Plant Pathology & Plant-Microbe Biology Projects

Below are past examples of projects that were planned for Summer Research Scholars. For details on 2022 projects, please check back in the future. 

1. BEAT IT!

Cercospora beticola, the causal agent of Cercospora leaf spot (CLS) is one of the most destructive foliar, fungal pathogens of table and sugar beets in the United States and causes significant annual losses in yield and productivity for growers. To cause disease Cercospora species also produce a phytotoxin called cercosporin and the gene cluster responsible for its synthesis is well characterized. If you love beets, joins us in a voyage of discovery to evaluate the genetics regulating pathogenicity in C. beticola. An added bonus will be visits to see the disease in the field, understanding its impact and management options available to table beet growers."

  • Field:20%, Lab: 80% (split coming soon)
  • Faculty: Pethybridge

2. Un-beet-able fungi? Rhizoctonia solani and table beet production

New York is the nation's second-largest producer of table beets (Beta vulgaris ssp. vulgaris). Recent industry expansion has increased the need for sustainable disease management strategies, especially for root rot caused by the Rhizoctonia solaniR. solani is a yield-limiting pathogen of table beets, sugar beets, and many other vegetable and grain crops. In beets, current control options are limited to in-furrow applications of azoxystrobin fungicides. The summer scholar will work in the lab and in the field to investigate alternative disease management strategies, including biocontrols/biofungicides. Additional skills will be developed collecting and characterizing isolates by anastomosis group determination and population studies. 

3. Something new under the sun?  

Our program has pioneered the use of ultraviolet light to suppress plant diseases. (View video.)  A critical issue is what effects the treatments have on non-target organisms on treated plants.  Are any harmed, and if so which ones?  Do yeast and bacterial populations rebound after exposure to therapeutic UV treatments?  How long does that take?  You’ll be the first in the world to answer these questions. 

  • Lab: 50%, Field: 50%
  • Faculty: Gadoury

4. The orchard is on fire!

Fire blight, caused by the bacterial pathogen Erwinia amylovora, is one of the most devastating diseases of apple production worldwide, capable of destroying entire orchards in unforeseen epidemics and costing farmers millions of dollars in the United States annually. Modern management of fire blight relies almost exclusively on antibiotic sprays, such as streptomycin, which have come under scrutiny due to the potential development of antimicrobial resistance in both pathogen and off-target bacterial populations. Each year numerous biological control options are developed for managing fire blight, but they often provide poor control and are not optimized for temperate production regions. Scholars will examine alternative management programs, including plant growth regulators and biological controls, for managing fire blight. In addition, scholars will investigate the distribution and movement of E. amylovora strains and potential implications for management utilizing CRISPR genotyping techniques. Scholars will have opportunities to visit actual fire blight outbreaks and learn about modern apple production.

  • Lab: 50%, Field: 50% 
  • FacultyCox

5. Endangered apples!

Apple Scab caused by the fungus Venturia inaequalis has limited the sustainable production of apples in temperate climates. The pathogen has become resistant to many of the safest and most environmentally responses fungicides. Multi-drug resistant V. inaequalis has caused disastrous production failures in apple production operations throughout the eastern US apple industry. Scholars will determine how farm management practices impact the evolution of resistant populations of V. inaequalis to help growers produce disease free apples safely and sustainably. They will look at population changes in fungicide target site genes and microscopic growth. In addition, scholars will have opportunities to visit orchards with disease outbreaks and learn about modern apple production.

  • Lab: 50%, Field: 50% 
  • FacultyCox

6. Mildew Mission

Apple powdery mildew (Podosphaera leucotricha) is a fungal disease found in most apple-growing regions of the world. P. leucotricha spreads on new growth as apple trees break dormancy in the spring, reducing tree vigor and hindering blossom development. The pathogen is obligate (meaning it requires its host to survive), which makes study difficult. Historically, P. leucotricha management in the orchard has relied on a narrow group of fungicides to maintain control. Little is known whether P. leucotricha populations have developed resistance to these compounds. Scholars will aid in the development of an in vitro culturing method for P. leucotricha to allow study, as well as establish a detached-leaf fungicide assay with which to test fungal isolates’ relative fungicide resistance. Scholars will also learn DNA extraction, PCR, and sequence analysis protocols to evaluate isolates for known resistance mutations to commonly-used fungicides. In addition, scholars will have opportunities to visit research and commercial orchards to learn about modern apple production.

  • Lab: 80%, Field: 20%
  • FacultyCox

7. Don't let their size fool you...

Despite their small genomes and lack of cellular machinery, viruses still pack a big punch: plants infected with viruses show a number of symptoms ranging from leaf discoloration to fruit deformities or death. You will learn how to use genetically engineered grapevine fanleaf virus to study how plant viruses cause symptoms in their host. You will also use proteomics techniques to probe the protein-protein interaction underpinnings of symptom development. You will gain skills in molecular biology, plant virus biology, and diagnosing virus infection, as well as protein extraction, detection, and proteomic analysis.

  • Lab: 90%, Greenhouse: 10%
  • FacultyFuchs

8. A virus’ arm race with host defenses

RNA silencing plays a critical role in plant resistance against viruses. To evade the antiviral host defense through RNA silencing, plant viruses have evolved RNA silencing suppressors that are potent arms in the arm race between plant and invading viruses. Research will involve the characterization of the RNA silencing suppressor of grapevine fanleaf virus using cell, biochemical, genetic and molecular technologies to improve our basic knowledge about plant-virus interactions and unravel the mechanisms of suppression of RNA silencing by this virus.

  • Lab: 80%, Greenhouse: 20%
  • FacultyFuchs

9. Grapes and a virus and an insect and symbionts: Oh my!

Red blotch is a recently recognized viral disease of grapevines that is caused by a DNA virus named grapevine red blotch virus. This virus is transmitted by the three-cornered alfalfa hopper.  There is much to uncover regarding the multitrophic interactions between the host, the virus, the treehopper vector, and symbiotic bacteria within the treehopper. You will use techniques such as nucleic acid extraction, polymerase chain reaction, dissection, and confocal microscopy to address questions about virus transmission and insect biology. You will take an active role in designing, optimizing, and implementing experiments, as well as analyzing and presenting data.

  • Lab: 80%, Greenhouse: 20%
  • FacultyFuchs

10. Code red: When a virus attacks!

Grapevine red blotch virus is the recently identified causal agent of red blotch disease of grapevine. This virus is vectored by the three-cornered alfalfa hopper in vineyards. You will contribute to research aimed at developing efficient transmission assays of the virus by its vector, to both grape and alternative hosts, to help characterize the transmission mode. You will design and optimize assays using techniques such as plant inoculation with infectious virus clones, nucleic acid extraction, polymerase chain reaction, dissection, sequencing, and microscopy while also learning insect rearing techniques.

  • Lab: 70%, Greenhouse: 30%
  • Faculty: Fuchs

11. No gut, no glory!

The three-cornered alfalfa hopper vectors a DNA virus named grapevine red blotch virus. Little is understood about the landscape-level movement of this viral transmitter; yet virus spread is occurring although grape is not a reproductive host and the hoppers are only found in vineyards during brief summer months. This project will look at the optimization of molecular gut content analysis to address feeding preferences of the treehoppers in a vineyard ecosystem. Research will involve insect rearing, feeding trials, dissections, molecular dietary composition, PCR, sequencing, and other laboratory techniques, to unveil virus-vector-host interactions.

  • Lab: 70%, Greenhouse: 30%
  • Faculty: Fuchs

12. Fighting an Old Battle with Modern Weapons: Can We Defeat Fire Blight With Next-Gen Genomics?

Fire blight, caused by the gram-negative bacterium Erwinia amylovora, is one of the most destructive bacterial diseases of apple trees. In recent years, research has been revolutionized due to increased throughput technologies and a reduction in genome sequencing costs. You will be involved in a project that takes advantage of high-throughput genomics and phenomics to better understand host-pathogen interactions. With this information we can characterize natural resistance sources in apples, identify genomic regions (QTLs), molecular markers, and underlying genes using the genetic diversity available at the US apple germplasm repository in Geneva, NY. You will inoculate apple trees in the greenhouse to determine susceptibility to fire blight and then participate in mapping out the genetic resistance source. In addition, you will use chlorophyll fluorescence, infrared thermal, and multispectral imaging to detect early symptoms in response to fire blight infection and to quantify disease susceptibility/resistance. Results of this research will ultimately be used for genetic enhancement of fire blight resistance in apples by deploying resistance alleles in commercially favored backgrounds.

  • Lab: 50%, Greenhouse: 50%
  • FacultyKhan

13. Can Machines be Taught to Accurately Diagnose Diseases in Apple Orchards?

Apple orchards suffer from large numbers of diseases that can incur serious damage to trees, fruits, and the industry. Rapid and accurate disease diagnosis is critical in commercial apple orchards for timely control and to implement successful and environmentally-sound management. Appearance of disease symptoms can vary based on image capture conditions or traits of host and disease making it challenging for computer vision models to accurately distinguish between the many symptoms of many diseases. Large datasets of high-quality images are critical to train computer vision models. You will help collect, annotate, and classify high-resolution images of biotic and abiotic stresses using digital cameras and smart phone during the growing season. This image dataset will be used to develop automated image-based disease classification and quantification of symptoms of biotic and abiotic stresses of apple for the accelerated and automated stress diagnostics and management in apple orchards. Students at Cornell Tech in NYC will use these images to develop and train machine learning models for automatic disease detection, and you will collaborate with them to test the models.

  • Computer: 50%, Greenhouse: 50%
  • FacultyKhan

14. The Key to Appealing Apples: Apple Scab Fungal Population Diversity, Virulence, and Host Genetic Resistance

Apple scab, caused by Venturia inaequalis, is a destructive fungal disease of major apple cultivars worldwide, most of which are moderately to highly susceptible. Cultivar resistance is the best long-term solution to reduce overall production costs and preserve fruit quality. Isolates of V. inaequalis vary in their ability to overcome resistance genes found among the commercial apple cultivars used in breeding programs for decades. You will participate in a project to characterize virulence of fungal isolates and the genetics of apple scab resistance. This will involve collection and culture of V. inaequalis isolates and their phylogenetic analysis based on genome resequencing data. Additionally, the project will require artificial inoculation and resistance/susceptibility evaluation of a genetic mapping population and a differential host set in the greenhouse,  as well as field data collection in an apple orchard with a diverse apple germplasm collection from all over the world.

  • Lab: 50%, Greenhouse: 50%
  • FacultyKhan

15. Do bacterial effectors affect an effect during tomato infection?

That's right! If you can say it, you'll certainly enjoy working on it.

Plant pathogens enjoy eating vegetables as much as we do. To promote disease, plant pathogens use an array of molecular mechanisms against their hosts. Effectors are proteins that pathogens deploy to manipulate the host metabolism and thus support their own growth. In this project, you will perform whole genome analyses of several strains of Xanthomonas cynarae pv. gardneri to fish for putative effectors. The methodology will include bioinformatics to align the genomes and lab work to validate the presence of these effectors in inoculated tomato leaves.

  • Lab: 80%, Greenhouse: 20%
  • FacultyC. Smart

16. Solving the root of our problems with microbes

Industrial hemp is a newly emerging economic crop throughout the country with numerous uses ranging from grain and fiber production to CBD supplements. Common soil pathogens such as Fusarium spp. and Pythium spp. are common causal agents of root rot and vascular wilt, which occur when these pathogens infiltrate the root systems and prevent water transport to the shoots. Our goal is to determine if biological additives can increase root growth and help hemp seedlings escape the devastating effects of root rot. In this project you will learn techniques to isolate fungal pathogens from field samples, analyze hemp root growth with various biologicals added, and gather imaging data using RhizoVision software.

  • Lab: 50%, Greenhouse: 50%
  • FacultyC. Smart

17. A spoonful of sugar helps the pathogen go down!

Cucurbit crops are susceptible to a variety of fungal and oomycete pathogens that can attack their roots, crown, leaves, and fruit. The soilborne pathogen Phytophthora capsici is notorious for causing blight on all parts of the host plant, and here we are especially interested in fruit rot of winter squash, Cucurbita sp. Some cultivars are less susceptible to fruit infection as a result of innate immunity, including rind thickness and sugar content. In this project, you will investigate the inhibitory effect that sugar may have on P. capsici and learn techniques to isolate pathogens from field samples. 

  • Lab: 65%, Greenhouse: 35%
  • FacultyC. Smart

18. Light, pathogens, action!

Reflectance spectroscopy is a newly-established but highly effective tool for non-destructively assessing plant disease physiology, and can be used to detect early, and even pre-symptomatic, pathogen infection. This project will explore early detection of grape powdery mildew and grape downy mildew in the field with non-destructive spectroscopy. Through this project, you will gain skills in applied precision agriculture research and data analysis in R. This project will directly contribute to a broader effort of building an early disease detection system for NY state grape growers. An added bonus will be visits to see the diseases in the field, understanding their impact and management options available to grape growers.

  • Field: 40%, Computation: 60%
  • Faculty: Gold

19. Jet Pathogen Laboratory: Vineyard disease detection with NASA sensors

The Jet Propulsion Laboratory’s Airborne Visible and Infrared Imaging Spectrometer Next Generation (AVIRIS-NG) is the highest quality imaging spectrometer (aka hyperspectral imager) on Earth. This project will explore early detection of grapevine diseases in commercial vineyards with NASA’s AVIRIS-NG. Through this project, you will gain skills in applied precision agriculture research, hyperspectral imaging, data analysis in python, and working with remote sensing data in QGIS. This project will directly contribute to a broader effort building global and regional disease warning systems for US grape growers. An added bonus will include virtual visits and opportunities to interact with NASA Jet Propulsion Laboratory scientists working with the Gold lab on this project.

  • Computation: 100%
  • Faculty: Gold

20. PhytoPatholoBot: The scout of the future!

PhytoPatholoBot (PPB) is the next generation of vineyard scouts: fully autonomous and fully robotic! This project will help develop PPB’s ability to scout for disease by teaching him how to differentiate between grape downy mildew and powdery mildew. Through this project, you will gain skills in precision agriculture research, applied robotics, data analysis in python, and computer vision. This project will directly contribute to a broader effort of building an early disease detection system for NY state grape growers. An added bonus will be visits to see the diseases in the field and collaborating with computer scientists and engineers.

  • Field: 50%, Computation: 50%
  • Faculty: GoldJiang

21. Hitchhikers beware: monitoring for soilborne pathogen transport on global dust currents

Global dust storms bring more than just dust with them when they blow, there is a growing body of evidence that shows that they’re also bringing along soilborne plant pathogen hitchhikers! This project will study how changing pathogen properties impact Fusarium oxysporum’s ability to hitchhike on global dust currents. Through this project, you will gain skills in precision agriculture research, bioinformatics, data analysis in python, and visualizing remote sensing data in QGIS. This project will directly contribute to a broader effort building global and regional disease warning systems for global agriculture. An added bonus will include virtual visits and opportunities to interact with NASA Jet Propulsion Laboratory scientists working with the Gold lab on this project.

  • Computation: 100%
  • Faculty: Gold