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: Course Coordinator:

Kenneth H. Nealson Ms Shana Rapoport

USC Wrigley Professor of Geobiology phone: 213-821-2511
knealson@usc.edu, (213) 821-2271 email: rapoport@usc.edu

Guest Lecturers:

1. Prof. Johannes Gijsbrecht Kuenen, Technical University of Delft, Holland

2. Prof. Victoria Orphan, CalTech
3. Prof. Dianne Newman, CalTech
4. Prof. Robert Blankenship, Washington St. Louis University
5. Prof. Greg Ferry, Penn State University
6. Prof. Yuri Gorby, J. Craig Venter Institute
7. Prof. Mandy Ward, USC

Course Assistants and Technical Advisors:

1. Ms Andrea Cheung, USC
2. Dr. Greg Wanger, J. Craig Venter Institute

This will be an intensive lecture/laboratory 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. 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%).

Please Note: Lectures will be in the morning from 0900 to 12:30

Laboratory (chemostat work) will be from 1315 to 1700
8 students are registered for the lectures and lab
Others are welcome to sit in on the lectures: For these students (auditors), please
note that for the first two days of the course, lectures will also be in the afternoon
Detailed Schedule: a = 0900 – 1030; b = 1100 – 1230
c = 1330 – 1445; d = 1500 - 1700
April 5 (Monday)
Morning
a. Introduction, thermodynamics principles/ Eh-pH diagrams GK
b. The Monod and Pirt models for microbial growth GK

Afternoon
c. Chemostats as an indispensible tool for physiological studies GK
d. Exercises in the use of chemostats, including calculations GK

April 6 (Tuesday)
a. Role of central metabolic pathways for carbon metabolism KN
b. Diversity of fermentative routes and the redox balance GK
Afternoon
c. Diversity of metabolism and selective enrichments GK
d. Composition of growth media (chemostat discussion) GK

April 7 (Wednesday)
a. Mitchell hypothesis, Energetics, and Aerobic respiration KN
b. Anaerobic respiration KN
c. Mixotrophic metabolism GK
D, Chemostat lab, discussion, exercises GK

April 8 (Thursday)
a. Metabolic Regulation (I) KN
b. Physiology of Shewanella YG
Afternoon -- Chemostat lab, discussion exercises GK

April 9 (Friday)
a. Metabolic Regulation (II) KN
b. Mixed cultures and competition in the chemostat DN
Afternoon -- Chemostat lab, discussion, exercises

April 10: Party at KN’s house -- relax, talk about microbes !!

April 12 (Monday)
a. Bacterial Photosynthesis BB
b. Bacterial Photosynthesis (II) BB
Afternoon – Chemostat lab, discussion, exercises

ADJUSTED LECTURE PROGRAM , SEE NEXT PAGE:

April 13 (Tuesday)
a. The chemostat and genomic studies GK
b. Chemolithotrophy and reverse electron transport GK
Afternoon – Chemostat lab, discussion, exercises

April 14 (Wednesday)
a. Extracellular electron transport YG
b. Single cell biology/ nanoSIMS VO
Afternoon – Chemostat lab, discussion, exercises

April 15 (Thursday)
a. Riboswitches: regulatory and KN
controlling roles of small RNAS’s
b. Bacterial Behavior (taxis) I MW
Afternoon – Chemostat lab, discussion, exercises

April 16 (Friday
a. Anaerobic ammonium oxidation (Anammox) GK
b. Bacterial behavior (quorum sensing, signaling) KN
Afternoon – Chemostat lab, discussion, exercises

Weekend: RUNNING CHEMOSTATS

April 19
a. Methanogenesis GF
b. Methanogenesis II GF
Afternoon – Chemostat lab, discussion, exercises

April 20
a. Anaerobic methane oxidation VO
b. Oxidaton and reduction of metals DN
Afternoon – Chemostat lab, discussion, exercises

April 21
a. Sulfur oxidizing bacteria GK
b. Anammox applications GK
Afternoon – Chemostat lab, discussion, exercises

April 22: Questions and Discussion

April 23: Exam & Lab exam