Dr. Craig Moyer & Marion Brodhagen's

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Biology 405/545G - MICROBIAL ECOLOGY

Course Outline

Microbial Ecology Course Syllabus Updated 04/15/08
Term paper Instructions Updated 04/15/08
Evaluation Tool for Peer Reviews Updated 05/18/08

Lecture #1: What is Microbial Ecology?
Color slides 3 per page notes

Reading Assignments:

Micobial Ecology, Text Chapter 1 (McArthur, 2006)
Uncharted Microbial World (AAM, 2008)
Environmental Microbiology: Chaps 12, 13 & 14 (Hurst et al., 2007)

Lecture #2: "Microbial" Origins of Life
Color slides 3 per page notes

Reading Assignments:

From Geochem to Biochem (Russell & Hall, 2002)
The Rocky Roots of Acetyl-CoA (Russell & Martin, 2004)
Life As We Do Not Know It: Chapters 1 & 2 (Ward, 2005)
Origins of Life, Text Chapter 2 (McArthur, 2006)

Lecture #3: Methods in Microbial Ecology
Color slides 6 per page notes

Reading Assignments:

Molecular Microbial Methods (Moyer, 2001)
In silico T-RFLP (Engebretson & Moyer, 2003)
Species Concept, Text Chapter 3 (McArthur, 2006)

Lecture #4: Microbial Diversity
Color slides 6 per page notes

Reading Assignments:

Book as Metaphors for Microbial Communities (Schloss & Handelsman, 2007)
Are they the Same? (Schloss, 2008)
Microbial Biogeography (Hughes et al., 2006)
Rarefaction & Microbial Inventories (Hughes & Hellman, 2005)
Community Structure & Diversity, Text Chapter 11 (McArthur, 2006)

Lecture #5: Growth & Adaptation
Color slides 6 per page notes

Reading Assignments:

The Origin of Mutants (Cairns et al., 1988)
Stress-Induced Mutagenesis in Bacteria (Bjedov et al., 2003)

Lecture #6: Habitats: Freshwater & Marine

Reading Assignments:

The Superficial Life of Microbes (Kolter & Greenberg, 2006)
Arctic Bacterioplankton in Lakes & Streams (Crump et al., 2007)
Nutrient Enrichment on Bacterioplankton Production (Apple et al., 2004)

Lecture #7: Habitats: Soils
Color slides 6 per page notes

Reading Assignments:

Identifying MOs in soil suppression (Borneman & Becker, 2007)
Soil Microbial Dynamic under Global Change (Panikov, 1999)

Lecture #8: Habitats: Lithosphere & Marine
Color slides 6 per page notes

Reading Assignments:

SLIMES (Nealson et al., 2005)
Deep Subsurface Biomass (Whitman & Weibe, 1998)
Microbial Life in Ocean Crust (Santelli et al., 2008)
Shotgun Sequencing of the Sargasso Sea (Venter et al., 2004)

Lecture #9: Plant Microbe Interactions
Color slides 6 per page notes

Reading Assignments:

Pathogen-driven Forest Diversity (Nature News & Views, 2000)
Soil Biota & Exotic Plant Invasion (Callaway et al., 2004)
Stress Tolerance in Plants (Rodriguez et al., 2008)
Stress Tolerance via Fungal Symbiosis Review (Rodriguez & Redman, 2008)
Soil Fungal Abundance & Diversity (Broz et al., 2007)
The Unseen Majority: Soil Microbes (van der Heijen et al., 2008)

Lecture #10: Biofilms & Quorum Sensing
Color slides 6 per page notes
Color slides 6 per page notes

Reading Assignments:

Perspective on Biofilms (Battin et al., 2007)
Species Interactions in Biofilms (Hansen et al., 2007)
Sociomicrobiology (West et al., 2006)

Lecture #11: Human Microflora
Color slides 6 per page notes

Reading Assignments:

Human Microflora (Dethlefsen et al., 2007)
Gut Microbes Modulate Human Metabolic Phenotypes (Li et al., 2008)

Lecture #12: Nutrient & Mineral Cycling
Color slides 6 per page notes
Color slides 6 per page notes
Color slides 6 per page notes
Color slides 6 per page notes

Reading Assignments:

Nitrosomonas Genome Analysis (Chain et al., 2003)
Reverse TCA cycle in Marine Autotroph MC-1 (Williams et al., 2006)
Reverse Methanogenesis (Hallam et al., 2004)
Carbon Assimilation and Ammonia Oxidation in Marine Crens (Hallam et al., 2006)

Student Presentations:
Allen R. - Normal Flora of the Gut
Tori T. - Soil Effects on Diversity
Julian H. - Microbial Fuel Cells
Rachel B. - Bioremediation
Sean M. - Viral Impact on Evolution
Tom D. - Myxococcus xanthus
Sasha L. - Gingivitis
Leslie W. - Oral Biofilms

Course Links:

 List of Prokaryotic names with Standing in Nomenclature
Fifty Rules to Good Writing
Adobe Acrobat Reader
Biology Department Homepage