that would provide downstream benefit to the health of consumers and profitability of producers.

Scholars interested in the system would gain hands on experience in fungal culturing, molecular characterization, fungicide screening bioassays, statistical analyses in R Studio and last but not least get to work in an idyllic apple orchard in Upstate NY. 

Lab: 75%, Field: 25%

Mentors: Kerik Cox, Riley Harding

25. 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%

Mentors: Kerik Cox, McKenzie Schessl