Syllabus
BISC 599 (13602D) – Advanced Microbial Physiology
Spring 2010, Special Session: April 5-23
9am-12 noon and 1-4pm MTWHF
Preparation: Basic biology, chemistry, and biochemistry. Permission of instructor
required.
Instructor:
Kenneth H. Nealson
USC Wrigley Professor of Geobiology
knealson@usc.edu, (213) 821-2271
SHS 560 – 12 noon to 1pm daily.
Guest Lecturers:
Prof. Johannes Gijsbrecht Kuenen
Technical University of Delft, Holland
Prof. Victoria Orphan
CalTech
Prof. Dianne Newman
M.I.T.
Prof. Robert Blankenship
Washington St. Louis University
This will be an intensive seminar-type course in microbial physiology, a course that does
not presently exist at USC or at any of the other major teaching institutions in the Los
Angeles basin. With the rapid rise in interest in functional genomics, an understanding of
microbial physiology is the fundamental guide to enable one to ask the right biologically
relevant questions, and to interpret the interactions of microorganisms with their
environment (both biotic and abiotic). The course will fill a niche in our own curriculum
in biology, molecular sciences, engineering, marine sciences, and earth sciences. The
laboratory component will provide instruction in the use of a specialized cultivation
device called the chemostat. (This instruction is not otherwise currently available in the
U.S. Gijs Kuenen, one of the world’s leading experts in the area of high pH-tolerant
microbes, teaches this subject in Holland.)
Grades will be assigned by: 1) participation in course discussions (10%), 2) homework
assignments (10%), 3) a written final exam (30%); and final exam in practical
demonstrated performance in the laboratories (50%).
Because this is a special topics course, there will be no required textbook. Readings will
be provided to students based on current and extremely recently (within a few months of
the course’s start date) published papers for each subject. Journals will include:
Geobiology Journal, Isme Journal, Nature, Science, PNAS (Proceedings of the National
Academy of Science,) Journal of Bacteriology, and Environmental Microbiology.
Detailed Schedule:
April 5
a.
b.
c.
d.
April 6
a.
b.
c.
d.
April 7
a.
b.
c.
Introduction, thermodynamics principles/ Eh-pH diagrams
Mitchell hypothesis and energetics
The Monod and Pirt models for microbial growth
Chemostats as an indispensible tool for physiological studies
Exercises in the use of chemostats, including calculations
GK
KN
GK
GK
Role of central metabolic pathways for carbon metabolism
Diversity of fermentative routes and the redox balance
Aerobic respiration
Diversity of metabolism and selective enrichments
KN
GK
KN
GK
Anaerobic respiration
Theoretical and experimental growth yield and YATP
Metabolism under different growth conditions
Chemostat Lab
KN
GK
April 8
a. Mixotrophic metabolism and use of dual substrates
b. Anaerobic respiration of perchlorate (chlorine)
c. Chemostat Lab
April 9
a. Chemolithotrophy and reverse electron transport
b. Chemostat Lab
GK
KN
GK
GK
April 12
a. Metabolic regulation -- Global and local
b. Bacterial photosynthesis
c. Chemostat Lab
KN
RB
April 13
a. Bacterial photosynthesis
b. Chemostat Lab
RB
April 14
a. Anaerobic methane metabolism
b. Chemostat Lab
VO
April 15
a. Anaerobic ammonia metabolism
b. Chemostat Lab
GK
April 16
a. Mixed Cultures in the chemostat/selection, etc.
b. Chemostat Lab
GK
April 19
a. Methanogenesis & methanogens
b. Methanotrophy & methanotrophs
c. Chemostat Lab
KN
GK
April 20
a. Sulfur reduction and SRBs
b. Sulfur oxidation
c. Chemostat Lab
KN
GK
April 21
a. NOx reduction
b. N oxidation
c. Chemostat Lab
KN
GK
April 22
a. Metal oxidation and reduction
b. Chemostat Lab
April 23
a. Exam
b. Lab Exam
KN/DN