| Topics: |
Required readings: |
Other sources: (not required) |
Class Lectures |
|
| January 10 |
Introduction to geomicrobiology |
ASM Geobiology paper (handout in
class) |
||
| January 15 |
Overview of microorganisms &
habitats |
Konhauser, Ch. 1 Link to basic microbiology information: http://www.bact.wisc.edu/Microtextbook/index.php |
||
| January 17 |
Microbial habitats and growth |
Konhauser, Ch. 1 |
slides |
|
| January 22 |
Microbial energetics (free
energy change, redox potentials) |
Konhauser, Ch. 2, pgs. 36-64 |
practice problems |
slides |
| January
24 |
Microbial
energetics (chemiosmosis, fermentation, respiration) |
Konhauser, rest of Ch. 2 (to page 92) |
practice
problems ANSWERS |
slides |
| January 29 |
Photosynthesis and microbial mats |
Konhauser, pgs. (within
Ch. 2) and pgs. 240-246 (Photosynthetic mats) |
slides |
|
| January
31 |
UNIVERSITY
CLOSED--SNOW |
|||
| February 5 |
Geomicrobiology methods |
PubMed
link GeoRef link |
slides |
|
| February 7 |
Geomicrobiology methods | Overview
of cloning and DGGE Overview of PCR Linking function and identification of uncultured microbes |
DGGE
article FISH overview Spectroscopy methods |
slides |
| February 12 |
Geomicrobiology methods |
Homework 1 DUE |
slides |
|
| February 14 |
Stable isotopes and biomarkers |
Minireview of stable isotopes and biomarkers | Sulfur
preference of early Archaean microbes (article) |
slides |
| February
19 |
CLASS
CANCELLED |
|
||
| February 21 |
Cell
surface interactions |
Konhauser, Ch. 3 (up to section
3.4) |
Surface adhesion tutorial | slides |
| February 26 |
Mineral formation |
Konhauser, Ch. 3 (section 3.7) |
slides |
|
| February 28 |
Fe and Mn Reduction | 1. Geomicrobiology ebook, Ch. 14
and 15 (see link above) 2. Iron metabolism at neutral pH [Straub, et. al. (2001)] 3. Fe reduction section [Weber, et. al. (2006)] |
Recommended
reading: 1. Fe and Mn reduction review [Lovley, et. al. (2004). Advances in Microbial Physiology, V49, pp. 219-286. ] 2. Bo Thamdrup, 2000. Bacterial Manganese and iron reduction in aquatic sediments. Advances in Microbial Ecology, V. 16, pp. 41-84. |
slides |
| March 4 |
Fe and Mn oxidation and cycling |
1. Overview of Fe and Mn
oxidation [Emerson (2004)] 2. Fe oxidation section [Weber, et. al. (2006)] 3. Mn oxidation [Tebo, et. al. (2005)] |
slides |
|
| March 6 |
Fe isotopes,
BCM |
1. Konhauser, pg. 174-179 2. Bazylinski and Frankel, 2003 (MSA review) |
slides |
|
| March
10-14 |
NO CLASS (spring recess) | |||
| March 18 |
Sulfur biogeochemistry |
1. Konhauser, pp. 74-76,
169-174, 272-276 2. Geomicrobiology ebook, Ch. 17 |
slides |
|
| March 20 |
Sulfur reduction,
disproportionation |
1. Earths 'great oxidation
event' (Farquhar,
et al. 2000) 2. Sulfur isotope geochemistry review (Seal, II, 2006) |
slides |
|
| March 25 | Sulfur
oxidation |
1. Konhauser, pp. 211-230 2. Sulfide oxidation review (Nordstrom and Southam, 1997) |
1. Acid Mine
Biogeochemistry (Druschel
et al., 2004) 2. Negative pH waters (Nordstrom et al., 2000) |
slides |
| March 27 |
Bioleaching, desulfurization |
(see Konhauser above) |
1. Sulfuric acid speleogenesis (Engel
et al., 2004) 2. Cave microbiology (Barton and Jurado, 2007) |
slides |
| April
1 |
Toxic metal(loid)s | 1.
Ecology of Arsenic (Oremland
and Stolz, 2003) 2. As and Se in microbial metabolis (Stolz et al., 2005) |
1.
As, microbes and contaminated aquifers (2005) |
slides |
| April 3 |
Carbonates, phosphates, silicates | Konhauser, pp. 192-211 |
1. Silicate weathering review
(Bennet et al., 2001) |
slides |
| April
8 |
Presentations |
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| April
10 |
Presentations |
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| April 15 |
Presentations |
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| April 17 |
Presentations |
|||
| April
18-19 |
Class
field trip: Soap Lake |
|||
| April 22 |
Early Earth and life |
Konhauser, Ch. 7 Habitat and nature of early life (Nisbet and Sleep, 2001) |
1. Hot ancient bacteria (Gaucher
et al., 2008) 2. Cold origin of life (Price, 2007) 3. Photosynthetic mats 3.4Ga (Tice and Lowe, 2004) |
slides |
| April 24 |
Early Earth and life |
(Guest: Dr. Tom Williams) |
slides |
|
| April 29 |
Early Earth and life |
(same as April 22) |
slides |
|
| May 1 |
Up to Eukarya evolution |
1. Life and Earth's atmosphere (Kasting
& Siefert, 2002) |
slides |
|
| May
5-9 |
FINAL
EXAM WEEK |
Geol 418/518
final: 10-12, Friday, May 9, 2008 |