GEOL 467/667‐010 Geomicrobiology Fall 2009 Syllabus

Meeting times and location: Tuesday/Thursday 2:00‐3:15pm Penny Hall 209

Professor: Clara Chan 106 Penny Hall [email protected]

Office hours: Wednesday 10:30 am‐12 pm and by appointment. Although I am often in my office, I prefer that you make an appointment. I welcome questions by email, but if the answers are extensive, I may ask that you meet me in person.

Course Description: An exploration of the interface between geological and biological processes. Focused on the mutual effects of microorganisms and Earth's chemistry. Topics include biomineralization, origin and evolution of life, microbial weathering and rock formation, and influences on environmental problems.

Course Website on Sakai

Required textbook: Introduction to Geomicrobiology by Kurt Konhauser

Recommended textbook: Biology of Microorganisms (or Brock Biology of Microorganisms) by Madigan et al. 8th or later edition is fine (current is 12th ed.; older ones are cheaper but still very useful)

I will also assign research articles and other required reading.

Grading: Assignments 55% (including papers, presentations, short writing assignments) Midterm Exam 15% Final Exam 20% Participation 10%

Short assignments will be graded ✔+ (check plus), ✔(check), ✔‐ (check minus), or 0 (zero) for excellent, good, below average, and no effort (respectively). Longer assignments will be given letter grades. Participation includes attendance and engagement in discussion.

Late work policy: I have low tolerance for late work, as it delays grading and return of work to your classmates. A grade level will be deducted from your score for every day your work is late. You must still let me know when to expect your work or I will automatically give you a zero. The only exceptions are for extended fieldwork and incapacitating illness. Also, unless you are seriously ill, exams cannot be postponed. I reserve the right to ask for evidence for any excuse.

GEOL 467/667‐010 Geomicrobiology Fall 2009 Syllabus

Course outline

I. Introduction to geomicrobiology a. What is geomicrobiology? Why study it? b. Relevant basics of microbiology II. Microbial metabolism and energetics a. Redox and thermodynamics b. Electron donors and acceptors in geologic environments c. Diversity of microbial metabolism d. Microbial metabolism presentations III. Microbial surfaces a. Cell surface structure and chemistry b. Interactions with metals c. Case studies, environmental applications IV. Biomineralization a. Direct and indirect biological mineral precipitation b. Properties of biominerals c. Case studies, examples of mineralization pathways V. Microbial weathering a. How microbes dissolve minerals b. Examples (including acid mine drainage and cave formation) VI. Microbes on the early Earth (and maybe other planets!) a. Biosignatures and life detection b. Origin and evolution of microbial life VII. Final presentations on geomicrobiology topics of choice

In addition to the subjects mentioned above, we will cover various techniques for studying geomicrobiology.

Special guests! The Geological Sciences department will be hosting three geomicrobiologists as part of our weekly seminar series. These scientists will visit our class to talk about how they got started in geomicrobiology and discuss their research and related science. I will give you some background on each scientist before his or her visit. I also highly recommend you attend their seminars, which are listed below. These will be held in Penny 209 (same room as class) on Thursdays at 3:30pm (right after class).

Sept 24: Bryn Kimball (Pennsylvania State University) Biogeochemical Processes Affecting Copper Mobility in Acid Mine Drainage: From Mineral to Microbe

Oct 22: Ken Williams (Lawrence Berkeley National Laboratory) Electrode Techniques for Monitoring Microbial Activity in the Environment

Nov 19: Nathan Yee (Rutgers) Selenium Oxyanion Reduction by Subsurface Microorganisms