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Unit Chapters
Genomics
Proteins & Proteomics
Evolution & Phylogenetics
Microbial Diversity
Introduction
Microbes as the First Organisms
The Diversity of Microbial Metabolism
Archaea and Bacteria
The Universal Tree of Life
Studying Unculturable Microbes with PCR
Microbes and the Carbon Cycle
Microbes and the Cycling of Nitrogen
Biofilms
Biofilms Formation and Bacterial Communication
Impact of Biofilms on Humans
Communication Between Bacteria and Eukaryotes
Microbes in Mines
Microbial Leaching of Ores
Coda
Emerging Infectious Diseases
HIV & AIDS
Genetics of Development
Cell Biology & Cancer
Human Evolution
Neurobiology
Biology of Sex & Gender
Biodiversity
Genetically Modified Organisms
The Universal Tree of Life

Starting in the 1970s Carl Woese proposed that variation in the sequences of DNA encoding ribosomal RNA (rRNA) in different organisms would provide valuable information regarding evolutionary relatedness. rRNA is an integral part of ribosomal structure, so it is found in all organisms. After comparing the small variations between the genes for rRNA from many organisms, Woese suggested that the Archaea constitute a unique domain of life, a grouping broader than kingdom. The genomes of several members of the Archaea have been entirely sequenced and have been compared with the genomes of other organisms. Such studies confirm that Archaea constitute a separate group: These organisms contain hundreds of genes with no counterparts in Bacteria or Eukarya. Unexpectedly, ribosomal proteins from Archaea were found to be more similar to those of Eukarya than to Bacterial ribosomal proteins. So, Archaea and Eukarya seem more closely related than Bacteria and Eukarya. (See the Evolution and Phylogenetics unit.)

Can we construct a tree illustrating the relatedness of the three domains, with one common ancestor for all life? Woese and his colleagues have argued -- based on phylogenetic methodology and data from several genes -- that there is a common ancestor. They further argue that Archaea and Eukarya are more closely related to each other, and that Bacteria diverged from the common ancestor first. (See the Evolution and Phylogenetics unit.)

Other biologists have countered that the true universal tree of life may be more complicated than the picture that Woese and his colleagues presented. The complication is lateral gene transfer, where individuals exchange genes between one another. Although not generally exhibited in Eukarya, mechanisms for lateral gene transfer (also known as horizontal gene transfer) are well known in Bacteria. Genes are exchanged between bacterial species by the action of viruses and by conjugation (cell-to-cell contact in which DNA copied from a plasmid or chromosome is transferred to a recipient cell). Under special conditions, some bacteria are known to take up "naked" DNA from the environment.

Lateral gene transfer, if restricted to very similar organisms, would not pose a problem for constructing a universal tree of life. However, there is evidence that genes have been exchanged between very distant organisms. Eukarya acquired mitochondrial and chloroplast DNA from Bacteria. Nuclear genes in eukaryotes seem to be derived from Bacteria as well, not just from Archaea. Genes are also shared between Archaea and Bacteria.
Figure 3. The "Shrub of Life"
Twenty-four percent of the genome of the bacterium Thermotoga maritima contains archaen DNA. Similarly, the archaean Archaeoglobus fulgidus has numerous bacterial genes. Some scientists believe that a more diverse community of primitive cells gave rise to the three domains and that the notion of a single universal ancestor might be replaced. W. Ford Doolittle (Dalhousie University) has suggested that lateral gene transfer among early organisms has generated a "tree of life," which more closely resembles a shrub with untreelike links (shared genes) connecting the branches (Fig. 3).

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