Credits: 1 to 19, but it is recommended that students sign up for 1 or 2 credits only in Spring 2014. One credit is interpreted as about 3 hrs of work per week for an entire semester, or 40-45 hours total, including listening to online lectures, reading related materials, taking quizzes, and, especially, engaging in hands-on activities.

If you do more work than initially planned, you may sign up for the additional credit earned the next time the course is scheduled (planned for spring 2015). See how it goes once you get into it!

Spring 2014 Students will be allowed (to allow work with more fresh material), to extend work into the summer, finishing by August (or other negotiated time). A grade of incomplete would be given at the end of spring semester if this is done. Alternatively, see note above about signing up for additional credit in the future.

Coordinator: Anton Baudoin


Fungi: Anton Baudoin

Nematodes: Jon Eisenback

Prokaryotes: Boris Vinatzer

Viruses: Xiaofeng Wang

Collaborators/contributors: Several, including Elizabeth Bush, Mary Ann Hansen, and Gary Griffin. Others will be listed as contributions are received. Off-campus students should seek a local coordinator for assistance with any logistics, and perhaps administration of quizzes (quizzes with on-campus instructors may also be arranged by phone, Skype, or email).

Rationale: The current PPWS graduate course line-up, with very few graduate plant pathology courses containing a lab component, leaves plant pathology students short on hands-on and practical experience in identifying and working with plant pathogens.

This course will provide a number of online introductions or lectures on identification of plant pathogens in general and of selected groups, accompanied by a choice of exercises that students can complete on a flexible schedule, with faculty guidance as needed. This allows students at off-campus locations to complete this course. And it allows off-campus faculty to participate in teaching this class, while the team-taught nature will keep the time commitment of each faculty member modest.

Coverage: Identification and working with selected groups of fungi, prokaryotes, nematodes and viruses, with focus on major plant pathogens but also including common saprophytes. Students may elect to study material on all pathogen groups, or focus on only one or several. Materials will include cultures and dried specimens, as well as specimens that students collect themselves. The idea is not to provide comprehensive coverage of all pathogen groups, but enough of a variety of examples to provide students with basic competency.

Pre- or corequisite: Coverage of pathogens equivalent to that offered in PPWS 4104, Plant Pathology. Expected: Plant Pathogenic Agents, PPWS 5054, but introductory material will be available for motivated students without this background.

Each “section” is expected to contain:

  1. Introductory lecture and/or explanation in different format (e.g., Powerpoint file with narration script; if you would rather listen than read, contact course instructor)
  2. A quiz or test on this introductory material
  3. Instructions for possible ACTIVITIES (e.g., examination of fungal cultures, dried plant samples, etc., see below)


  1. Review of the basics on fungi. Introduction, overview of fungi and fungus-like organisms as plant pathogens. Classification and identification.
  2. Microscope use (Eisenback)
  3. Techniques: collecting, preserving, slide preparation (staining? thin sections?) and preservation, photography, resources on techniques, biosassay of fungicide sensitivity
  4. A general approach to identifying microfungi on plants (Hansen)
  5. Major groups
    1. Classification and identification of Oomycota
      • Phytophthora (Bush)
      • Pythium (Bush)
      • Downy mildews
    2. Classification and identification of Ascomycetes
      • Cryphonectria parasitica (Griffin, cultures available with 2 wks notice)
    3. Classification and identification of Deuteromycota
      • Introduction to Deuteromycota or Fungi Imperfecti
      • Fusarium (Schmale)
      • Powdery mildews
      • Sclerotinia
      • Common foliar fungi: Mycosphaerella, Cercospora, Septoria, Phyllosticta, etc.
    4. Classification and identification of Basidiomycota
      • Rhizoctonia
      • Rusts
      • Smuts
  6. A general approach to identifying nematodes (Eisenback)
  7. Major groups of plant-parasitic nematodes (Eisenback)
    1. Classification and identification of Tylenchids
      • Meliodogyne
      • Globodera
      • Heterodera
      • Pratylenchus
      • Hoplolaimus
      • Helicotylenchus
      • Tylenchorhynchus
    2. Classification and identification of Criconematids
      • Criconema
      • Paratylenchus
      • Gracilacus
      • Hemicycliophora
    3. Classification and identification of Aphelenchs
      • Aphelenchoides
      • Aphelenchus
      • Bursaphelenchus
    4. Classification and identification of Dorylaims
      • Trichodorus and Paratrichodorus
      • Xiphinema
      • Longidorus

Modules on prokaryotes and viruses to be added.

Activities, assignments and grading

  1. Online lectures (we aim to provide choices).
  2. Quizzes based on online lectures (may be online quizzes, or paper quizzes that students may arrange to take in faculty offices, or oral quizzes – sample question: “tell me about some of the major things you learned from this lecture.” Negotiable. These are generally expected to be relatively short (10-30 minutes; you will be warned about outliers).
  3. Examination of samples (cultures, herbarium material, fresh collections) and reports
  4. Required: collection of unknowns, with brief reports on observations and attempted identifications
  5. Identifying common contaminants
  6. Isolation of Phytophthora from roots on selective media, observation of cultures under microscope, production of sporangia.
  7. Baiting (Phytophthora?)
  8. Anastomosis group testing (Rhizoctonia)
  9. Inducing sporulation and/or sexual reproduction, variety of techniques
  10. Measuring structures (e.g., spore size)
  11. Determining spore concentration
  12. Browsing the book shelf (techniques, identification keys, etc.)
  13. Other possibilities that may emerge from studying materials and resources on plant pathological techniques (see references)
  14. Observations of key Phytophthora morphological characteristics (sexual and asexual structures, hyphal swellings, chlamydospores); production of zoospores, zoospore observation, use of hemocytometer and producing single zoospore colony.

Grade will be based on quiz results and lab activity reports/notes. Weighting will vary depending on percent of effort (i.e., some students may take fewer quizzes than others but complete more activities). Course completion will be by discussing your accumulated activity reports with an appropriate course instructor.


  1. Online lectures will be posted in Scholar as the material becomes available, and students will be notified. You should schedule and pace yourself. Contact appropriate instructor (or off-campus contact) to set up an appointment when ready to take a quiz on a particular module; see above for more information on quizzes.
  2. Hands-on activities, general: Some of these you can schedule yourself (for example, creating a collection of specimens); for others, contact instructor to schedule availability of materials, “Open House” lab times, and personalized instruction (but don’t assume the instructor knows everything). Please keep a log of time spent, and keep a notebook on all your activities. This notebook may be on paper, or electronic (MS Word file or whatever format is deemed suitable), or a mix of the two. It should contain notes on work accomplished, line drawings, photos, and other suitable materials. Consult with instructor once you have gotten a start, and preferably several additional times, to determine whether contents are suitable. Although you should aim to include observations and identifications, if you spend an hour looking through resources on how to culture or stimulate sporulation of fungi, those activities count, and brief notes on those activities should be included as well.
  3. Collection: Start keeping your eyes open for possible specimens that you may encounter yourself. This should include the following:
    • Plant diseases
    • Dead plant material with sporulating fungal pathogens and saprophytes
    • Isolation attempts and whatever grows from those, both pathogens and contaminants

Collect specimens and try to identify. Keep records: host, collection date and location, symptoms (if any) and any observations on fungi present. Photographs (macro and micro) encouraged, and preserved slides may be saved. Aim for diversity and representation of different taxonomic and ecological groups.

  1. Materials that can be made available:
    • Cultures
    • Dried plant material
    • In-season: fresh plant material, and the "Catch of the Day" from the Plant Disease Clinic
    • Some reference books
    • Microscopes may be used in Price Hall (classroom 400), or in the lab facilities where you work. Digital cameras mounted on microscopes are available in Price 417 (but it's difficult to get good illumination for the one on the dissecting microscope; working to improve this).
    • Assistance: Let an instructor know when you need help. We'll organize "open house" times, and your suggestions as to what would work well for you will be helpful in doing this most effectively.
  2. Students are encouraged to share findings, for example, when they find and collect interesting specimens, or when they produce interesting structures.
  3. Field trips? Why not? Probably best once the weather warms up. We could aim for morel season!