BIO540 – Mycology

Course Information – Fall 2016

Jessie Uehling, Biological Sciences, Room 344, 660-7369,
Rytas Vilgalys, Biological Sciences Room 346, 660-7361,

Location &Time:
FFSC 1244, Tuesday/ Thursday 8:30AM-11:30AM

Students will gain the skills necessary to:

  • Understand basic fungal biology
  • Be familiar with major fungal lineages
  • Collect and identify fresh fungi
  • Culture and barcode fungi using PCR
  • Create and interpret phylogenetic trees using molecular sequence data
  • Understand how fungi are utilized and encountered every day
  • Describe various fungal ecological strategies
  • Analyze and explain methods and results from primary scientific research literature

Class Structure:
Classes will meet on Tuesday and Thursday from 8:30-11:30AM in French 1244, including both lecture and lab. Unless otherwise noted, classes will begin with lectures about topics indicated on the schedule. The lab portion of each class will consist of a discussion about the assigned readings, and allotted time for specific lab activities introducing methods, concepts, and protocols. Papers will include both recent and seminal manuscripts from scientific journals.

Date Lecture Topic Lab Activity Quiz/Due date
30-Aug Introduction to fungi, collections, & ID Reading, EOL, & flash phyla signup, fungal isolation set up, field trip  
1-Sep Fungal Tree of Life Media preparation, culture methods flash fungal phyla presentations
6-Sep Basidiomycetes I: Agaricomycete families & poisonous fungi Field trip  
8-Sep no class    
13-Sep Basidiomycetes II: Agaricomycete families cntd. sterile technique & field trip  
15-Sep Environmental culture ID & microscopy photography cultures, microscopy  
20-Sep Fungal toxins Discussion 1: fungal toxins papers Quiz 1
22-Sep Medical mycology Discussion 2: medical mycology papers First blog post due on Sunday (9/25)
27-Sep Basal basidiomyetes, mating compatibility, population biology    
29-Sep Wood rotting fungi Discussion 3: rust papers  
4-Oct Plant Pathogenic Fungi Plant Pathogens labDiscussion 4: wood rot papers Quiz 2
6-Oct Ascomycetes Ascomycete lab  
11-Oct FALL BREAK (no class)    
13-Oct Molecular Systematics, species, speciation, & barcoding PCRs for pure cultures  
18-Oct Mycorrhizal Ecology PCR gel analysis & field trip  
20-Oct Mushroom cultivation BLASTing & mushroom kit making  
25-Oct Industrial mycology/ Biotechnology Field trip to Mystery Brewing  
27-Oct Ethnomycology Discussion 5: ethnmycology papers  
1-Nov Mycorrhizal community ecology Mycorrhizal community ecology lab Quiz 3
3-Nov Lichenized fungi Lichens lab  
8-Nov Chytridiomycota and other aquatic fungi Chytrids lab  
10-Nov Zygomycetes Discussion 6: zygomycete papers  
15-Nov Oomycete biology & slime molds Discussion 7: slime & water molds  
17-Nov Plant Fungal Interaction Genomics Discussion 8: interaction genomics papers  
24-Nov thanksgiving week (no class)   EOL pages due
29-Nov open lab for special topics    
1-Dec open lab for special topics    
6/8 Dec Symposium: class presentations & banquet


Assignments and Grading:

Item points total points % grade
flash talks (2) 50 100 10%
blog post/specimens (8) 50 400 25%
quizzes   (3) 40 120 10%
EOL page aka quiz 4 (1) 50 50 5%
Discussion leader (1) 200 200 15%
attendance/ participation 100 100 10%
term paper & blog post 300 300 25%
  • Quizzes: Quizzes will be administered bi-weekly and will cover materials presented in the previous two classes and labs.
  • Encyclopedia of Life (EOL) Page: Each student will create and contribute a page for the Encyclopedia of Life (EOL) website. The topic will be a zygomcete fungal species of the students choosing. Relevant information can include macro- and microscopic photos, taxonomic information, links to publications, and genome statistics if available.
  • Specimen collection & blog: A representative, well-documented and preserved collection of 12 field-collected specimens will be required of each student (that’s one species per wk). Collections should reflect diversity of fungi you encounter along with information about the species, identified to genus and species, with photos and notes on fresh and microscopic characteristics, spore prints, and other data used in their identification. Descriptions and photos of your  specimens will be published in the class blog.
  • Class discussion & presentations: Each student shall help lead a weekly discussion on a particular subject area within mycology.  The papers will be posted on our blog site. Everyone reads the papers and participates in discussion- discussion leaders should be prepared to lead discussion with questions.
  • Individual project: Each student will write a term paper on a selected topic in Mycology, and give a presentation at the end of the class. Previous research topics have included: Fungal communities on wood and litter, Strategies for spore dispersal, Unusual fungal niches: aquatic, marine, deserts, polar regions, Mycology of food, brewing and baking, Evolution of truffles and other hypogeous fungi, Interesting fungal diseases, Mycorrhizal ecology, Orchid and their mycorrhizae, Fungal decomposition on wood or litter, or other substrate, Mushroom cultivation, Population biology, clonality and individualism in fungi, Pathogenic chytrids & global amphibian decline, Nutrient cycling by fungi, Fungal pharmacology, Ethnomycology, Fungi on/in plants (endophytes), and Fungi on/in insects.


  • Keep cell phone usage minimal, no cell phones or lap tops during quizzes.
  • No cheating. Plagiarism reports will go to the Dean’s office.
  • Turn in your work on time.
  • Communicate about foreseeable absences.
  • Come on time and be respectful to your peers and instructor.

Resources for students regarding academic problems:

Academic Resource Center (ARC),
which contains 3 relevant programs:

Other relevant resources:

The Writing Studio, where students can attend workshops and individual appointments to improve brainstorming, formatting, and writing skills.

The Academic Advising Center (AAC), which offers students advising in field specific aspects such as choosing a major, utilizing resources within Duke’s scientific community, making progress toward career goals, and maximizing your experience at Duke.