15.3: Two or Three Domains?

At the very highest levels of life on Earth, we find three major cell lines, the domains. The domain Archaea includes unique single-celled organisms found throughout the ocean and also in extreme environments (e.g., hot pools, high-salinity ponds). Bacteria, the most diverse domain of life, comprise another unique type of single-celled organism found virtually everywhere on Earth (e.g., Coleman et al. 2021). The third domain, the Eukarya, includes single-celled and multicellular organisms with yet another unique type of cell. This is our domain.

Applications of genetic sequencing in the late 1970s set the stage for establishing the three-domain system in use today. American microbiologist Carl Woese (1928–2012)—hailed as “one of the most significant biologists of the 20th century” (Illinois IGB 2013)—had a hunch that gene sequences could be used to learn something about the evolution and origins of life on Earth (Luehrsen 2014). What he figured out and accomplished—not without controversy—shattered long-held ideas in biology (Nair 2012). In a paper published in 1977, Woese and then-postdoctoral microbiologist George Fox (b. 1945) presented RNA-sequence evidence for a third “domain” of life, the Archaea. Prior to publication of this paper, biologists believed that bacteria and eukaryotes were the only cell lines on Earth. Though met with skepticism, their discovery of the domain Archaea has come to be acknowledged as “one of the most influential in microbiology and arguably, all of biology” (Nair 2012).

Subsequent work over the ensuing decades provided support for three domains. Archaea, Bacteria, and Eukarya each occupied a major branch of a three-branched phylogenetic tree of life. Significantly, the tree of life and its three major branches validated the theory of common descent, the idea that all life on Earth shared a universal ancestor, the last universal common ancestor, or LUCA (e.g., Fox et al. 1980; Doolittle 1999; Weiss et al. 2016; Crapitto et al. 2022). As Darwin put it, “All the organic beings which have ever lived on this earth have descended from some one primordial form” (Darwin 1860). The tree of life depicts this common ancestry and the branching that has occurred since life originated some 3.9 billion years ago.

Until recently, the Archaea, Bacteria, and Eukarya were considered distinct domains on a three-domain tree of life. But an ever-widening body of evidence supports the existence of only two domains—the Archaea and the Bacteria—on a two-domain tree of life (e.g., Rayman et al. 2015; Williams et al. 2020; Doolittle 2020). The Eukarya belong to a branch of the Archaea and either arose within that group (e.g., Williams et al. 2020) or evolved via endosymbiosis (endo meaning “within”; symbiosis meaning “living together”), a “merging” of two organisms (e.g., López-García and Moreira 2020). Some trees depict the Eukarya as an offshoot of the Archaea branch (e.g., Castelle and Banfield 2018), while others depict the Eukarya as a third branch formed between the Archaea and Bacteria branches (e.g., Skejo and Franjevic 2020).

All of these concepts and definitions serve to bring into focus the evolutionary lineages of life on Earth. But the history of life on Earth is only one part of the story, for life and Earth evolved together, as we shall now see.