This schedule is subject to change as the semester progresses; click on the title of any posted Topic or Module to go to that web page.

Section Topics Modules Date

Introduction Course Overview
Chapter 1 of the textbook
Course Overview Aug 17

Context & Historical Baggage

Chapter 2 of the textbook
What is Microbial Diversity?
The fundamental similarity of all living things

The evolution of evolutionary thought Aug 19
Taxonomy and phylogeny
The false eukaryote/prokaryote dichotomy

Phylogenetic analysis How to do a phylogenetic analysis

Chapters 3 and 4 of the textbook
Step 1: Deciding on sequences for analysis Aug 22
    Step 2 : Obtaining the sequence data
    Step 3 : Identifying homologous residues
Alignment problem set
    Step 4 : Tree-construction
Tree construction problem set
Aug 24
    Step 5 : Interpreting the phylogenetic tree
Tree interpretation problem set
    Example analysis : ES-2
    Discussion session : A second transmissible cancer in Tasmanian Devils Aug 26

Chapters 5 and 6 of the textbook
Alternative substitution models Aug 29
    Alternative treeing algorithms
    Alternatives to ssu-rRNA Aug 31
    Other methods for identification
    Discussion session : Phylogenetic Analysis problems sets Sep 2
  Labor Day - No class Sep 5
  What does this all mean?

Chapter 7 of the textbook
A review of "The Big Tree" Sep 7
  Rooting the Universal Tree
  The caveat - horizontal transfer
  Discussion session : The Hot Spring of Yellowstone
The Hot Springs of Yellowstone slideshow
Sep 9

Midterm Exam #1 No class - take the exam in the DELTA Testing Center Sep 12–13

The Bacteria Primitive Thermophilic Bacteria

Chapter 8 of the textbook
Phylum Aquificae (Aquifex and relatives) Sep 14
Phylum Thermotogae (Thermotoga and relatives)
Other primitive thermophiles
Thermophilic ancestry of Bacteria
Life at high temperatures

Discussion session : The Great Tree of Life Sep 16

Green Phototrophic Bacteria

Chapter 9 of the textbook
Phylum Chloroflexi (Green non-sulfur Bacteria) Sep 19
Phylum Chlorobi (Green sulfur Bacteria)
Phylum Cyanobacteria (Blue-green algae)
Other Green phototrophs
Bacterial photosynthesis
Carbon fixation


Chapter 10 of the textbook
Class α-proteobacteria Sep 21
Class β-proteobacteria
Class γ-proteobacteria
Class δ-proteobacteria
Class ε-proteobacteria
The concept of Proteobacteria

Discussion session : Can cyanobacteria see? Sep 23

Gram-positive Bacteria

Chapter 11 of the textbook
Phylum Firmicutes (Low G+C Gram-positive Bacteria) Sep 26
Phylum Actinobacteria (high G+C Gram-positive Bacteria)
Bacterial Development
Bacterial Multicellularity

Spirochaetes & Bacteroids

Chapter 12 of the textbook
Phylum Spirochaetes Sep 28
Phylum Bacteroids (Sphingobacteria, or Bacteroides/Flavobacterium/Cytophaga)
Bacterial Motility

Discussion session : Plagues aren't what they used to be Sep 30

Deincocci, Chlamydia & Planctomycetes

Chapter 13 of the textbook
Phylum Deinococci (Deinococcus/Thermus) Oct 3
Phylum Chlamydiae (Chlamydia and relatives)
Phylum Planctomycetes (Planctomyces & relatives)
Reductive evolution in parasites

Bacterial phyla with few or no cultivated species

Chapter 14 of the textbook
Phyla with few cultivated species Oct 5
  Phyla with no cultivated species
  Phylogenetic groups at all levels are dominated by uncultivated sequences
  How much of the microbial world do we know about?

Fall Break - No class Oct 7


Chapter 16 of the textbook
Unikonts Oct 10

Viruses & Prions

Chapter 17 of the textbook
The origin of viruses Oct 12

Discussion session : Nanobacteria, Fact or Fiction? Oct 14


Chapter 15 of the textbook
Phylum Euryarchaea Oct 17
Phylum Nanoarchaeum

Phylum Crenarchaea Oct 19
Phylum Korarchaea
Archaea as...

Discussion session : Pelagibacter ubique Oct 21

Midterm Exam #2 No class - take the exam in the DELTA Testing Center Oct 24–25

Microbial Populations The identifications of uncultivable organisms

Chapter 18 of the textbook
Determining the phylotype of the Octopus Spring pink filaments organism Oct 26
  Cultivation and isolation of the pink filaments organism, Thermocrinus ruber
  Discussion session : TBA Oct 28
  Sequence-based microbial surveys
(including 454 sequencing)

Chapter 19 of the textbook
Molecular phylogenetic analysis of bacterial symbionts of the deep-sea hydrothermal vent scaly snail Oct 31
  The Human Microbiome Nov 2
  Discussion session : The human microbial hand-ome Nov 4
  Molecular fingerprinting of microbial populations

Chapter 21 of the textbook
Denaturing Gradient Gel Electrophoresis Nov 7
    Different bacteria in different temperature zones of a Tibetan hot spring.
    Terminal Restriction Fragment Length Polymorphism
    Realtime PCR
    Changes in oral microflora after treatment for peridontal disease
  Linking phylotype and phenotype

Chapter 22 of the textbook
Stable Isotope Probing Nov 9
    Identification of ciliate grazers of autotrophic Bacteria in ammonia-oxidizing activated sludge by RNA stable isotope probing
    Discussion session : Class microbiome project Nov 11
    Metagenomics Nov 14
    Evidence for a new type of phototrophy in the sea


Chapter 23 of the textbook
How to sequence a genome Thermotoga maritima and evidence for lateral gene transfer Nov 16
    Discussion session : New tree of life? Nov 18
  Metagenomics The metagenome of the Sargasso Sea Apr 21

Thanksgiving Break - No class Nov 23-25


Chapter 24 of the textbook
The time scale A 3.2 billion year old fossilized ecoystem Nov 28
The Last Common Ancestor
The RNA World
The emergence of Life

TBA     Nov 30
    Discussion session : TBA Dec 2

Final Exam - schedule your exam in the DELTA Testing Center Dec 5-9