Microbial Ecology

Winter 2004
LH2 Wednesdays, 6-9:45

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Microorganisms are by far the most abundant forms of life on this planet, with enormous impacts on all other aspects of life. This program is designed for MES students and advanced science students with a need and interest in understanding the basic principles and interactions in microbial systems and their roles in the broader ecology of earth. You are expected to have read the assignments before coming to class and be prepared to take active part in discussions. (Work outside of class should take 8 h weekly.)
Texts: Brock Biology of Microorganisms -- Madigan et al. -- 10th edition -- this book is expensive but very well done and will also be an excellent resource for more specialized topics well into the future
The Killers Within - Shnayerson and Plotkin

Planned activities include:
Illustrated lectures on broad ideas and patterns
Readings-based small- and large-group discussions of basic concepts in microbiology and microbial ecology, including important experimental techniques -- using books and handouts
Talks on such topics as archae (those microbes that grow under greater extremes of temperature, pH, etc.), biofilms, fish pathogens, gut microbiology, E. coliO157, role of bacteriophages in maintaining microbial balance in nature, and other topics of special interest to the group
Student-researched presentations on case studies and/or microbes of particular interest. Presentations will take place primarily during the last 4 weeks of the quarter, and students will be encouraged to work in pairs in carrying out the research and presentations.

Syllabus - Microbial Ecology - draft as of Dec. 2, 2003 -

This will be finalized in conjunction with the class, reflecting their particular needs and interests, and will include both student and faculty presentations.


Topics and Activities


In Brock unless otherwise specified.

Week 1

Discussion groups: how do you see microbial ecology as being relevant in your life and work? What are some of the key questions you would like to explore this quarter? We will use your discussion here, along with information on the backgrounds of everyone in the class, to revise and complete the syllabus.

The Microbial World -- general overview, roles on our planet, history of life Brock xxi-37; 322-329

Week 2

Microbial ecology: -- further defining the questions:
Seminar: The Killers Within.

614-629, 633-643,330-344;
The Killers Within pg. 3-159

Week 3

Microbial molecular genetics: (much of this should be review for many of you, so you will be at different places on the "spiral of learning", but the concepts are crucial.) Workshop on basic molecular principles

39-53, 168-192, 312-318

Week 4

** how much more deeply we go into the physiology and energetics will depend on the background and interests of the group; we may well set it up for students to work at a couple of different levels depending on background, and/or for students who have had Molecule to Organism to do parts of these presentations.

Basic microbial structure and physiology 59, 64-110;

Week 5

Student presentation: nitrogen, sulfur and iron cycles (build from 662-669)
Student presentation: Microbial bioremediation of natural compounds (build from 669-676)

Carbon cycle: 652-662; Plant interactions: 679-694

Week 6

Student presentation: Marine microbiology (build from pg. 643-652)
Seminar: The Killers Within - rest of the book

Essentials of Viruses and Phages: 232-262

Week 8


Week 9


Week 10





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