Introduction to microbial diversity. What is microbial diversity?; Context and historical baggage; Phylogenetic information; Constructing a phylogenetic tree; Tree construction complexities; Alternatives to small-subunit rRNA analysis; The tree of life -- The microbial zoo: Primitive thermophilic bacteria; Green phototrophic bacteria; Proteobacteria; Gram-positive bacteria; Spirochetes and bacteroids. Deinococci, chlamydiae, and planctomycetes; Bacterial phyla with few or no cultivated species; Archaea; Eukaryotes; Viruses and prions -- Microbial populations. Identification of uncultivated organisms; Sequence-based microbial surveys; Fluorescent in situ hybridization surveys; Molecular fingerprinting of microbial populations; Linking phenotype and phylotype -- Conclusions: The phylogenetic perspective. Genomics, comparative genomics, and metagenomics; Origins and early evolution