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Frontiers in Microbiology - IV. Microbes and the Three Domains

Taxonomy is the theory and practice of describing, naming, and classifying earth’s diverse organisms. Some people regard taxonomy as rigid and uninteresting. In fact, it is a dynamic discipline that responds to our ever-changing understanding of earth’s biodiversity. As mentioned previously, over the past several decades it has become apparent that the majority of biodiversity is found among microbes. This realization has caused taxonomists to change their classification schemes in light of new information.

Carolus Linnaeus is regarded as the father of taxonomy. In 1758, he developed a system whereby each type of organism was identified by a unique two-word name corresponding to its genus and species. Linnaeus further grouped organisms into larger categories based on their similarities and differences. The groups were arranged in a hierarchical fashion. Linnaeus originally used four classification categories but our modern system uses seven. In the Linnaeus system, species that share many characteristics are grouped together in the same genus. Likewise, related genera are grouped together in the same family. This process repeats all the way up to the kingdom category.

Originally, biologists recognized just two kingdoms, Plantae (plants) and Animalia (animals). When microbes were first identified, they were assigned to one of these two kingdoms. During the middle of the 19th century, Ernst Haeckel proposed creating a third kingdom called Protista. Within the Protista kingdom were placed unicellular organisms. Bacteria were a major group within this kingdom. In the early part of the 20th century, it was recognized that bacteria differed in fundamental ways from other organisms with regard to their cell structure. A fourth kingdom called Monera was created to set them apart. Finally, in the 1950s, Robert Whittaker expanded the system still further by adding a fifth kingdom called Fungi. Viruses are not part of this classification system since they are not composed of cells, being just nucleic acid surrounded by a protein coat.

Whittaker’s five-kingdom system was widely accepted by biologists but just 20 years later another sweeping change occurred in taxonomy. Previous classification systems relied on visible traits to describe and classify organisms. Carl Woese was analyzing invisible traits, namely DNA sequences. Specifically, he compared sequences from a gene for ribosomal RNA across many species. Woese realized that an organism’s DNA provided an historical record of its evolution. By comparing sequences across species he could describe evolutionary relationships independent of the traditional use of visible traits. Evolutionary trees constructed from molecular data generally yield identical or similar trees to those constructed from morphological data. This agreement represents some of the best proof supporting the theory of evolution.

Nevertheless, comparisons of the rDNA sequences did produce some surprises. Woese found that most of the sequence diversity occurred within the microbes. Analysis of this data suggested to Woese that a new category of classification, the domain, was needed (Woese et al., 1990). The rDNA sequences from bacteria fell into two distinct groups—the true bacteria and the ancient bacteria (meaning those thought to be living fossils of the first bacteria to have evolved on earth). These two groups of microbes are as different from one another as either are to eukaryotic organisms. Woese proposed a classification system that featured three domains called Bacteria, Archaea, and Eukarya. Domain Bacteria includes the true bacteria. Domain Archaea includes all of the ancient bacteria. For example, methanogenic bacteria are members of the Euryarchaeota branch of the Archaea. They are strictly anaerobic and tend to be heat tolerant, suggesting an ancient origin. Today, there are confined to environments such as cow intestines and the soils beneath flooded rice paddies. Domain Eukarya includes all the organisms within the four eukaryotic kingdoms—Animalia, Plantae, Protista, and Fungi. An evolutionary tree based on Woese’s three-domain classification system shows the dominance of microbes on earth. Plants and animals are depicted as a couple of twigs on the tree.

Molecular sequence data are increasingly being used to investigate evolutionary relationships (Driskell et al. 2004). After two species diverge from each other, they begin to collect sequence mutations independent of one another. This means that two species that are closely related to each other will have DNA (or amino acid) sequences that are more similar to each other than two species that are more distantly related. Such sequence analysis can be used to construct family trees of organisms. This data is not without its drawbacks however.

The assumption made in phylogenetics is that DNA sequences are passed on only from parent to offspring. This is usually an accurate assumption. Microbes however present a more complex situation. Many species of microbes can pass on genetic information not just to their progeny, but also to other individuals in the same population or even to members of other species. This is called horizontal transfer or lateral transfer. When horizontal transfer occurs, the introduced gene brings into the cell its own history, which does not reflect that of the host cell. An extreme case of horizontal transfer took place about one billion years ago when Eubacteria entered into a symbiosis with Archaea-type host cells that led to the development of some organelles (mitochondria and chloroplasts). It remains to be seen just how much horizontal transfer will limit our ability to tease out evolutionary relationships among the microbes.

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