SES: Microbial Methods in Ecology

2019 Semester


Joe Vallino (Starr 330, x7648,
Kristin Gribble (Lillie 305, x7194,
Emil Ruff (Starr 325, x7758,
TA: Rachel Clifford (

Listed below are lectures and other materials for the Microbial Methods in Ecology elective. See the Semester in Environmental Science web site for information on the overall course. This site will be updated as lectures and course materials become available.

Course 2019 Syllabus
Course 2019 Reading assignments
The 12th ed. of Brock can be ordered on amazon here.  Used versions were available for $15 or less, but the prices can very over time.


Note, these files are from last year unless marked as 2019. Files will be updated to 2019 versions as they are presented in class.  Assigned readings below do not include those assigned in Brock, so check Reading Assignments above.  The lecture notes are published here as pdf files, but can be obtained as power point files by contacting Joe Vallino.
  1. Introduction (2019)

  2. Bacterial Abundance (2019)

  3. Bacterial Production (2019) and Liquid Scintillation Counter (2019) (Instructors: Ruff and Vallino) 

  4. Extracellular Enzyme Assays (2019)

  5. Microbial Food Webs: Flagellate and ciliate grazing on bacteria (2019)

  6. Microbial Biogeochemistry: Metabolism in Winogradsky columns (2019)

  7. Molecular Techniques: PCR  (Instructor: Kristen Gribble)

  8. Microbial Food Webs: Bacteria-phytoplankton competition (2019)

Problem Sets 

Problem sets will be posted here as they are assigned.  In general, problem sets are due on the next Thursday following the end of module (see syllabus above).  It is preferred that problem sets be turned in as Word documents via email. 

Some Past Experimental Results

Interesting Links

Winoblog: A blog on Winogradsky Columns.  Feel free to post our results there!

Very good interactive site on Microbial Ecology of Winogradsky columns

Winogradsky columns as art: Here, here, here and here

The making of a Giant Winogradsky column.

Microbial mat at Great Sippewissett Saltmarsh, MA. and "Pink Berries" at Little Sippewissett.

Microbial fuel cells

Winogradsky columns

The Microbial World (archived)

Digital learning center for microbial ecology

EPA Info on coliform counts (See chapter 17)

Protist images

Introduction to Freshwater microorganisms

Harmful algal blooms

Archaea that grows at autoclave temperatures!

Micrographia.  Site contains many images and descriptions on microorganisms

Micro*scope  (now at Carleton)

Micobial Life - Educational Resouces