Table of Contents
1 Cover
2 Preface
5 SECTION I: Introduction to Microbial Diversity 1 What Is Microbial Diversity? Facets of microbial diversity The fundamental similarity of all living things 2 Context and Historical Baggage The evolution of evolutionary thought Taxonomy and phylogeny The false eukaryote-prokaryote dichotomy 3 Phylogenetic Information Deciding which organisms and sequences to use in the analysis Obtaining the required sequence data Assembling sequences in a multiple-sequence alignment 4 Constructing a Phylogenetic Tree Tree construction: the neighbor-joining method How to read a phylogenetic tree Example analysis 5 Tree Construction Complexities Substitution models Treeing algorithms Bootstrapping 6 Alternatives to Small-Subunit rRNA Analysis SSU rRNA cannot be used to distinguish closely related organisms Alternative sequences Alternatives to sequence-based methods 7 The Tree of Life Major lessons of the “Big Tree of Life” Rooting the “Tree of Life” The caveat of horizontal transfer
6 SECTION II: The Microbial Zoo 8 Primitive Thermophilic Bacteria Phylum Aquificae (Aquifex and relatives) Phylum Thermotogae (Thermotoga and relatives) Other primitive thermophiles Thermophilic ancestry of Bacteria Life at high temperatures 9 Green Phototrophic Bacteria Phylum Chloroflexi (green nonsulfur bacteria) Phylum Chlorobi (green sulfur bacteria) Phylum Cyanobacteria (blue-green algae) Other green phototrophs Bacterial photosynthesis Carbon fixation 10 Proteobacteria Phylum Proteobacteria (purple bacteria and relatives) Class Alphaproteobacteria Class Betaproteobacteria Class Gammaproteobacteria Class Deltaproteobacteria Class Epsilonproteobacteria The concept of “proteobacteria” 11 Gram-Positive Bacteria What does being gram positive mean? An alternative view of gram-positive bacteria Phylum Firmicutes (low-G∙C gram-positive bacteria) Phylum Actinobacteria (high-G∙C gram-positive bacteria) Bacterial development Bacterial multicellularity 12 Spirochetes and Bacteroids Phylum Spirochaetae Phylum Bacteroidetes (sphingobacteria or Bacteroides/Flavobacterium/Cytophaga group) Bacterial motility 13 Deinococci, Chlamydiae, and Planctomycetes Phylum Deinococcus-Thermus Phylum Chlamydiae (Chlamydia and relatives) Phylum Planctomycetes (Planctomyces and relatives) Reductive evolution in parasites 14 Bacterial Phyla with Few or No Cultivated Species How do we know about these organisms? Phyla with few cultivated species