Geosc 409W
Course Syllabus
link to schedule
Jenn Macalady
210 Deike Building
Office telephone: 865-6330
Office hours: by appointment
  Class Meetings: 240 Deike Bldg., T & Th 11:15-12:30  
  Prerequisites: (1) CHEM 112 and (2) Introductory geology (GEOSC 001, GEOSC 020, GEOSC 040, or EARTH 002) or BIOL 110 or MICRB 201  
  Course Website:
The website contains the syllabus and will be updated often throughout the semester. Bookmark this site!!
  Grading: The grading scheme for the course will be as follows:
Exam 1 (20%)
Exam 2 (15%)
Homework (35%)
Writing Assignments (30%)
(10%) paper #1 (graded)
(15%) paper #2 (graded w/ rewrite)
(5%) discussion journal/class participation
Assignments are due by 5:00 pm on the due date unless otherwise noted in the syllabus below. Late assignments will be penalized 5% per day unless you have made prior arrangements.
  Readings: The required text is Brock's Biology of Microorganisms (12th ed.), by Madigan et al. This is an excellent reference and is the microbiology text of choice for geoscientists interested in microorganisms. Readings listed below are from this text unless otherwise noted. A copy is on reserve in the geosciences library. Used copies of the 10th or 11th editions are also available, but you will need to translate the page number for reading assignments. Other readings will be taken from the scientific literature.

Web "readings": There is an enormous body of geomicrobiology-related information that is accessible on the web. One of my goals for the course is to introduce you to good web resources on geomicrobiology-related topics. You will find that some of the assigned "readings" are actually web explorations. These are required and fair game for exams unless marked "optional". If you find particularly useful or interesting web resources that are not listed, please let me know!

Reading assignments should be completed before class on the day they are listed.
  Writing: Effective communication of scientific discoveries to a broad audience is among the most challenging and important tasks scientists must tackle. You will be asked to write two papers and keep a discussion journal for this course. A more detailed description of the writing assignments is given here.

  Schedule: Class discussion topics and assignments are listed on the schedule. Be aware that these are subject to change as the semester progresses! Assignment due dates and exams are in red.  
  Note: If you have a disability that affects your participation in the class, please let me know as soon as possible so we can discuss ways to accommodate your needs.  
Good bedtime reading on geomicrobiology topics



Library resources
You can look for books in the library under subjects including "geomicrobiology", "microbial ecology" or "environmental microbiology". Be aware that geomicrobiology is changing so rapidly that books published before ~ 2005 may be significantly out of date! The following may be useful:

Banfield, J. F. and K. H. Nealson (eds.). 1997. Geomicrobiology: Interactions between microbes and minerals, Reviews in Mineralogy Vol. 35, Mineralogical Society of America, Washington D.C. (result of a MSA short course)

Banfield, J.F., Cervini-Silva, J. and K. H. Nealson (eds.). 2005. Molecular Geomicrobiology. Reviews in Mineralogy Vol. 59, Mineralogical Society of America, Washington D.C. (result of a MSA short course)

Ehrlich, H. L. 1996. Geomicrobiology, 3rd. ed. Marcel Dekker, Inc., New York, 719 pp.

Fenchel, T., King, G. M., and T. H. Blackburn. 1998. Bacterial Biogeochemistry, 2nd. ed. (a graduate-level text, difficult to read)

Canfield, D. E., Thamdrup, B. and E. Kristensen. 2005. Aquatic Geomicrobiology. Advances in Maine Biology Vol. 48, Elsevier Academic Press, New York. (graduate-level text, highly recommended)
Nature and Science (weeklies where the latest, most important discoveries are reported. Special issues:
Science issue on Environmental Microbiology, 2002, Vol. 296, Issue 5570
Science issue on Microbial Ecology, 23 May 2008, Vol 320

Environmental Microbiology
Applied and Environmental Microbiology (has sections for geomicrobiology, microbial ecology, and environmental microbiology)
FEMS Microbiology Ecology
American Mineralogist (see the special issue on Geomicrobiology, 1998, Vol. 83, Issues 11-12)
Microbial Ecology
ISME Journal
Other bioscience journals with geomicrobiology content:
Journal of Bacteriology
Microbial and molecular biology reviews
Microbiology (Reading, UK)
Trends in Microbiology
Other geoscience journals with geomicrobiology content:
Earth and Planetary Science Letters
Geochimica Cosmochimica Acta
Limnology and Oceanography
Nature Geoscience
Virtual Journal of Geobiology
a collection of geobiology-related articles collected monthly from Elsevier journals; access is free
Databases for literature searches
Web of Science
Pubmed (access from National Center for Biotechnology Information, NCBI)
Geomicrobiologists on the Web
One of the best ways to learn about developments in geomicrobiology is to check out what geomicrobiologists are up to. Here are some links to websites maintained by scientists doing geomicrobiology research (by no means an exhaustive list!):
Penn State (Geosciences): Chris House, Kate Freeman, Sue Brantley, Jenn Macalady
UC Berkeley: Jill Banfield (click on faculty-->Jill Banfield-->etc.)
Caltech (Geology and Planetary Sciences): Dianne Newman (nice introduction to geomicrobiology) , Alex Sessions, Victoria Orphan
Massachusetts Institute of Technology (MIT): Ed Delong (marine geomicrobiology), Roger Summons (lipid biogeochemistry)
U. Mass Amherst: Derek Lovely (lots of pdfs of recent publications)
Harvard: Ann Pearson
Michigan State University (Center for Microbial Ecology): Jim Tiedje (pollutant degradation, soil microbiology)
Woods Hole Oceanographic Institute (WHOI): Katrina Edwards
UC Santa Barbara (Geological Sciences Dept.): Dave Valentine
Max Planck Institute for Marine Microbiology: (many interesting pages, see Bo Jorgensen, Dirk DeBeer, Antje Boetius, Rudy Amann and many others)
Max Planck Institute for Terrestrial Microbiology (Dept. of Biogeochemistry): (many interesting pages)

Good Bedtime Reading
Margulis and Sagan (1986) Microcosmos: Four Billion Years of Microbial Evolution

Richard Dawkins (1990) The Selfish Gene

Andy Knoll (2003) Life on a Young Planet

Bob Hazen (2005) Genesis: The Scientific Quest for Life's Origins

Other geomicrobiology-related web sites:
The Astrobiology web (a bit high on hype, but somegood links)
American Type Culture Collection (ATCC)
German Collection of Microorganisms and Cell Cultures (DSMZ)
NASA Astrobiology Web
National Center for Biotechnology Information (NCBI)

The 2 courses below are unfortunately not open to undergrads, but are great things to do in graduate school:
MBL Microbial Diversity Summer Course
USC Geobiology Training Course