PPEM 425: Biology of Fungi (Fall 2017)

This course is a hands-on survey of fungal diversity, covering a wide variety of topics in fungal biology: phylogenetics, morphology, ecology, evolution, population biology, fungi as food, fungi as sources of toxins, ethnomycology, fungi as agents of plant and animal disease, fungi as sources of pharmaceuticals, and industrial uses.


  • Plant Pathology and Environmental Microbiology


Course Logistics

Instructor: Dr. David M. Geiser, Professor of Plant Pathology and Environmental Microbiology
Office: 121 Buckhout Lab
Phone: 814-865-9773
Email: or via Canvas
Office Hours: Tuesdays, 9:30-10:30 a.m., or by appointment. If not in 121 Buckhout, try 118 or 119 Buckhout Lab. After lecture and/or during/after laboratory time is generally the best time to ask questions.

Class Meeting Times:

  • Lecture: Tues/Thurs | 1:35-2:50 p.m.
  • Lab: Tues/Thurs | 3:05-5:35 p.m.

Class Location: 103 Buckhout Lab
Class Communication: I will contact you through Canvas email frequently, so you will need to make sure you are reachable.

Teaching Assistant: Phillip Martin
Email: or via Canvas

Materials: There is no required textbook for this course.

  1. REQUIRED: A three-ring binder in which to place your handouts for lecture and laboratory. All handouts will be hole-punched.
  2. OPTIONAL: You may wish to buy a field guide for yourself. These are recommended for use in the northeastern U.S. There will be several copies of these available in the laboratory. Class copies are NOT to be taken home for any reason.
    • National Audubon Society Field Guide to North American Mushrooms, by Lincoff. This is a sturdy and inexpensive field guide that you will find useful on and after field trips. Copies will be available in the classroom. $12-$15.
    • North American Mushrooms: A Field Guide to Edible and Inedible Fungi by Orson K. Miller, Hope H. Miller. $15-$20.
    • Mushrooms of the Northeastern United States and Eastern Canada by Timothy J. Baroni. <$20. This is a brand-new guide that I am trying for the first time in 2017.

Course Syllabus

Lecture and lab topics subject to change.

DayDateTopicLab/Other Info
1 8/22 Introduction to fungi Phylogenetics exercise
2 8/24 Introduction to fungi Microscope use and maintenance
3 8/29 Introduction to fungi FIELD TRIP 1*
4 8/31 Introduction to fungi, turn in study questions Identification of field-collected specimens
5 9/5 Basidiomycota I - Intro, Agaricomycotina FIELD TRIP 2*
6 9/7 Basidiomycota II - Agaricomycotina Identification of field-collected specimens
7 9/12 Basidiomycota III - Agaricomycotina FIELD TRIP 3*
8 9/14 Basidiomycota IV - Agaricomycotina, turn in study questions Identification of field-collected specimens
9 9/19 Basidiomycotina V - Ustilaginomycotina/Urediniomycotina Gasteromycetes
10 9/21 Basidiomycota VI - Urediniomycotina Jelly fungi
11 9/26 Ascomycota I - Introduction Smuts and rusts
12 9/28 Ascomycota II - Intro, Taphrinomycotina Yeasts
13 10/3 Ascomycota III - Saccharomycotina, turn in study questions DNA identification exercise
15 10/10 Ascomycota IV - Pezizomycotina DNA identification exercise
16 10/12 Ascomycota V - Pezizomycotina Polymerase Chain Reaction
17 10/17 Ascomycota VI - Pezizomycotina MRC Tour
18 10/19 Ascomycota VII - Pezizomycotina, Fungal ID projects due Asexual Ascomycota I
19 10/24 Ascomycota VIII - Pezizomycotina Asexual Ascomycota II
20 10/26 Ascomycota IX - Pezizomycotina, turn in study questions Cleistothecia
21 10/31 Ascomycota X - Pezizomycotina Perithecia I
22 11/2 Ascomycota XI - Pezizomycotina Perithecia II
23 11/7 Glomeromycota, Zygomycota I Sequence identification
24 11/9 Zygomycota II, Chytridiomycota I Other Ascomycota
25 11/14 Oomycota I, turn in study questions Mucoromycotina
27 11/28 Oomycota II Set up baits for zoosporic fungi
28 11/30 Slime molds, term paper due Zoosporic fungi
29 12/5 CATCH UP Zoosporic fungi
30 12/7 CATCH UP, turn in study questions Slime molds
Week of 12/11-15 FINAL EXAM - TBA, Includes a midterm style portion that specifically covers material from 11/14 to the end of the course (last 5 sessions)

*There may be more than three field trips, depending on the availability of field-collected specimens and other factors.

Course Activities

Lectures: 75 minutes is reserved for lecture every day. The instructor will write the lecture material on the whiteboard, and you must take copious notes. This course has no required textbook, and my lecture notes will not be made available to you in any form. Requests to make audio recordings of lectures may be granted; no still or video photography is allowed. Exam material will be based on what is covered in the lecture and laboratory. Occasional handouts pertaining to lecture material will be provided. At the end of most lectures, a PowerPoint presentation will show photographs and other information pertinent to the lecture presented. These PowerPoint files – which are NOT comprehensive of the lecture material and NOT a substitute for lecture notes – will be posted via Canvas at some point after the presentation.

Why so little PowerPoint? Unfortunately, to learn mycology you need to learn a lot of terms and life cycles – there is no way to avoid it. Note-taking is a key part of the learning process for students, and my writing material on the board keeps the pace of the lecture manageable.

You will need to use a pen/pencil and paper to take notes; I strongly recommend using loose-leaf notebook paper that can be placed into a three-ring binder along with course handouts. A laptop or tablet will only work for the text portions of the lecture material - diagrams and illustrations comprise a large portion of the material covered. In reproducing diagrams, you do not have to be a good artist, but you should be able to provide a schematic that answers the question.

Students who do best in the course not only take good notes, they curate them into a personal study guide.

Laboratories: After a ten- to fifteen-minute break following lecture, 2 hours and 30 minutes are reserved for the laboratory period. The prepared laboratory activities should not take that long, and the remaining time is available for you to work on projects and lab reports. No one will dismiss you from laboratory – you are free to leave when you have completed your work for the day. However, I recommend that you not run off as soon as you can: wisely utilize this time in your schedule.

Field Trips: We will take three to five field trips to local forests to collect fungi, depending on conditions. If fungal fruiting is poor, we may replace one or two of these trips with prepared labs. You will work in groups to identify what you collect and produce herbarium reports based on the results (see “Herbarium Project” handout to come). The field trips will occur during the lab periods on Tuesdays, starting in late August and possibly as late as mid-October. On field trip days we may leave earlier than the official beginning of lab period! I may change the dates of field trips based on the weather and availability of specimens.

Clothing: Tuesday field trips are mandatory and will be canceled/postponed only if the weather is very bad. We will proceed with trips in light-to-moderate rain, so make sure you are prepared with wet-weather clothing. We will be on easy trails, but there may be poor footing, and, if we are lucky, mud. So wear strong, closed-toed shoes with good traction, that you do not mind getting dirty.


Grades will be based on the following percentage scale. The total point value for the semester will depend on the actual number of assignments given, but will be in the range of 1250-1600 points.

A 93-100
A- 90-92.99
B+ 87-89.99
B 83-86.99
B- 80-82.99
C+ 77-79.99
C 70-76.99
D 60-69.99
F <60

Points will be given for the following:

  1. Midterm exams (2 x 150 = 300 points): Two midterm exams will be given covering lecture AND lab material, on OCTOBER 5 and NOVEMBER 16. Each exam will be worth 150 points. Students generally take from 45-90 minutes to complete these exams; rarely do students need or want more time, but I will try to provide as much time as you need.

    Each exam will have at least two portions, a short-answer portion (about 75-80 percent of the total points) and a fill-in-the-blank portion. Most or all of the short-answer questions will be chosen from “study questions” (see below) distributed beforehand. The total number of study questions provided during a full mid-term exam period (August 22 to September 28; October 3 to November 9) will be 60-80; a proportional number will be provided for the remainder of the semester. Approximately ten of these study questions will be chosen for the full mid-term exams, and a proportionate number will be chosen covering the last three weeks of the course on the final exam. The fill-in-the- blank questions will mostly test your knowledge of terms and taxonomy.
  2. Laboratory reports (approximately 200-300 points total): For most laboratories, you must turn in a short report; a handout will usually be provided telling you what to include. Most of these will be worth ten to thirty points each and will be returned to you after grading.
  3. Fungal identification project (~200 points): You will collect fungi and identify them in the laboratory. More on this later.
  4. Term paper on a fungus or group of fungi (OPTIONAL: 200 points): More on this later.
  5. Study questions (approximately 150 points): You will be given “study questions” related to the lecture and lab material on a regular basis. These same questions will make up approximately three-fourths of the midterm exam material (see above). In addition, you will be given a “taxonomy table” listing all of the organisms covered in the course, organized taxonomically. Approximately every two weeks, you will turn in your answers to the study questions during class. A number of questions will be selected for grading. The questions will be returned to you during the lab period.
  6. Final exam (200 + 75 = 275 points total): The final exam will consist of two portions: 1) a portion structured like the midterm exams, covering the material covered from November 15 to the end of the course, worth 75 points, and 2) a multiple choice/matching/fill-in-the-blank portion that is cumulative, worth 200 points.

What is hard about this course: The amount of material covered is very large. If you do not 1) come to class, 2) take good notes, and 3) study on a regular basis to keep up, you will be overwhelmed. Trust me.

The good news is that despite the mammoth amount of material covered, students tend to do pretty well. The small size of the course encourages students to get involved and be fully engaged. Those that don’t participate fully tend not to do as well. This should be a fun class – fully engage yourself in it and enjoy this rare opportunity where you can interact with the instructors and your classmates. Most students do this.


Your attendance will be noted every session. This is a small class, and I know who is present and absent on a daily basis. If you miss class for any reason, legitimate or not, it is a good idea to tell me why.

Missed exams and laboratories: Make-up exams will be given only in extremely special circumstances. Circumstances that do not warrant make-up exams include exams being given in other classes on the same day or travel for weddings or other non-emergency situations. Circumstances that may warrant make-up exams include bereavement, significant health issues, and crucial research or other academic activities. Most laboratory activities require special preparation and cannot be made up after the fact. Proof may be required for any excused absence. If you have a reason in advance for missing class, whether it is an acceptable excuse or not, it is important that you inform me of these things as far ahead of time as possible.

Flu Protocols: In compliance with Pennsylvania Department of Health and Centers for Disease Control recommendations, students should NOT attend class or any public gatherings while ill with influenza. Students with flu symptoms (respiratory symptoms accompanied by significant fever) will be asked to leave campus if possible and to return home during recovery. The illness and self-isolation period will usually be about a week. It is very important that individuals avoid spreading the flu to others.

Courtesy and Good Citizenship

Being on time: Lecture begins PROMPTLY at 1:35 p.m., whether you have arrived or not. You are expected to show up on time for every lecture. If you know you need to miss a class or lab for a legitimate reason ahead of time, let me know and I will do what I can to accommodate it. If you cannot make the 1:35 p.m. start time, I suggest that you take a different course.

Phones: Turn them off or to vibrate and do not use them during the lecture period. During lab period, as well as between lecture and lab, you may come and go as you please, but do not make or receive phone calls in the classroom – go out in the hallway.

Laptops and tablets: You must not use laptops or tablets except for legitimate classroom activities. The use of lecture or lab time for internet surfing or other illegitimate computer use will not be tolerated – it is rude, a distraction to your classmates, and very foolish if you want to do well in this course.

Academic Honesty: Students will work together in the laboratory, and study groups are encouraged both for answering study questions and for exam preparation. However, with the exception of group assignments specifically labeled as such, ALL material turned in must be the original work of each individual student, and students must not copy the work of other students, from websites, publications, or other material, either for the class projects or for the exams. Copying even portions of descriptions of Fungi or other published material for any projects is plagiarism. Such misrepresentation will be dealt with as a matter of academic dishonesty, which will result in any combination of a zero grade on the assignment, an F grade in the class, and/or disciplinary action by the university in accordance with the policies described below.

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