| Topics: |
Required readings: |
Other sources: (strongly recommended) |
Class Lectures |
|
| January 15 |
Introduction to geomicrobiology |
ASM Geobiology paper (handout in
class) |
||
| January 20 |
Microbiology basics |
Konhauser, Ch. 1 |
Link to basic microbiology
information: http://www.bact.wisc.edu/Microtextbook/index.php |
|
| January 22 |
Microbiology basics |
Konhauser, Ch. 1 |
Bacterial
evolution article by Carl Woese (1987) |
slides |
| January 27 |
Geology basics (Jen Hinds) |
slides |
||
| January
29 |
Geology
basics (Jen Hinds); early Earth rocks |
1) 4.4
Ga zircons (Wilde et al., 2001, Nature) 2) A cool early Earth? (J.W. Valley, Scientific American, Oct. 2005, pp. 58-65 ), OR a similar article in Geology |
Old
diamonds and the upper crust (I.A. Williams, 2007, Nature) What's new on early Earth? (A. Halliday, 2006, Elements) |
slides |
| February 3 |
Microbial energetics (free energy change, electrode potentials) | Konhauser, Ch. 2 (pp. 36-66) | practice problem set |
slides |
| February 5 |
Energy conservation (phosphorylations) |
Above, and pgs. 240-246 (Photosynthetic mats) | slides |
|
| February 10 |
Geomicrobiology methods | PAPER #1 |
slides |
|
| February 12 |
Geomicrobiology methods |
Overview
of cloning and DGGE Overview of PCR Linking function to ID |
DGGE
article FISH overview Spectroscopy methods |
slides |
| February 17 |
Stable isotopes and biomarkers |
Minireview of stable isotopes and biomarkers | slides |
|
| February 19 |
NO
CLASS |
|
||
| February 24 |
Mineral formation |
Konhauser, Ch. 3 |
Surface adhesion tutorial | slides |
| February 26 |
Fe and Mn Reduction | 1. Konhauser, Ch. 2 2. Geomicrobiology ebook, Ch. 14 and 15 (see link above) 3. Iron metabolism at neutral pH [Straub, et. al. (2001)] |
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, 16, pp. 41-84. |
slides |
| March 3 |
Fe and Mn oxidation and cycling |
1. Overview of Fe and Mn
oxidation [Emerson (2004)] 2.Geomicrobiological cycling of Fe [Kappler & Straub, 2005] |
Mn oxidation [Tebo, et. al. (2005)] | slides |
| March 5 |
NO CLASS |
|||
| March 10 |
Fe isotopes, BCM |
1. Konhauser, pg. 174-179 2. Fe isotopes, Johnson & Beard, 2006 Bazylinski and Frankel, 2003 (MSA review) |
Iron
Isotope Biosignatures, Beard et al., 1999. |
slides |
| March 12 |
Acid Rock Drainage (AMD/ARD) |
Konhauser, pp. 211-230 | 1. Acid Mine
Biogeochemistry (Druschel
et al., 2004) 2. Negative pH waters (Nordstrom et al., 2000) |
slides |
| March
17, 19 |
NO CLASS (spring recess) | |||
| March 24 |
Sulfur biogeochemistry, sulfate
reduction |
1. Konhauser, pp. 74-76,
169-174, 272-276 2. Geomicrobiology ebook, Ch. 17 |
1. Earths 'great oxidation
event' (Farquhar,
et al. 2000) 2. Sulfur isotope geochemistry review (Seal, II, 2006) |
slides |
| March 26 | Sulfur oxidation |
sulfide oxidation review (Nordstrom and Southam, 1997) | Chemolithotroph bloom in
sulfidic waters (Lavik
et al., 2009) |
slides |
| March 31 |
Caves and carbonates |
Cave microbiology (Barton and Jurado, 2007) | 1. Sulfuric acid speleogenesis (Engel
et al., 2004) |
slides |
| April
2 |
Dolomite
precipitation |
1.
Konhauser, pp. 160-166 2. Microbial carbonate formation review (pp. 3-7) |
Microbial
dolomite precipitation (Sanchez-Roman
et al., 2008) |
slides |
| April 7 |
Weathering | 1. Konhauser, Ch. 5 pp. 192-211 2. Colonization of silicates (Rogers, 2002) |
slides |
|
| April
9 |
Methane |
1.
Konhauser,
pp. 277-280 2. AOM short review (Valentine, 2002) |
1.
AOM review (Boetius,
2009) 2. Methane consuming Archaea (Orphan et al., 2001) |
slides |
| April
14 |
Origins
of life |
1.Konhauser,
Ch. 7 pp. 293-305 2. Origin of life (Forterre & Gribaldo, 2007) |
1.
Hot ancient bacteria (Gaucher
et al., 2008) 2. Cold origin of life (Price, 2007) |
slides |
| April 16 |
Early
life geobiology |
Konhauser, Ch. 7 pp. 305-340 Habitat and nature of early life (Nisbet and Sleep, 2001) |
1.Photosynthetic mats 3.4Ga (Tice
and Lowe, 2004) 2. MISS formations (Noffke, 2008) |
slides |
| April 21 |
Early
life geobiology |
Konhauser, Ch. 7 pp. 341-349 | Life and Earth's atmosphere (Kasting & Siefert, 2002) | slides |
| April
23 |
Rise
of O2 & Eukarya |
1. Atmospheric O2 (Kump,
2008) 2. Eukaryotic evolution (Embley & Martin, 2006) |
1. Nickel and methanogen
collapse (Konhauser
et al., 2009). 2. Evolution of O2 photosynthesis (Buick, 2008). |
slides |
| April 28 |
Presentations |
Kate, Chris, Justin |
||
| April 30 |
Presentations |
Kelle, Stephanie, Sarah |
||
| May 5 |
Presentations |
Tom, Kara, Grant |
||
| May 7 |
Wrap-up |
|||
| May
12 |
FINAL
EXAM WEEK |
Geol 418/518
final DUE: 12pm, Tuesday, May 12 |
EXAM 2 answers (briefly) |