Plant Path. & Plant-Microbe Biology Projects

What project will you work on during your internship as a Summer Research Scholar? You should choose three (3) projects from the list below and note them in order of preference (e.g., 2, 4, 1) at the top of the APPLICATION FORM. We will do our best to accommodate your top choice.

Faculty members associated with each project are also listed. You can read more about their programs by clicking on their names.

1. Flying fungi

FungiInvestigate the remarkable processes that fungi have evolved for dispersal and survival in an introduction to the sciences of aerobiology and plant epidemiology. As part of a research team, you'll learn how fungal plant pathogens move anywhere from microns to thousands of kilometers to cause disease. Plant systems involved include wine grapes, fruit and vegetable crops.
Lab 50%, Field 50% Faculty: Gadoury

2. Bacteria that Prevent Disease

girl in vineyardStudy how to detect Agrobacterium vitis that cause crown gall disease and other bacteria that stimulate freezing injury that are called ice nucleation-active (INA) bacteria in grapevines.  The different genera that are isolated will be characterized.  Study the survival of A. vitis and INA bacteria on grapevines and on other plant species in vineyards (weeds and cover crops) and determine how prevalent they are.
Lab 50%, Field 50% Faculty: Burr

3. Don't let their size fool you...

Despite their small genomes sizes 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 to death of the plant.  In this project, you will learn how to design, construct, and use genetically engineered viruses to study how plant viruses cause symptoms in their host.  You will gain skills in using molecular biology software, performing traditional molecular cloning, inoculating plants with viruses, and detecting virus infections.
Lab 70%, Greenhouse 30% Faculty: Fuchs

4. The orchard is on fire!

fire blight on leavesFire blight, caused by the bacterium Erwinia amylovora is one of the most devastating diseases of modern apple orchards and destroys 100s of acres of high-value apples each year. While antibiotics are the most effective way to manage the disease early in the season, they are ineffective at later stages of the disease. Moreover, organic apple producers are unable to use antibiotics and are left with few viable options. 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 the use of plant growth regulators and biological controls for managing fire blight. Scholars will have opportunities to visit actual fire blight outbreaks and learn about modern apple production.
Lab 50%, Field 50% Faculty: Cox

5. Smile!

fungiThis project requires familiarity with software for creation of Computer-Generated Animation (CGA) and digital imagery.  The student will be embedded within the research program of a major national research project on strawberry diseases involving Cornell University, The University of Florida and the US Department of Agriculture, with the goal of producing the CGA and digital image content required for educational videos depicting various aspects of pathogen growth and infection.
Lab 80%, Greenhouse/Field 20% Faculty: Gadoury

6. Endangered apples!

apple scabApple 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 in an effort 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% Faculty: Cox

7. “In short, if all the matter in the universe except the nematodes were swept away, our world would still be dimly recognizable-...” (N. A. Cobb, 1915)

CarrotWith such a big statement, why wouldn’t you want to study nematodes! Have you ever wondered – how collegial are nematodes? Do they hang around together or individually? How damaging are they? If so, well this is the project for you!  In this project we will focus on quantifying the impact of plant-parasitic nematodes on potato production.  This will involve characterizing the spatial characteristics of real-life epidemics using geostatistical-based modelling and learning a variety of techniques (traditional enumeration, bioassays, and molecular) for quantifying nematode population densities.
Lab 50%, Field 50% Faculty: Pethybridge

8. Lights Out!

pathogenic fungiLight has a poorly understood regulatory role in the production and release of inoculum by several plant pathogenic fungi. Be part of a team that is exploring how light intensity, quality, and timing can be used to moderate or inhibit sporulation, and thereby affect the incidence and severity of disease.
Lab 90%, Field 10% Faculty: Cadle-Davidson, Gadoury

9. Outside, inside, out, Clavibacter’s livin’ la vida loca

TomatoClavibacter michiganensis subsp. michiganensis is the causative agent of bacterial canker of tomato. This disease is an internationally devastating pathogen and a problem in New York tomato production. We do not yet have a full picture of what makes this bacterium a pathogen, but interestingly enough, it appears to be inside tomato cells, which would be unusual for a plant pathogen. This summer we will use plant bioassays, confocal microscopy, and other lab techniques to determine if and when the bacteria might be entering the tomato cells. 
Lab 75%, Field 25% Faculty: C. Smart

10. Chillin' in the Hopyard!

Hop yardThose cool early summer nights may be great for sleeping, but they aren't so good for some plant diseases! Investigate how cold temperatures can kill the fungus that causes hop powdery mildew, and how those same cold temperatures can also make hop plants more resistant to infection. This work will involve both hop yard investigations into how leaf temperatures supercool at night and how the disease spreads in the early season, as well as laboratory studies where the Scholar will learn various microscopy skills, including scanning electron microscopy! If you like working outside, but also want to improve your microscopy skills, Chillin' in the Hopyard is just for you!
Lab 50%, Field 50% Faculty: Cadle-Davidson, Gadoury

11. Magical rusts and where to find them

RustNew York State is one of the leading producers of shrub willow as a bioenergy feedstock.  However, a fungal rust pathogen aims to thwart our progress.  In this project, you will help decipher the genetic structure of Melampsora spp. isolates using a genome-wide-strategy to gain a clearer picture of these organisms’ populations.  You can expect to be smitten with the bright orange spores, while expanding your knowledge of microbiology and molecular techniques.
Lab 70%, Field 30% Faculty: C. Smart

12. Modern next-gen genomics weapons to better fight fire blight disease

plant injectionThe gram-negative bacterium Erwinia amylovora is one of the most destructive bacterial diseases of apples. Progress has been made in understanding interactions between host and pathogen, but managing fire blight, the disease caused by the bacterium, remains problematic. You will be involved in research that takes advantage of next-gen genomics technologies, such as genome and transcriptome sequencing, to understand host-pathogen interactions, characterize resistance in apples, and identify genomic regions (QTLs), molecular markers, and underlying genes using genotypes from the national apple germplasm repository. You will inoculate apple trees in the greenhouse to determine susceptibility and then map out the genetic source.
Lab 50%, Greenhouse/field 50% Faculty: Khan

13. Protecting peppers, pumpkins, and zucchini from a devastating pathogen

pumpkinsPhytophthora capsici is a devastating pathogens on many vegetable crops, including peppers, pumpkins, and zucchini. This project involves testing plant breeding lines for resistance, studying the pathogen, and bioinformatics on DNA sequence. As part of our search for host plant tolerance to this oomycete pathogen, you will inoculate and evaluate zucchini and pumpkin plants for disease susceptibility in replicated trials in the greenhouse and field. You will also gain skills in the lab as you extract, sequence, and analyze DNA from isolates to characterize the genetic diversity of the pathogen.
Lab 70%, Field 30% Faculty: C. Smart

14. Multi-dimensional visualization of disease progress for apple gene identification

​​Erwinia amylovora Symptoms developed by apple trees in response to the attack by the gram-negative bacterium Erwinia amylovora can be visualized and quantified to assess disease severity. The variation in response can then be correlated with changes at the host cellular and gene expression levels to identify genes for improving disease resistance.  You will work on developing real-time imaging of fire blight infection in susceptible/resistant apples to monitor disease progress, with concurrent sampling of transcripts and the metabolome to identify specific spatio-temporal resistance mechanisms at the genetic, cellular and molecular levels.
Computer Lab 60%, Greenhouse/field 40% Faculty: Khan

15. Spread of the red

grape virusGrapevine red blotch-associated virus (GRBaV) is a recently recognized DNA virus causes red blotch disease of grapevines. Help understand the epidemiology of this virus and contribute to research efforts addressing spread of GRBaV by testing the transmission attributes of its treehopper vector and searching for alternative hosts. Laboratory work will consist of designing, optimizing, and implementing experiments based on nucleic acid extractions, polymerase chain reactions, insect dissection, and nucleotide sequencing.
Lab 70%, Greenhouse 30% Faculty: Fuchs