Chapter Summary


  • Elements of life were formed through nuclear reactions within stars that exploded into supernovas before the birth of our own Sun.
  • Reduced molecules compose Earth’s interior. Oxidized minerals are found only near the surface. Early Earth had no molecular oxygen (O2).
  • Archaean rocks show evidence for life based on fossil stromatolites, isotope ratios, and chemical biosignatures. Fossil stromatolites appear in chert formations formed 3.4 Gyr ago. Isotope ratios for carbon indicate photosynthesis at 3.7 Gyr ago and sulfate reduction at 3.47 Gyr. Cyanobacterial hopanoids appear at 2.5 Gyr ago.
  • Microfossils of filamentous and colonial prokaryotes date to 2.0 Gyr ago. At 1.2 Gyr, larger fossil cells resemble those of modern eukaryotes.
  • Early metabolism involved anaerobic oxidation-reduction reactions. Likely forms of early metabolism include sulfate respiration, lightdriven ion pumps, iron phototrophy, and methanogenesis.
  • Banded iron formations reflect the cyclic increase and decrease of oxygen produced by cyanobacteria and consumed through reaction with reduced iron. After all the ocean’s iron was oxidized, oxygen increased gradually in the atmosphere.


  • Prebiotic soup models propose that the fundamental biochemicals of life arose spontaneously through condensation of reduced inorganic molecules.
  • Metabolist models propose that components of intermediary metabolism arose from self-sustaining chemical reactions that connected nucleotides with amino acids, forming the basis of the genetic code.
  • The RNA world model proposes that in the first cells, RNA performed all the informational and catalytic roles of today’s DNA and proteins.
  • Thermophile or psychrophile? Classic models of early life assume thermophily, but Earth may actually have been cold when the first cells originated.
  • A world of methane? If the first cells were methanogens, methane production could have led to the first greenhouse effect, warming the Earth and enabling evolution of other kinds of life.
  • Origin on Earth or elsewhere? Isotope ratios suggest the presence of complex metabolism by 3.7 Gyr ago, shortly after Earth cooled (3.9 Gyr ago). Simpler cells existing before 3.9 Gyr ago may have evolved much faster than life today. A more speculative possibility is that life first evolved on another planet.


  • Phylogeny is the divergence of related organisms. Organisms diverge through random mutation, natural selection, and reductive evolution.
  • Molecular clocks are based on mutation rate. Given a constant mutation rate and generation time, the degree of difference between two DNA sequences correlates with the time since the two sequences diverged from a common ancestor.
  • Different sequences diverge at different rates. Under selection pressure, the actual divergence rates of sequences depend on structure and function of the RNA or protein products.
  • Phylogenetic trees are based on sequence analysis. The more different the two sequences are, the longer is the branch representing time since divergence from the common ancestor. Rooting a tree requires comparison with an outgroup.
  • The tree of life diverges to three domains: Bacteria, Archaea, and Eukarya. Eukaryotes are distinguished by the nucleus, lacking in archaea and bacteria. Archaea possess ether-linked isoprenoid lipids rare or absent in bacteria and eukaryotes, and they are never pathogens. The machinery of archaeal gene expression resembles that of eukaryotes.


  • Horizontal gene transfer occurs between different species. Horizontal transfer is most frequent between closely related species or between distantly related species that share a common habitat.
  • Genomes include informational genes and operational genes. Informational genes involve central processes of gene expression; they tend to be transferred vertically. Operational genes involve metabolic processes that function independently of other components. They are more likely to be transferred horizontally.
  • Horizontal gene transfer is important for adaptation to new environments and for pathogenesis. Gene transfer among pathogenic and nonpathogenic strains leads to emergence of new pathogens.


  • Microbial species are defined based on sequence similarity of vertically transmitted genes such as SSU rRNA sequences and multiple orthologous genes. The species definition should be consistent with the ecological niche or pathogenicity.
  • A pan-genome includes core genes possessed by all isolates of a species plus accessory genes found in some isolates but not others. A pan-genome may be open (infinite) number of genes or closed (finite) set of available genes.
  • Taxonomy is the description and organization of lifeforms into classes (taxa). Taxonomy includes classifi- cation, nomenclature, and identification.
  • Classification is traditionally based on a hierarchy of ranks. Groups of organisms long studied tend to have many ranks, whereas recent isolates have few.
  • DNA sequence relatedness defines microbial taxa. Below genus level, however, the definition of bacterial species can be problematic.
  • Practical identification is based on phenotypic and genetic traits. Methods of identification include the dichotomous key and the probabilistic test battery. Both methods assume a predefined set of organisms.


  • Symbiosis is the intimate association of two unrelated species. A symbiosis in which both partners benefit is called mutualism. If one partner benefits while harming the other, this is called parasitism.
  • Symbiotic partners undergo coevolution, the evolution of two species in response to one another. Coevolution involves reductive (degenerative) evolution, in which each partner species loses some functions that the other partner provides.
  • An endosymbiont lives inside a much larger host species. Many microbial cells harbor endosymbiotic bacteria whose metabolism yields energy for their hosts.
  • Many invertebrates harbor endosymbiotic bacteria. The bacteria are required for host survival and in some cases for pathology caused by a parasitic invertebrate.
  • Mitochondria evolved from endosymbionts. The ancestor of mitochondria was an alphaproteobacterium related to rickettsias.
  • Chloroplasts evolved from endosymbionts. The chloroplast ancestor was a cyanobacterium.