Plant Pathology & Plant-Microbe Biology Projects

2022 projects

1. 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.

Computer work/data analysis: 40% effort, Field and greenhouse: 40%, Lab: 20%

Faculty: Gold

2. 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 mapping individual crops within fields and early detection of grapevine diseases in commercial vineyards with NASA’s AVIRIS-NG. High resolution space borne instruments are now available at a global scale. 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.

Computer work/data analysis: 100%

Faculty: Gold

3. 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.

Computer work: 50%, Field: 50%

Faculty: Gold

4. 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.

Computer work/data analysis: 100%

Faculty: Gold

5. Tomatoes under attack: how varieties of tomato respond to a bacterial pathogen

Description: Plants get sick just as we do. Bacteria in the genus Xanthomonas are especially good at infecting a wide array of different economically important crops, tomato plants included, causing a disease called bacterial spot of tomato. This disease causes nasty dark spots in the fruits making them unmarketable. Bummer! During your summer internship, you will be involved with a field experiment evaluating the pathogenicity and virulence of the bacterial spot pathogen on about 20 different tomato varieties from around the US.  Work will range from learning microbiological techniques, growing bacteria in the lab, and inoculating tomato plants, to rating the disease in the field. You will also learn lab techniques including DNA extraction, PCR, and performing greenhouse experiments to assess the role of specific bacterial genes in virulence on tomato. You will be part of a diverse and inclusive environment in our lab!

Lab: 40%, Field: 40%, Greenhouse: 20%

Faculty: C. Smart

6. The “root” of the problem in hemp cultivation

Description: The root systems of hemp plants are highly susceptible to fungal rots, particularly in wet soils. In this project, you will examine root architecture using digital imaging, test root growth-promoting microbes, and analyze the role root exudates may play in disease development. There will be lab, greenhouse, and field work where you will learn to culture root pathogens, treat plants with growth-promoting microbes, and develop strategies to characterize hemp root exudates.

Greenhouse: 36%, Lab: 48% lab, Field: 16%

Faculty: Smart

7. Rhubarb, really??

Description: Come learn about the amazing rhubarb plant while also learning about one of its fungal leaf spot pathogens. You will collect field samples from several locations in New York, culture the pathogen, extract DNA, inoculate the host, and help determine how many different fungi are attacking our delicious rhubarb. If interested, the project may also include extracting DNA from rhubarb leaves to determine the genetic diversity of the crop. 

Lab: 60%, Field: 30%, Greenhouse: 10%

Faculty: C. Smart

8. The Little Green Friend

The three-cornered alfalfa hopper, Spissistilus festinus, has become of growing interest for its role in vectoring grapevine red blotch virus (GRBV). S. festinus can be found in vineyards but are not the only “little green friends” to be present. Several other treehopper species are believed to feed and interact with similar plant species as S. festinus in vineyard ecosystems. There is currently no information on the genetic divergence of these species. Here, you will investigate three buffalo treehoppers and test how genetically related these species are and whether they can ingest GRBV. Research will involve insect DNA extractions, characterization of target insect and virus genes by PCR and sequencing, and other laboratory techniques, to unveil phylogenetic diversity.

Laboratory: 100%

Faculty: Fuchs

9. A virus a day keeps the apples away?

An unexplained collapse of young apple trees is a growing source of concern for growers, extension specialists, and researchers alike. Many hypotheses have been proposed about the causal factor(s) of this phenomenon, from novel pathogens to abiotic stresses, but to date, the culprit(s) remain unidentified. Our goal is to determine whether latent viral pathogens of apple trees are involved in tree decline and collapse. Despite their global distribution and high prevalence in apple orchards, relatively little is understood about the impacts of these viruses on apple production. For this project, you will investigate the effects of several latent viruses on the health of young apple trees, as well as their potential role in tree decline. You will optimize and implement nucleic acid extraction techniques and molecular diagnostic assays to detect and quantify viruses in plant tissues, in addition to assessing tree health in experimental and commercial apple orchards.

Laboratory: 70%, Field: 30%

Faculty: Fuchs

10. Hydroponic virus factories

Grapevine fanleaf virus (GFLV) causes fanleaf degeneration in Vitis spp and is present in most vineyards worldwide. We utilize the model host Nicotiana benthamiana to investigate molecular mechanisms of virus-host interactions. We are studying how GFLV causes symptoms, and how it affects foliar traits and root growth in a plant. The goal of this project is to quantify these traits in a high-throughput manner. You will gain experience in molecular biology techniques, RNA isolation of plant tissue, virus inoculations of plants, virus detection and hydroponic plant growth systems. Machine learning based phenotyping and RStudio will be utilized but no prior programming or computational knowledge is required.

Laboratory: 60%, Greenhouse/Growth chamber: 25%, Computation/Programming: 15%

Faculty: Fuchs

11. Behaving ‘Graply’

Spissistilus festinus (the three-cornered alfalfa hopper) vector grapevine red blotch virus (GRBV) but their relationship with their grapevine host is antagonistic. S. festinus is not a natural pest of Vitis spp. and struggle to complete reproductive cycles on wine grapes. Nonetheless, S. festinus transmit GRBV in vineyards. The presence of S. festinus as an agricultural concern for the grape and wine industries was previously disregarded but, as knowledge of GRBV transmission increases, so does the need to establish an understanding of the relationship between S. festinus and Vitis spp. This summer you will investigate the behavior of S. festinus on distinct Vitis spp. by looking at tissue preferences, instar development capabilities, and GRBV acquisition. Research will involve insect rearing, feeding trials, behavioral analysis, insect DNA isolations, PCR analysis of GRBV, and other laboratory techniques, to unveil virus-vector-host interactions.

Laboratory: 50%, Greenhouse/Growth chamber: 50%

Faculty: Fuchs

12. Break the silence!

RNA silencing is an effective and conserved antiviral defense mechanism utilized by plants to fight against viral infections. To counteract this host defense, plant viruses have evolved to encode proteins that act as RNA silencing suppressors and interfere with specific steps of the antiviral RNA silencing pathways. You will contribute to research aimed at exploring the mechanisms of suppression of RNA silencing by grapevine fanleaf virus (GFLV) in the model host Nicotiana benthamiana. You will use fluorescence imaging, biochemical, genetic, and molecular tools to improve our understanding of plant-GFLV interactions.

Laboratory: 80%, Greenhouse/Growth chamber: 20%

Faculty: Fuchs

13. Vectors, they’re grape!

Grapevine red blotch virus is a significant threat to grapevine production. The virus is transmitted by an insect vector, the three-cornered alfalfa hopper in vineyard settings. You will contribute to research aimed at optimizing transmission assays of the virus by its vector and further understand transmission capabilities of the insect. 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.

Laboratory: 70%, Greenhouse/Growth chamber: 30%

Faculty: Fuchs

14. Virus plus virus equals no symptoms?

Grapevine fanleaf virus (GFLV) shows stark vein-clearing symptomology on the model plant host Nicotiana benthamiana. We identified select host protein candidates that likely interact with GFLV for symptom development. To validate some of these host candidates, you will use another virus in RNA interference experiments to knock down the expression of these genes and assess whether vein clearing symptoms caused by GFLV are absent or still present. This exciting venture will investigate the molecular underpinnings for viral infection and symptom development. You will explore and gain experiment in RNA isolation from plant tissue, characterization of host genes by PCR, virus inoculation techniques, virus-induced gene silencing, and virus detection.

Laboratory: 70%, Greenhouse/Growth chamber: 30%

Faculty: Fuchs

15. 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, molecular markers, and phenomics to better understand genetics of fire blight resistance in apples. This research experience will involve characterization of natural resistance sources in apples, identification of genomic regions (QTLs), and underlying genes using the genetic diversity in apples and genetic mapping populations. 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/field: 50%

Faculty: Khan

16. Know Your Roots: Rootstock-regulated Disease Resistance in Apples

In apple orchards, a superior ‘scion’ fruit cultivar is grafted onto rootstock genotypes to maintain its genetic identity. Rootstock can impact tree size, tree vigor, plant-associated soil microbial communities, and biotic and abiotic stress tolerance of grafted scion cultivars. Identifying and characterizing the exact mechanism regulating rootstock-derived tolerance or resistance can benefit apple productivity and disease management. In this project you will participate in characterizing the role of rootstocks in regulating fire blight susceptibility of grafted scion. This will involve quantifying the roots of apple rootstocks, developing new methods for root phenotyping, characterization of molecular mechanisms and differential gene expression in scion tissues of rootstocks with contrasting root systems. The data generated in this project will be used to help define the exact mechanism regulating rootstock-derived tolerance or resistance that can benefit apple productivity.

Greenhouse/field: 50%, Computer/Lab: 50%

Faculty: Khan

17. The Key to Appealing Apples: Genetic Mapping of Host Resistance to Apple Scab Fungus

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 commercial apple cultivars used in breeding programs for decades. You will participate in a project to genetically map apple scab resistance. This experience will involve collection and culture of V. inaequalis isolates, artificial inoculation and resistance/susceptibility evaluation of a genetic mapping population, molecular marker genotyping, QTL mapping, as well as field data collection in an apple orchard with a diverse apple germplasm collection from all over the world.

Lab: 50%, Greenhouse/field: 50%

Faculty: Khan

18. “Roads? Where We’re Going, We Don’t Need Roads”: The case study of Stemphylium vesicarium

Stemphylium vesicarium is a fungus responsible for an important disease of onion production in NY state, Stemphylium leaf blight (SLB). This project will study the aerobiology of S. vesicarium. The outcomes will depict the seasonality of spore concentrations and find weather variables associated with SLB. Together, these pieces of information will underpin the development of a forecasting system to reduce the use of pesticides in onion production, which will increase sustainability for the environment, produce healthier food for consumers, and reduce costs for growers. On this project, the summer scholar will work in the laboratory and the field. They will learn techniques in epidemiology and molecular biology; and plan, design, and conduct field experiments. By the way, the title of this summer scholar project is a quote from “Back to the Future: Part II” movie, which does not encompass all the story...

Faculty: Pethybridge

19. 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, germicidal light, 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

20. Endangered apples!

Apple Scab caused by the fungus Venturia inaequalis and other emerging fungal diseases have limited the sustainable production of apples in temperate climates. The apple scab pathogen has also become resistant to many of the safest and most environmentally responses fungicides. In response, producers are now relying on less-environmentally-friendly multi-site fungicides. There are also new regulations and restrictions being placed on multi-site fungicides leaving growers scrambling for options. Scholars will use horticulture, disease forecasting, and careful selection of biopesticides and single-site fungicides determine how to best help growers produce disease free apples safely and sustainably. In addition, scholars will have opportunities to visit orchards with disease outbreaks and learn about modern apple production.

Lab: 50%, Field: 50%

Faculty: Cox