BIOL 420 Environmental Microbiology Syllabus
Spring Quarter 2007
Dr. Holly Pinkart; phone: 963-2710; email: pinkarth@cwu.edu
Office hours: M 3:00-5:00, W 2-4 SCI 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 Chapter
Microbial evolution
Interactions among microbial populations
Plant-microbe interactions
Microbe-animal interactions
EXAM I
Development of microbial communities
Measurement of biomass and microbial activity
Microbial Diversity – phylogenetic, physiologic
and metabolic
Carbon, Nitrogen and Sulfur Cycling
EXAM II
Assorted biogeochemistry
Brock 2, 11, 14.2-14.4
BB
BB, Brock 19.19-.22
BB, Brock 19.11
Monday, April 16
BB, Brock 19.1-.3
Brock 18
Brock 12.1, 13.1, 14.9, 17
Brock 17.1-17.20, 17.28-17.29; 19.9-.14
Monday, May 14
Brock 17.18-.22, 19.15-.16
Waste treatment / Water quality
Biodegradation/bioremediation
Biofuels
Biocontrol, Industrial microbiology
Brock 28.1-.3
Brock 17.22-.24, 19.17-.18
BB
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”
Grade Breakdown is as follows:
93-100% = A
76-78 = C+
60-62 = D-
92-90 = A72-75 = C
<60 = F
86-89 = B+
69-71 = C-
82-85 = B
66-68 = D+
Evaluation:
Lecture Exams – 50%
Group project – 20%
Quizzes – 15%
2 write-ups (lab groups) – 15% (each weighted equally, 7.5% each)
79 – 81 = B63-65 = D
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
R
T
R
T
R
T
R
T
R
T
R
T
R
T
Date
3/29
4/3
4/5
4/10
4/12
4/17
4/19
4/24
4/26
5/1
5/3
5/8
5/10
5/15
Topic
Check in - epidemiology
Group projects outline & Winogradsky Columns
Soil moisture, pH and soil organic content, plate orgs
Soil moisture and soil organic content (cont’d)
Final plate counts and organic content, calculation of diversity
Alternative Counting techniques –AODC, DAPI
Soil DNA extraction, PCR, DGGE
DGGE results, calculation of diversity, discussion of results
Water Quality – Coliform, MPN, Colilert
Water Quality - Membrane filtration
Cellulose and lignocellulose to ethanol/ antibiotic production
Cellulose and lignocellulose to ethanol/ antibiotic production
Cellulose and lignocellulose to ethanol/ antibiotic production
Field Trip! To the Waste Treatment Plant
R
T
R
T
R
5/17
5/22
5/24
5/29
5/31
SOURCE
Group presentation work
Group presentation work
Group project - presentations
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
-Explain interactions 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 posted there 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.