The prokaryotes were alone on Earth for a very long time, adapting to new environments and to changes in existing environments. They have survived to this day, in massive numbers and incredible diversity, and they are found everywhere. In numbers of individuals, prokaryotes are far more abundant than eukaryotes. Individual prokaryotes in the oceans number more than 3 × 10²⁸—more than the number of stars in the universe. Closer to home, the individual bacteria living in your intestinal tract outnumber all the humans who have ever lived.

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Given our still-fragmentary knowledge of prokaryote diversity, it is not surprising that there are many different hypotheses about the relationships of the major groups of prokaryotes. In this book we use a classification system that has considerable support from nucleotide sequence data. We will discuss eight major bacterial groups that have the broadest phylogenetic support and have received the most study: hadobacteria, hyperthermophilic bacteria, firmicutes, actinobacteria, cyanobacteria, spirochetes, chlamydias, and proteobacteria (see Figure 25.1). Many other major groups of bacteria are known but are less thoroughly studied. We will then describe the prokaryotic archaea, whose diversity is even less well studied than that of the bacteria.