Aquatic Microbiology
Brief Course Description: Two-thirds of the earth is covered with water. The water is filled with microorganisms. A milliliter of Puget Sound or Pacific Ocean water contains millions of microorganisms. A gram of Lake Washington or Puget Sound sediment contains billions of bacteria. What are they all doing? How do you study organisms that are so small? Are they really important?

Register for FISH 490 or MICROM 490 to learn about the incredible microbes that live in the seas, lakes, and rivers on planet earth.
Quick Links
Course Schedule, 4/21/07 (Switched date for Sage's guest lecture)
Detailed Course Description, 3/27/07

Lecture Notes


Previous Exams
Exam 1
Exam 2
Final Exam


Environmenal Microbiology Web Sites

FISH/MICROM 490 Lecture Section Message Board

FISH/MICROM 490 Laboratory Section Message Board

FISH/MICROM 490 Laboratory Section Data (Sequence Data)


Future Scientists at Work in FISH/MICROM 490 Lab
Pipetting can be fun. Is this the right tube? Microorganisms are small. Inoculating petri dishes. Measuring chlorophyll a.
Pipetting can be fun. Is this the right tube? Microorganisms are small. Inoculating petri dishes. Measuring chlorophyll a.
Course Description

5-credit or 3-credit class offered Quarter Spring Quarter 2007. The 5 credit class consists of two 1.5-hour lecture periods and one 3-hour laboratory session each week. The 3 credit class does not include laboratory sessions.

FISH/MICROM 490 is appropriate for students in a variety of biological science and environmental fields.


Course Requirements
Recommend 15 credits of biological science and 10 credits of chemistry.

Information for Class
May 29 2007, 6:04 AM
New Readings on Web Site
Four new assigned readings (Dobbs, 2007; Sinigalliano 2007; Falkowski 2004; Venter 2004) and one new optional reading (Stepanauskas 2007) placed on the web site.

May 28 2007, 10:51 PM
Group Presentation PowerPoint Files
PowerPoint files from Groups 5, 6, and 7 are now on the web site.

May 28 2007, 10:38 PM
Lecture Notes
Notes for Lecture 13 (Molecular Methods) placed on web site.

May 21 2007, 1:12 PM
Lecture Notes
Notes for Lecture 12 (Fecal Pollution) placed on web site.

May 16 2007, 8:38 AM
Lecture Notes
Notes for week of May 14 placed on web site. Download Lectures 11 (shellfish biotoxins) and 11A (fish biotoxins).

May 1 2007, 1:09 PM
Lecture Notes in Two Formats
I will start to place my lecture notes onto the course web site in two digital formats - landscape and portrait. Pick the format you prefer.

FISH/MICROM 490, Spring 2007
Aquatic Microbiology

Instructor: Dr Russell P. Herwig
Email: herwig@u.washington.edu

Office: FSH 202B
Office Hours: By appointment only
Telephone: 206.685.2163

Meeting Times and Locations
Lectures: T Th 9:00 - 10:20. FSH 208

Lab Section: Monday 1:30 - 4:20. FSH 142


Assigned Readings

  1. Caron, D.A. 2002. Protistan community structure

FIRST MIDTERM EXAM MATERIAL TO HERE.

  1. Dobbs, F.C. 2007. Apre`s le de´luge: Microbial landscape of New Orleans after the hurricanes.
  2. Sinigalliano, C.D. 2007. Impacts of Hurricanes Katrina and Rita on the
    microbial landscape of the New Orleans area.
  3. Falkowski, P.G. 2004. Shotgun sequencing in the sea: a blast from the past?
  4. Venter, G.C. 2004. Environmental genome shotgun sequencing of the Sargasso Sea.
FINAL EXAM TO HERE

Optional Readings

1. Douglas, A.E. 2003. Coral bleaching - how and why?

2. Ott, R. 2005. Sound truth and corporate myths. Chapters 22 and 23.

SECOND MIDTERM EXAM MATERIAL TO HERE

  1. Stepanauskas, R. 2007. Matching phylogeny and metabolism in the
    uncultured marine bacteria, one cell at a time.
FINAL EXAM TO HERE

Figures and Video
  1. N Cycle. Revised figure (pdf) of the N cycle that includes anammox pathway.
  2. Hood Canal Bacteria Mats on Sediment Surface. Bacterial mat is composed of filamentous bacteria of the genus Beggiatoa. This genus consists of S-oxidizing bacteria. This is a wmv file (12 MB) that can be opened with QuickTime Player or Microsoft Windows Media Player. File provided by Dr. Joel Elliot, University of Puget Sound.
FIRST MIDTERM EXAM MATERIAL TO HERE
Student Group Presentations - PowerPoint Files
Group 1

Group 2

Group 3

Group 4

SECOND MIDTERM EXAM TO HERE

Group 5

Group 6

Group 7

FINAL EXAM TO HERE


Forms to Complete Following Your Presentation
  1. Group Presentation Self-Evaluation Form
  2. Group Presentation Peer-Evaluation Form

Study Questions for Group Presentations
Group Presentations 1-4 Study Questions

SECOND MIDTERM TO HERE

Group Presentations 5-7 Study Questions

FINAL EXAM TO HERE


List of Class Handouts
WEEK 1
1. Course Description
2. Course Schedule
3. First Day Student Survey (return to instructor)
4. Zonations in Oceans and Lakes
5. Phylogenetic Trees
6. Free Energy and Electron Tower

WEEK 2
7. Carbon Cycle, Trophic Levels, Cellulose, Chitin
8. Secondary Structures of Small Subunit Ribosomal RNA
9. Protists

WEEK 3
10. Nitrogen Cycle
11. Presentation Group Members
12. Presentation Instructions
13. Sulfur Cycle, Phosphate, and Silicon Cycles
14. Nitrogen Cycle, revised. Includes anommox pathway

FIRST MIDTERM MATERIAL TO HERE.

WEEK 4
15. Spread-plate and Pour-plate Methods
16. Biofilm Development and Co-aggregation

WEEK 5
17. n-Alkane Degradation Pathway
18. Aromatic Hydrocarbons

WEEK 6
19. Exxon Valdez Summary and Hg Cycle

WEEK 7
20.

SECOND MIDTERM MATERIAL TO HERE

WEEK 8

WEEK 9

WEEK 10
Send mail to: herwig@u.washington.edu
Last modified: 6/03/2007 10:57 AM