ESPM 131 Spring 2006 lecture: 10:00 - 11:00 am
Monday, Wednesday and Friday
Soil Microbial Biology location: 2312 Tolman Hall
course control number: 29384
webpage: http://plantbio.berkeley.edu/~bruns/espm131/
Instructors: Mary Firestone and Tom Bruns

Table of Contents
  • Description
  • Textbook
  • Grades
  • Prerequisites
  • Instructors
  • Syllabus
  • Additional Readings
  • Class Photo
    • top DESCRIPTION
    An introduction to soil microorganisms, diversity, ecology, and activity in the context of biogeochemical cycling, plant-microbial interactions, evolution and global environmental change.
    top TEXTBOOK
    Principles and Applications of Soil Microbiology 2    nd Edition, by Sylvia, Fuhrmann, Hartel and Zuberer. 2005. Publisher: Prentice Hall.
    top GRADES
    Midterm Exams: 40%
    Paper: 20%
    Final Exam: 40%

    possible topics for term papers: [click here]
    top PREREQUISITES
    listed as Biology 1A and 1B
    useful: Ecology, Microbiology and Soils
    top INSTRUCTORS
    Mary Firestone
    333 Hilgard Hall
    phone: 642-3667
    email: mkfstone@nature.berkeley.edu
    mailbox: 137 Mulford Hall
    Office hours Tues 1:30-2:30pm, Thurs 10:00-11:00am    		 Tom Bruns
    321C Koshland
    phone: 642-7987, 643-5483 (lab)
    email: pogon@berkeley.edu
    mailbox: 111 Koshland Hall
    Office hours Th 2:15-3:00, Fri 1:30-2:30
    top SYLLABUS
    date topic lecturer readings powerpoints
    week 1: Introduction to the course and soil
    1-18 Course Introduction Firestone/Bruns
    1-20 Soil as a habitat Firestone
    week 2: Soil as a habitat for microbes habitat.pdf
    1-23 Soil atmosphere Firestone firestone.pdf
    1-25 Soil water Firestone firestone.pdf
    1-27 Soil pH and temperature Firestone firestone.pdf
    week 3: How and where to live
    1-30 How to make a living (redox) Firestone firestone.pdf
    2-1 Where do they live Firestone firestone.pdf
    2-3 Rhizosphere as a habitat Firestone firestone.pdf
    week 4: Who’s there B and K Ch. 2
    2-5 Bacteria and Archaea Firestone firestone.pdf
    2-8 Fungi Bruns intro to fungi.pdf fungi [ppt] (40mb) [pdf]
    2-10 Fungi Bruns
    week 5: How do we know? B and K Ch. 22
    2-13 Traditional Methods Firestone
    2-15 Molecular Methods Bruns mol methods 1.pdf mol techniques 1 [ppt] [pdf]
    2-17 Molecular Methods Bruns mol methods 2.pdf mol techniques 2 [ppt] [pdf]
    week 6:
    2-20 President’s Day Holiday
    2-22 Molecular methods Bruns
    2-24 Mesofauna Firestone
    week 7: Interactions
    2-27 Mesofauna + Foodwebs Firestone
    3-1 Soil crusts Firestone
    3-3 Midterm #1
    week 8: Carbon
    3-6 Organic matter decomposition Firestone
    3-8 Humification Bird Kogel-Knabner 2002.pdf
    3-10 Carbon continued Firestone
    week 9: Xenobiotics
    3-13 Methane production + consumption Firestone
    3-15 Biodegradation Firestone
    3-17 Biodegradation
    week 10:
    3-20 Nitrogen: mineralization Firestone
    3-22 Nitrification Firestone
    3-24 Denitrification and reductive processes Firestone
    week 11:
    4-3 N2 fixation Sims N fix handout.pdf N-fix 1 [ppt] [pdf]
    4-5 N2 fixation Sims N-fix 2 [ppt] [pdf]
    4-7 Mycorrhizal types Bruns mycorrhizae.pdf arbuscular
    mycorrhizae [ppt] [pdf]
    week 12:
    4-10 Mycorrhizae Bruns ecto and ericoid
    mycorrhizae [ppt] [pdf]
    4-12 Acquisition and transport of nutrients
    in mycorrhizae    		 Bruns acquisition and
    transport [ppt] [pdf]
    4-14 MID-TERM # 2
    week 13:
    4-17 Mycorrhizal Community Structure outline Bruns Bever et al. review.pdf community
    structure [ppt] [pdf]
    4-19 Pathogenic interactions Bruns
    4-21 Pathogenic interactions Bruns other symbiotic
    interactions [ppt] [pdf]
    week 14:
    4-24 Communication DeAngelis
    4-26 Application of ecological concepts Bruns Jessup et al.pdf Microbial Diversity [ppt] [pdf]
    4-28 Metagenomic analysis of communities Hugenholtz
    week 15:
    5-1 Iron Dubinsky
    5-3 Chromium and Uranium Brodie Metals, Radionuclides and
    Bioremediation [ppt] [pdf]
    5-5 Sulfur and Phosphorus Firestone
    week 16: Firestone
    5-8 Wrap up and review Firestone/Bruns
    5-15 FINAL EXAM – Group 7 8-11am
    top ADDITIONAL READINGS
    top CLASS PHOTO
    click on photos for a larger version
    last updated: 5/12/06