Jan Sapp opens with a history of the study of microbes, which he divides into four eras: germ theory, molecular genetics, molecular phylogenetics based on small subunit ribosomal DNA, and analyses based on full bacterial genomes.
Norman Pace covers the large scale structure of the Tree of Life and the division into Bacteria, Archaea, and Eucarya. And Wolfgang Ludwig and Karl-Heinz Schleifer focus on the phylogeny of the bacteria: phyla and many subgroups are well supported, though their relationships are not.
Two papers — W. Ford Doolittle's "If the Tree of Life Fell, Would We Recognize the Sound?" and William Martin's "Woe is the Tree of Life" — argue for a dominant role for horizontal gene transfer (HGT). Most of the other papers attribute much less weight to HGT, but Kurland's "Paradigm Lost" is a vehement attack on claims for its ubiquity and consequences.
Carl Woese argues that HGT dominated only very early on, and that a kind of annealing happened as replication systems improved and passed through a "Darwinian threshold"; the earliest evolution involved cells rather than genomes.
Radhey Gupta suggests that approaches to phylogeny using distinctive insertions and deletions (indels) produce robust trees and evidence for a stable core of genes and proteins that is minimally affected by factors such as HGT. He also argues that the eukaryotic cell evolved from symbiosis between a gram-negative bacterium and an Archaea, in an aerobic environment dominated by antibiotic-producing organisms.
James Lake et al. argue for eukaryotic origins from a symbiosis between something like a purple sulfur bacteria and an eocyte, linked by hydrogen and sulfur metabolism. They suggest HGT is widespread and significant, but not so much so as to prevent construction of a meaningful Tree of Life.
Some endosymbiotic events are less controversial. The origin of mitochondria as alpha-proteobacteria is now accepted, but Michael Gray considers further questions about their evolution. And John Archibald and Patrick Keeling give an account of the origin and evolution of plastids, with one primary endosymbiotic event followed by multiple secondary and even tertiary endosymbioses.
Hannah Melnitsky, Frederick Rainey and Lynn Margulis present a karyomastigont model for the origin of eukaryotes, involving symbiosis between a Thermoplasma-like archaebacteria and a spirochete, and compare it to alternatives. And Michael Dolan looks at the origin of the microtubule cytoskeleton and the relationship of tubulin to the prokaryotic protein FtsZ.
A couple of papers are peripheral to the central debates. Harold Morowitz and others offer a biochemists' perspective on evolution, finding robust patterns in intermediate metabolism and arguing for a phenotype-first approach. And John Werren looks at how vertically transmitted parasites can influence host reproduction, focusing on the bacteria Wolbachia, which manipulates eukaryote hosts through cytoplasmic incompatibility and sex-ratio control.
All up Microbial Phylogeny and Evolution is a fascinating collection, covering some of the most exciting topics in the history of life.