Plant Path. & Plant-Microbe Biology Projects

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These are the Plant Pathology and Plant-Microbe Biology projects that our Summer Research Scholars will be tackling in 2019.  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. Shedding light on bacterial lifestyle: studying the potential for intracellular colonization of the bacterial canker pathogen of tomato.

The Gram-positive bacterium, Clavibacter michiganensis subsp. michiganensis (Cmm), is the causal agent of bacterial canker of tomato. Cmm is a seed-borne pathogen that can spread systemically through the plant causing wilt, cankers, necrosis, and fruit lesions. In order to develop new strategies to control this disease, we must learn more about the pathogen’s biology. Preliminary evidence shows the potential for the bacterium to be intracellular, which is uncommon for bacterial plant pathogens. This project will use plant bioassays, protoplast preparation, confocal microscopy, and other lab techniques to determine the range of cells that the pathogen may affect and to search for intracellular bacteria in intact cells.
Lab: 50% Greenhouse: 25% Microscopy: 25% Faculty: C. Smart


3. 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 to death of the plant. In this project, you will learn how to use genetically engineered viruses 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 70%, Greenhouse 30% Faculty: Fuchs


4. The orchard is on fire!

fire blight on leavesFire 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, chiefly 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% 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. Beat it!

Cercospora 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 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 genes regulating cercosporin production and 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.
Lab 80%, Field 20% Faculty: Pethybridge


7. 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


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

Phytophthora capsici is a devastating pathogen of many vegetable crops, including peppers, tomatoes, pumpkins, and zucchini. Currently, there are no resistant zucchini or pumpkin varieties commercially available for growers. The objective of this project is to develop disease-resistant varieties and elucidate the genetic basis of this trait. As part of our research team, you will inoculate and evaluate breeding lines in replicated trials in the greenhouse and field. You will also gain experience in genomics as you map loci involved in resistance and develop and test molecular markers. 
Field 60%, Lab 40%     Faculty: C. Smart


10. Mildew Mission

apple powdery mildewApple 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% Faculty: Cox


11. 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


12. 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


13. Modern weapons for an old battle: can we win the fight against fire blight with next-gen genomics?

plant injectionFire 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 next-gen genomics, including genome and transcriptome sequencing, to better understand host-pathogen interactions, characterize natural resistance sources in apples, and 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 map out the genetic resistance source. 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/field 50% Faculty: Khan


14. Spread of the red

red blotchRed blotch is a recently recognized viral disease of grapevines that is caused by a DNA virus named grapevine red blotch virus. Contribute to research efforts addressing virus transmission by its treehopper vector and searching for alternative hosts. Research will involve designing, optimizing, and implementing experiments utilizing techniques such as nucleic acid extraction, polymerase chain reaction, dissection, agroinoculation, sequencing, and fluorescence microscopy.
Lab 70%, Greenhouse 30% Faculty: Fuchs


15. Early detection of disease symptoms and multi-dimensional visualization of disease progress in real time for gene identification

imagingPlants develop symptoms in response to pathogen attacks that can be visualized and quantified. Fire blight, caused by the gram-negative bacterium Erwinia amylovora, is one of the most destructive bacterial diseases to apples. So far, there are no reliable, precise and high-throughput methods to detect early symptoms in response to pathogen attack and to quantify disease susceptibility/resistance. You will be involved in testing chlorophyll fluorescence and infrared thermal imaging for early disease detection. You will also work on developing real-time imaging of fire blight infection to monitor disease progress with concurrent sampling and characterization of transcripts to identify specific spatiotemporal molecular mechanisms. This research will provide new insights into physiological changes in response to disease development and lead to more fire blight resistant apples through the identification of novel molecular markers.
Computer/lab 60%, Greenhouse/field 40%, Faculty: Khan


16. Assessing white mold on industrial hemp

hemp white moldIndustrial hemp is Cannabis sativa with low levels of THC production and has recently made a return to New York State after almost a century. Industrial hemp has a wide range of uses and there are growing potential markets in fiber, oilseed, and pharmaceutical production. While hemp has not been grown in New York State for many years, observations in other areas where hemp has been grown for longer have proved that white mold (Sclerotinia sclerotiorum) will likely be one of the most important diseases to affect hemp. Understanding how various cultivars of hemp stand up to this fungus will be an important piece of information for both new growers and the hemp breeding program here at Cornell. You will gain useful plant pathology skills as you inoculate cultivars and evaluate their susceptibility in the greenhouse. This research will help to inform future field trials and experiments to better understand how we can deal with this disease as Industrial hemp becomes a more widespread crop in New York.
Lab 40%, Greenhouse 60% Faculty: C. Smart