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Archaea — timeline of the third domain

Key Points

  • Studies of the Archaea have had a substantial impact on the field of biology.

  • Carl Woese carried out several pioneering studies, examining the evolution of the genetic code, the translation apparatus and the cell as a whole, and the insight gained from his early work led to the discovery of the third domain.

  • Defining moments in the history of archaeal research include the construction of a universal tree of life and the rationalization of the phylogeny of small-subunit ribosomal RNA, aminoacyl-tRNA synthetases and other protein sequences, leading to the three-domain view of life.

  • Seminal advances were made through probing the biochemistry, physiology, genetics and evolution of methanogens, extreme halophiles and thermoacidophiles.

  • The nature of archaea as extremophiles can now be placed into context with the knowledge that archaea are abundant and ubiquitous throughout the Earth's biosphere, including in the vast cold reaches of the planet.

  • Archaea play a key part in maintaining important biogeochemical cycles, and several contemporary advances have been made in our understanding of the importance of archaea in global ecology.

  • Technological advances have greatly enhanced the output from the field; particularly noteworthy are the impact of DNA sequencing, and the dawning of the genomics era and application of metagenomics, as well as breakthroughs that have been made through the development of tractable genetic systems.

Abstract

The Archaea evolved as one of the three primary lineages several billion years ago, but the first archaea to be discovered were described in the scientific literature about 130 years ago. Moreover, the Archaea were formally proposed as the third domain of life only 20 years ago. Over this very short period of investigative history, the scientific community has learned many remarkable things about the Archaea — their unique cellular components and pathways, their abundance and critical function in diverse natural environments, and their quintessential role in shaping the evolutionary path of life on Earth. This Review charts the 'archaea movement', from its genesis through to key findings that, when viewed together, illustrate just how strongly the field has built on new knowledge to advance our understanding not only of the Archaea, but of biology as a whole.

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Figure 1: Trends in the growth of knowledge about the Archaea.
Figure 2: Phylogenetic tree of the Archaea.

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Acknowledgements

I dedicate this Review to Carl Woese, who pioneered, led and continues to inspire the field with his brilliance. I am indebted to C. Robertson, who generously constructed the phylogenetic tree, and M. DeMaere, who processed the RefSeq data. I also thank my many colleagues who informally and formally commented on the manuscript, in particular N. Pace, T. Kolesnikow, F. Lauro, H. Ertan and M. Dyall-Smith. This Review could not be exhaustive and I regret not being able to cite all of the relevant literature. Research in my laboratory is supported by the Australian Research Council.

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NCBI Taxonomy Datbase

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RefSeq

Glossary

Domain

The highest level of taxonomic division; the three domains are the Archaea, Bacteria and Eukarya. In descending order, the other levels include: kingdom, phylum, class, order, family, genus and species.

Extremophile

An organism that requires extreme environments for growth, such as extremes of temperature, salinity or pH, or a combination of these.

Methanogen

An anaerobic organism that generates methane by the reduction of carbon dioxide, acetic acid, or various one-carbon compounds such as methylamines or methanol.

Halophile

An organism that requires high concentrations of salt (typically greater than 1M NaCl) for growth.

Thermoacidophile

An organism that requires high temperatures (typically greater than 60 °C) and a low pH (typically less than pH 3) for growth.

Heterotroph

An organism that uses organic compounds as nutrients to produce energy for growth.

Phototrophic

Pertaining to the growth of an organism: able to use sunlight to generate energy for growth.

Hyperthermophile

An organism that requires extremely high temperatures (typically greater than 80 °C) for growth.

Autotroph

An organism that can grow on carbon dioxide as a sole source of carbon.

Small-subunit rRNA

The ribosome is the core biological machine of the translation apparatus and is essential for converting the genetic code described in DNA and mRNA into protein. Ribosomal RNA (rRNA) is the RNA component of the ribosome and forms two subunits, the small subunit (SSU) and the large subunit. SSU rRNA is highly conserved in all cellular forms of life and is commonly used for describing the phylogeny of organisms.

Lateral gene transfer

Horizontal transfer of genes between unrelated species, as opposed to vertical inheritance within a species.

Bootstrap value

A computationally derived measure of confidence about tree topology: the closer the bootstrap value is to 100, the more confidence we can have in the topology of the tree.

Monophyletic

Pertaining to a natural taxonomic group or clade: consisting of individuals that share a common ancestor.

Reverse methanogenesis

The methanogenesis pathway functioning in reverse to consume methane and produce cellular carbon and energy; this process leads to the anaerobic oxidation of methane.

Chemolithoautotrophically

Pertaining to an organism: able to derive energy from a chemical reaction (chemotroph) using inorganic substrates as electron donors (lithotroph) and CO2 as a carbon source (autotroph).

Ammonia-oxidizing members of the Crenarchaeota

An archaeon with the ability to grow chemolithoautotrophically with near-stoichiometric conversion of ammonium cations (NH4+) to nitrite ions (NO2) using carbonic acid (H2CO3) and ammonium (NH4) as the sole sources of carbon and nitrogen, respectively.

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Cavicchioli, R. Archaea — timeline of the third domain. Nat Rev Microbiol 9, 51–61 (2011). https://doi.org/10.1038/nrmicro2482

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