BIOL 420 Environmental Microbiology Syllabus
Spring Quarter 2007
Dr. Holly Pinkart; phone: 963-2710; email:
Office hours:M 3:00-5:00, W 2-4SCI 236D
Course goals: The goal of this course is to investigate environmental microbiology and microbial ecology through the study of microbial interactions with other microbial populations, plants and animals, biogeochemical cycling, applied microbiology, and through the use of molecular techniques.
Text: Brock Biology of Microorganisms, 11th ed.
Additional readings will be on BlackBoard under”Course Documents”
My Expectations of You: I expect that you will have had the proper prerequisites for this course (BIOL 323 and CHEM 362). You will be familiar with prokaryotic cell structure, and familiar with microbial structure, growth and metabolism, and microbial genetics. These are covered in Unit I, IV and V of the Brock text. I expect academic honesty in all matters (see Appendix B in CWU catalog). Cheating and/or plagiarism will not be tolerated.
Topics to be covered (subject to minor changes):
Topic
/ Text ChapterMicrobial evolution / Brock 2, 11, 14.2-14.4
Interactions among microbial populations / BB
Plant-microbe interactions / BB, Brock 19.19-.22
Microbe-animal interactions / BB, Brock 19.11
EXAM I / Monday, April 16
Development of microbial communities / BB, Brock 19.1-.3
Measurement of biomass and microbial activity / Brock 18
Microbial Diversity – phylogenetic, physiologic and metabolic / Brock 12.1, 13.1, 14.9, 17
Carbon, Nitrogen and Sulfur Cycling / Brock 17.1-17.20, 17.28-17.29; 19.9-.14
EXAM II / Monday, May 14
Assorted biogeochemistry / Brock 17.18-.22, 19.15-.16
Waste treatment / Water quality / Brock 28.1-.3
Biodegradation/bioremediation / Brock 17.22-.24, 19.17-.18
Biofuels / BB
Biocontrol, Industrial microbiology / BB, Brock 30.1-.4
Final Exam / Tuesday, June 5 8:00-10:00
BB refers to material posted on BlackBoard; these can be found in the “Course Documents” folder called “Supplemental Material”
GradeBreakdown is as follows:
93-100% = A92-90 = A-86-89 = B+82-85 = B79 – 81 = B-
76-78 = C+72-75 = C69-71 = C-66-68 = D+63-65 = D
60-62 = D-<60 = F
Evaluation:
Lecture Exams – 50%Group project – 20%Quizzes – 15%
2 write-ups (lab groups) – 15% (each weighted equally, 7.5% each)
Course Exam Policies: If you miss an exam, you must take a comprehensive final (this applies to both lecture and lab). If you know ahead of time that you will miss an exam, you may take it early – you may not take it late. Quizzes will be posted on BlackBoard on Wednesday (and available until Friday 11:55 PM), except on an exam week. There are no make-ups for quizzes, but you may miss one without penalty. Those who haven’t missed any quizzes can drop their lowest score at the end of the quarter. THERE IS NO EXTRA CREDIT. The Final Exam will be 75% new material and 25% comprehensive.
Tentative Laboratory schedule:
Day / Date / TopicR / 3/29 / Check in - epidemiology
T / 4/3 / Group projects outline & Winogradsky Columns
R / 4/5 / Soil moisture, pH and soil organic content, plate orgs
T / 4/10 / Soil moisture and soil organic content (cont’d)
R / 4/12 / Final plate counts and organic content, calculation of diversity
T / 4/17 / Alternative Counting techniques –AODC, DAPI
R / 4/19 / Soil DNA extraction, PCR, DGGE
T / 4/24 / DGGE results, calculation of diversity, discussion of results
R / 4/26 / Water Quality – Coliform, MPN, Colilert
T / 5/1 / Water Quality - Membrane filtration
R / 5/3 / Cellulose and lignocellulose to ethanol/ antibiotic production
T / 5/8 / Cellulose and lignocellulose to ethanol/ antibiotic production
R / 5/10 / Cellulose and lignocellulose to ethanol/ antibiotic production
T / 5/15 / Field Trip! To the Waste Treatment Plant
R / 5/17 / SOURCE
T / 5/22 / Group presentation work
R / 5/24 / Group presentation work
T / 5/29 / Group project - presentations
R / 5/31 / Group Project - presentations
You are required to keep a lab notebook. Two experiments (your choice of which ones) will be written up in ASM format and turned in on May 31, along with your notebook. ASM format means you have to include an abstract, introduction, materials and methods, results, discussion and references. Examples of ASM journals are the Journal of Bacteriology and Applied and Environmental Microbiology. There is no page limit for your lab write-ups, just make sure that they are complete. The write up should not only include your data, but data from the other groups as well. The May 31 date is the last date that you can turn these in – feel free to turn them in early!!! You will turn them in via the Digital Drop Box in BlackBoard.
Course Outcomes
Students will be able to:
-Discuss microbial evolution
-Illustrate biogeochemical cycles and identify the roles of specific groups of microorganisms associated with each cycle
-Describe the development of microbial communities
-Calculate microbial diversity using appropriate indices
-Explaininteractions within and between microbial populations in terms of parasitism, predation, competition, commensalism, synergism and mutualism
-Describe, in ecological terms, the interactions between microorganisms and plants, and microorganisms with animals
-Measure microbial biomass and various metabolic activities related to microbial ecology and water quality
-Develop a grant proposal
-Collect samples from terrestrial and aquatic environments
-Elucidate various biodegradation pathways and describe methods of waste treatment
-Describe production of biofuels
-Discuss various forms of biocontrol
Some pertinent information and helpful hints:
1)I will use Blackboard for this course. All course materials (Powerpoint presentations, lab exercises, readings, syllabus, presentation information, etc) will be postedthere so you will have always have access to those as well as other course materials. Read the corresponding text chapters prior to class so you can follow course discussions.
2)Read the Lab manual or handouts prior to the corresponding lab period. In lab, you are graded on techniques and interpretation of microbiological analyses. If you miss any of the labs, it will hurt you. Also, it is quite a hassle to make up a lab if you have missed it.
3)Rewrite your notes soon after class – this will allow you to identify confusing points so you can ask questions.
4)Don’t use your cell phone in lab or class lecture. Step outside the classroom if it is an emergency.
5)There is no eating or drinking allowed in the laboratory. EVER.
6)Feel free to ask questions at any time. And please use my office hours! If you can not make it during my office hours, please make an appointment.
7)If you have a learning disability, it is your responsibility to let me know sometime during the first 2 weeks of class. This will give us the opportunity to coordinate with Disability Support Services well before the first exam. If you are colorblind, please let me know immediately so we can work out some alternative lab protocols.
8)Exams – if you know that you will not be in class on the day of an exam, you may arrange to take it early. If you miss an exam without notifying me ahead of time, you can take a comprehensive exam at the end of the quarter to make it up.
9)Quizzes will be posted on BlackBoard on Wednesday immediately after class, and will be available until 11:55 Friday night. I will drop your lowest quiz grade at the end of the quarter.