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. Access through your institution Buy or subscribe This is a preview of subscription content,

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REFERENCES * Cavicchioli, R. (ed) _Archaea: Molecular and Cellular Biology_ (American Society for Microbiology Press, Washington DC, 2007). A STRONG COLLECTION OF CHAPTERS FROM LEADERS IN

THE FIELD, INCLUDING A TESTAMENT ABOUT THE DISCOVERY OF THE ARCHAEA BY CARL WOESE. Book  Google Scholar  * Garrett, R. & Klenk, H.-P. _Archaea: Evolution, Physiology and Molecular

Biology_ (Blackwell, Oxford, UK, 2007). Google Scholar  * Rothschild, L. J. & Mancinelli, R. L. Life in extreme environments. _Nature_ 409, 1092–1101 (2001). Article  CAS  PubMed  Google

Scholar  * Kletzin, A. in _Archaea: Molecular and Cellular Biology_ (ed. Cavicchioli, R.) 14–92 (American Society for Microbiology Press, Washington DC, 2007). A COMPREHENSIVE OVERVIEW OF

THE MICROBIOLOGY, BIOCHEMISTRY AND ECOLOGY OF MANY TYPES OF ARCHAEA. Book  Google Scholar  * Makarova, K. S., Yutin, N., Bell, S. D. & Koonin, E. V. Evolution of diverse cell division

and vesicle formation systems in Archaea. _Nature Rev. Microbiol._ 8, 731–741 (2010). Article  CAS  Google Scholar  * Gribaldo, S., Poole, A. M., Daubin, V., Forterre, P. &

Brochier-Armanet, C. The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? _Nature Rev. Microbiol._ 8, 743–752 (2010). Article  CAS  Google

Scholar  * Walsby, A. E. A square bacterium. _Nature_ 283, 69–71 (1980). Article  Google Scholar  * Burns, D. G. et al. _Haloquadratum walsbyi_ gen. nov., sp. nov., the square haloarchaeon

of Walsby, isolated from saltern crystallizers in Australia and Spain. _Int. J. Syst. Evol. Microbiol._ 57, 387–392 (2007). Article  CAS  PubMed  Google Scholar  * Soppa, J. From genomes to

function: haloarchaea as model organisms. _Microbiology_ 152, 585–590 (2006). Article  CAS  PubMed  Google Scholar  * Cavicchioli, R., Curmi, P. M. G., Saunders, N. & Thomas, T.

Pathogenic archaea: do they exist? _Bioessays_ 25, 1119–1128 (2003). A DISCUSSION ABOUT THE CONCEPT OF ARCHAEAL PATHOGENS. Article  CAS  PubMed  Google Scholar  * Lepp, P. W. et al.

Methanogenic Archaea and human periodontal disease. _Proc. Natl Acad. Sci. USA_ 101, 6176–6181 (2004). Article  CAS  PubMed  PubMed Central  Google Scholar  * Qin, J. et al. A human gut

microbial gene catalogue established by metagenomic sequencing. _Nature_ 464, 59–65 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  * Brulc, J. M. et al. Gene-centric

metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. _Proc. Natl Acad. Sci. USA_ 106, 1948–1953 (2009). Article  PubMed  PubMed Central 

Google Scholar  * Burkhardt, F. & Smith, S. (eds) _The Correspondence of Charles Darwin:1856–1857_ Vol. 6 (Cambridge Univ. Press, Cambridge, UK, 1990). Google Scholar  * Woese, C. R. in

_Organization and Control in Prokaryotic and Eukaryotic Cells. 20th Symposium, Society for General Microbiology_ (eds Charles, H. P. & Knight, B. C. J. G.) 39–54 (Cambridge Univ. Press,

Cambridge, UK (1970). Google Scholar  * Woese, C. R., Sogin, M. L. & Sutton, L. A. Procaryote phylogeny. I. Concerning the relatedness of _Aerobacter aerogenes_ to _Escherichia coli_.

_J. Mol. Evol._ 3, 293–299 (1974). Article  CAS  PubMed  Google Scholar  * Crick, F. H. C. The biological replication of macromolecules. _Symp. Soc. Exp. Biol._ 12, 138–163 (1958). CAS 

PubMed  Google Scholar  * Zuckerkandl, E. & Pauling, L. Molecules as documents of evolutionary history. _J. Theor. Biol._ 8, 357–366 (1965). Article  CAS  PubMed  Google Scholar  * Fox,

G. E., Magrum, L. J., Balch, W. E., Wolfe, R. S. & Woese, C. R. Classification of methanogenic bacteria by 16S ribosomal RNA characterization. _Proc. Natl Acad. Sci. USA_ 74, 4537–4541

(1977). A CORNERSTONE OF THE DISCOVERY OF THE THIRD DOMAIN: THE FIRST SSU RRNA SEQUENCES OF METHANOGENS. Article  CAS  PubMed  PubMed Central  Google Scholar  * Woese, C. R. & Fox, G. E.

The phylogenetic structure of the procaryotic domain: the primary kingdoms. _Proc. Natl Acad. Sci. USA_ 74, 5088–5090 (1977). THE QUINTESSENTIAL DESCRIPTION OF THE THIRD DOMAIN THAT STARTED

IT ALL. Article  CAS  PubMed  PubMed Central  Google Scholar  * Woese, C. R. & Fox, G. E. The concept of cellular evolution. _J. Mol. Evol._ 10, 1–6 (1977). An important paper

describing the importance of the genotype–phenotype relationship in the evolution of life. Article  CAS  PubMed  Google Scholar  * Woese, C. R., Kandler, O. & Wheelis, M. L. Towards a

natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. _Proc. Natl Acad. Sci. USA_ 87, 4576–4579 (1990). THE PROPOSAL FOR THE FORMAL DESCRIPTION OF THE THREE

DOMAINS — A MUST-READ FOR ALL EDUCATIONAL PURPOSES. Article  CAS  PubMed  PubMed Central  Google Scholar  * Woese, C. R. in _Archaea: Molecular and Cellular Biology_ (ed. Cavicchioli, R.)

1–13 (American Society for Microbiology Press, Washington DC, 2007). A PROVOCATIVE TESTAMENT ABOUT THE ARCHAEA MOVEMENT. Book  Google Scholar  * Cavalier-Smith, T. The neomuran origin of

archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. _Int. J. Syst. Evol. Microbiol._ 52, 7–76 (2002). Article  CAS  PubMed  Google Scholar  *

Simonson, A. B. et al. Decoding the genomic tree of life. _Proc. Natl Acad. Sci. USA_ 102, 6608–6613 (2005). Article  CAS  PubMed  PubMed Central  Google Scholar  * Sapp, J. The

prokaryote-eukaryote dichotomy: meanings and mythology. _Microbiol. Mol. Biol. Rev._ 69, 292–305 (2005). AN EXTENSIVE AND REVEALING REVIEW ABOUT THE ARCHAEA MOVEMENT. Article  CAS  PubMed 

PubMed Central  Google Scholar  * Friend, T. _The Third Domain: the Untold Story of Archaea and the Future of Biotechnology_. (Joseph Henry, Washington DC, 2007). AN ENJOYABLE, EASY-TO-READ

AND INSIGHTFUL BOOK ABOUT THE HISTORY OF THE DISCOVERY OF THE ARCHAEA. Google Scholar  * Woese, C. R. & Goldenfeld, N. How the microbial world saved evolution from the Scylla of

molecular biology and the Charybdis of the modern synthesis. _Microbiol. Mol. Biol. Rev._ 73, 14–21 (2009). A CONTEMPORARY ESSAY CONCERNING HOW THE EVOLUTIONARY PROCESS HAS BEEN STUDIED IN

THE TWENTIETH CENTURY. Article  PubMed  PubMed Central  Google Scholar  * Iwabe, N., Kuma, K., Hasegawa, M., Osawa, S. & Miyata, T. Evolutionary relationship of archaebacteria,

eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. _Proc. Natl Acad. Sci. USA_ 86, 9355–9359 (1989). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Brown, J. R. & Doolittle, W. F. Archaea and the prokaryote-to-eukaryote transition. _Microbiol. Mol. Biol. Rev._ 61, 456–502 (1997). AN EXTENSIVE REVIEW OF THE EVOLUTION OF THE UNIVERSAL

TREE OF LIFE, WITH PARTICULAR EMPHASIS ON PROTEIN PHYLOGENY. CAS  PubMed  PubMed Central  Google Scholar  * Woese, C. R. On the evolution of cells. _Proc. Natl Acad. Sci. USA_ 99, 8742–8747

(2002). Article  CAS  PubMed  PubMed Central  Google Scholar  * Vetsigian, K., Woese, C. R. & Goldenfeld, N. Collective evolution and the genetic code. _Proc. Natl Acad. Sci. USA_ 103,

10696–10701 (2006). A MAJOR ADVANCE IN CONSIDERING THE ROLE OF DARWINIAN VERSUS LAMARCKIAN INFLUENCES ON THE EVOLUTION OF THE GENETIC CODE, THE TRANSLATION PROCESS AND CELLULAR ORGANIZATION.

Article  CAS  PubMed  PubMed Central  Google Scholar  * Woese, C. R., Olsen, G. J., Ibba, M. & Söll, D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process.

_Microbiol. Mol. Biol. Rev._ 64, 202–236 (2000). A COMPREHENSIVE REVIEW PLACING THE EVOLUTION OF AARSS IN THE CONTEXT OF THE REST OF THE TRANSLATION APPARATUS. Article  CAS  PubMed  PubMed

Central  Google Scholar  * Woese, C. R. A new biology for a new century. _Microbiol. Mol. Biol. Rev._ 68, 173–186 (2004). A REFLECTION ON THE SCIENTIFIC PROCESS INVOLVED IN REVEALING THE

ARCHAEA TO THE SCIENTIFIC COMMUNITY. Article  CAS  PubMed  PubMed Central  Google Scholar  * Kavran, J. M. et al. Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code

innovation. _Proc. Natl Acad. Sci. USA_ 104, 11268–11273 (2007). Article  CAS  PubMed  PubMed Central  Google Scholar  * Nozawa, K. et al. Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure

reveals the molecular basis of orthogonality. _Nature_ 457, 1163–1167 (2009). Article  CAS  PubMed  Google Scholar  * Fournier, G. P., Huang, J. & Gogarten, J. P. Horizontal gene

transfer from extinct and extant lineages: biological innovation and the coral of life. _Philos. Trans. R. Soc. Lond. B. Biol. Sci._ 364, 2229–2239 (2009). A PROVOCATIVE VIEW OF THE

EVOLUTION OF LIFE (IN PARTICULAR, CONCERNING WHAT MIGHT BE INFERRED ABOUT EXTINCT LINEAGES). Article  CAS  PubMed  PubMed Central  Google Scholar  * Pace, N. R. A molecular view of microbial

diversity and the biosphere. _Science_ 276, 734–740 (1997). AN INSIGHTFUL REVIEW CAPTURING THE EXCITEMENT EMERGING FROM THE USE OF DNA SEQUENCE DATA TO REVEAL THE EXTENT OF THE PREVIOUSLY

UNKNOWN PHYLOGENETIC AND FUNCTIONAL DIVERSITY IN THE MICROBIAL WORLD. Article  CAS  PubMed  Google Scholar  * Pace, N. R. Mapping the tree of life: progress and prospects. _Microbiol. Mol.

Biol. Rev._ 73, 565–576 (2009). AN UP-TO-DATE REVIEW ABOUT TREE CONSTRUCTION USING SSU RRNA SEQUENCES AND INFERENCES ABOUT THE UNIVERSAL TREE OF LIFE. Article  CAS  PubMed  PubMed Central 

Google Scholar  * Huber, H. et al. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. _Nature_ 417, 63–67 (2002). INSIGHT INTO AN INTERESTING NEW LIFESTYLE AS

WELL AS A NEW DIVISION WITHIN THE ARCHAEA. Article  CAS  PubMed  Google Scholar  * Elkins, J. G. et al., A korarchaeal genome reveals insights into the evolution of the Archaea. _Proc. Natl

Acad. Sci. USA_ 105, 8102–8107 (2008). INSIGHT INTO AN INTERESTING NEW DIVISION WITHIN THE ARCHAEA. Article  PubMed  PubMed Central  Google Scholar  * Brochier-Armanet, C., Boussau, B.,

Gribaldo, S. & Forterre, P. Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. _Nature Rev. Microbiol._ 6, 245–252 (2008). Article  CAS  Google Scholar 

* Casanueva, A. et al. Nanoarchaeal 16S rRNA gene sequences are widely dispersed in hyperthermophilic and mesophilic halophilic environments. _Extremophiles_ 12, 651–656 (2008). Article  CAS

  PubMed  Google Scholar  * Robertson, C. E., Harris, J. K., Spear, J. R. & Pace, N. R. Phylogenetic diversity and ecology of environmental Archaea. _Curr. Opin. Microbiol._ 8, 638–642

(2005). Article  CAS  PubMed  Google Scholar  * Ferry, J. G. Methanogenesis: Ecology, Physiology, Biochemistry and Genetics. _Chapman and Hall Microbiology Series_ (Chapman and Hall Inc.,

New York, 1993). A COMPENDIUM DESCRIBING ESSENTIALLY EVERYTHING THAT WAS KNOWN ABOUT METHANOGENS IN 1993. * Sohngen, N. L. Ueber bakterien, welche methan als kohlenstoffnahrung and

energiequelle gebrauchen. _Zentralbl. Bakteriol. Parasitik. Abt. I._ 15, 513–517 (1906) (in German). Google Scholar  * Wolfe, R. S. The sixth A. J. Kluyver Memorial Lecture. Methanogens: a

surprising microbial group. _Antonie Van Leeuwenhoek_ 45, 353–364 (1979). Article  CAS  PubMed  Google Scholar  * Dalton, H. The Leeuwenhoek Lecture 2000: the natural and unnatural history

of methane-oxidizing bacteria. _Philos. Trans. R. Soc. Lond. B. Biol. Sci._ 360, 1207–1222 (2005). Article  CAS  PubMed  PubMed Central  Google Scholar  * Barker, H. A. Studies upon the

methane-producing bacteria. _Arch. Mikrobiol._ 7, 420–438 (1936). Article  CAS  Google Scholar  * Kluyver, A. J. & van Niel, C. B. Prospects for a natural system of classification of

bacteria. _Zentralbl. Bakterol. Parasitenkd. Infectinskr. Hyg. Abt. II_ 94, 369–403 (1936). Google Scholar  * Barker, H. A. Studies upon the methane fermentation. IV. The isolation and

culture of _Methanobacterium omelianskii_. _Antonie van Leeuwenhoek J. Microbiol. Serol._ 6, 201–220 (1940). Article  Google Scholar  * Kandler, O. & Hippe, H. Lack of peptidoglycan in

the cell walls of _Methanosarcina barkeri_. _Arch. Microbiol._ 113, 57–60 (1977). Article  CAS  PubMed  Google Scholar  * Murray, P. A. & Zinder, S. Z. Nitrogen fixation by a

methanogenic archaebacterium. _Nature_ 312, 284–286 (1984). Article  CAS  Google Scholar  * Belay, N., Sparkling, R. & Daniels, L. Dintrogen fixation by a thermophilic methanogenic

bacterium. _Nature_ 312, 286–288 (1984). Article  CAS  PubMed  Google Scholar  * DiMarco, A. A., Bobik, T. A. & Wolfe, R. S. Unusual coenzymes of methanogenesis. _Annu. Rev. Biochem._

59, 355–394 (1990). Article  CAS  PubMed  Google Scholar  * Ferry, J. G. How to make a living by exhaling methane. _Annu. Rev. Microbiol._ 64, 453–473 (2010). Article  CAS  PubMed  Google

Scholar  * Scheller, S., Goenrich, M., Boecher, R., Thauer, R. K. & Jaun, B. The key nickel enzyme of methanogenesis catalyses the anaerobic oxidation of methane. _Nature_ 465, 606–608

(2010). Article  CAS  PubMed  Google Scholar  * Bult, C. A. et al. Complete genome sequence of the methanogenic archaeon, _Methanococcus jannaschii_. _Science_ 273, 1058–1073 (1996). A

HISTORICAL, EYE-OPENING ARTICLE DOCUMENTING THE FIRST GENOME SEQUENCE OF AN ARCHAEON, AND THE THIRD COMPLETE GENOME SEQUENCE OF AN ORGANISM. Article  CAS  PubMed  Google Scholar  * Orphan,

V. J., House, C. H., Hinrichs, K.-U., McKeegan, K. D. & DeLong, E. F. Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. _Proc. Natl Acad. Sci. USA_ 99,

7663–7668 (2002). Article  CAS  PubMed  PubMed Central  Google Scholar  * Knittel, K. & Boetius, A. Anaerobic oxidation of methane: progress with an unknown process. _Annu. Rev.

Microbiol._ 63, 311–334 (2009). A COMPREHENSIVE REVIEW OF ANAEROBIC METHANE OXIDATION. Article  CAS  PubMed  Google Scholar  * Alperin, M. & Hoehler, T. The ongoing mystery of sea-floor

methane. _Science_ 329, 288–289 (2010). Article  CAS  PubMed  Google Scholar  * Hinrichs, K. U., Hayes, J. M., Sylva, S. P., Brewer, P. G. & DeLong, E. F. Methane-consuming

archaebacteria in marine sediments. _Nature_ 398, 802–805 (1999). AN IMPORTANT BREAKTHROUGH IN REALIZING A ROLE FOR ARCHAEA IN ANAEROBIC METHANE OXIDATION. Article  CAS  PubMed  Google

Scholar  * Orphan, V. J., House, C. H., Hinrichs, K.-U., McKeegan, K. D. & DeLong, E. F. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis.

_Science_ 293, 484–487 (2001). Article  CAS  PubMed  Google Scholar  * Niemann, H. et al. Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink.

_Nature_ 443, 854–858 (2006). Article  CAS  PubMed  Google Scholar  * Zehnder, A. J. & Brock, T. D. Methane formation and methane oxidation by methanogenic bacteria. _J. Bacteriol._ 137,

420–432 (1979). CAS  PubMed  PubMed Central  Google Scholar  * Hallam, S. J. et al. Reverse methanogenesis: testing the hypothesis with environmental genomics. _Science_ 305, 1457–1462

(2004). AN ILLUSTRATION OF HOW METAGENOMICS CAN BE USED TO TEASE OUT A PREVIOUSLY UNKNOWN PATHWAY WHEN THERE IS EVIDENCE THAT THE PROCESS (IN THIS CASE, ANAEROBIC OXIDATION OF METHANE)

OCCURS. Article  CAS  PubMed  Google Scholar  * Dekas, A. E., Poretsky, R. S. & Orphan, V. J. Deep-sea archaea fix and share nitrogen in methane-consuming microbial consortia. _Science_

326, 422–426 (2009). Article  CAS  PubMed  Google Scholar  * Michaelis, W. et al. Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane. _Science_ 297, 1013–1015 (2002).

Article  CAS  PubMed  Google Scholar  * Raghoebarsing, A. A. et al. A microbial consortium couples anaerobic methane oxidation to denitrification. _Nature_ 440, 918–921 (2006). Article  CAS

  PubMed  Google Scholar  * Ettwig, K. F. et al. Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea. _Environ. Microbiol._ 10, 3164–3173 (2008). Article  CAS 

PubMed  Google Scholar  * Ettwig, K. F. et al. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. _Nature_ 464, 543–548 (2010). A LESSON IN WHAT CAN BE LEARNED BEYOND THE

ARCHAEA, FROM THE ARCHAEA. Article  CAS  PubMed  Google Scholar  * Hao, B. et al. A new UAG-encoded residue in the structure of a methanogen methyltransferase. _Science_ 296, 1462–1466

(2002). AN IMPORTANT DESCRIPTION OF PYRROLYSINE AND THE MECHANISM OF ITS INCORPORATION INTO PROTEINS. Article  CAS  PubMed  Google Scholar  * Soares, J. A. et al. The residue mass of

L-pyrrolysine in three distinct methylamine methyltransferases. _J. Biol. Chem._ 280, 36962–36969 (2005). Article  CAS  PubMed  Google Scholar  * Krzycki, J. A. Function of genetically

encoded pyrrolysine in corrinoid-dependent methylamine methyltransferases. _Curr. Opin. Chem. Biol._ 8, 484–491 (2004). Article  CAS  PubMed  Google Scholar  * Heinemann, I. U. et al. The

appearance of pyrrolysine in tRNAHis guanylyltransferase by neutral evolution. _Proc. Natl Acad. Sci. USA_ 106, 21103–21108 (2009). AN INTERESTING DESCRIPTION OF WHAT A NOVEL AMINO ACID AND

ITS COGNATE AARSS CAN EXPLAIN ABOUT EVOLUTION. Article  PubMed  PubMed Central  Google Scholar  * Farlow, W. G. in _United States Commission of Fish and Fisheries Part IV. Report for The

Commissioner 1878_ 969–973 (Government Printing Office, Washington DC, 1880). Google Scholar  * Kocur, M. & Hodgkiss, W. Taxonomic status of the genus _Halococcus_ Schoop. _Int. J. Syst.

Bacteriol._ 23, 151–156 (1973). Article  Google Scholar  * Sehgal, S. N., Kates, M. & Gibbons, N. E. Lipids of _Halobacterium cutirubrum_. _Can. J. Biochem. Physiol._ 40, 69–81 (1962).

Article  CAS  PubMed  Google Scholar  * Marshall, C. L. & Brown, A. D. The membrane lipids of _Halobacterium halobium_. _Biochem. J._ 110, 441–448 (1968). Article  CAS  PubMed  PubMed

Central  Google Scholar  * Fox, G. E. et al. The phylogeny of prokaryotes. _Science_ 209, 457–463 (1980). Article  CAS  PubMed  Google Scholar  * Oesterhelt, D. & Stoeckenius, W.

Rhodopsin-like protein from the purple membrane of _Halobacterium hatobium_. _Nature New Biol._ 233, 149–152 (1971). Article  CAS  PubMed  Google Scholar  * Oesterhelt, D. & Stoeckenius,

W. Functions of a new photoreceptor membrane. _Proc. Natl Acad. Sci. USA_ 70, 2853–2857 (1973). Article  CAS  PubMed  PubMed Central  Google Scholar  * Henderson, R. & Unwin, P. N. T.

Three-dimensional model of purple membrane obtained by electron microscopy. _Nature_ 257, 28–32 (1975). AN IMPORTANT BREAKTHROUGH, NOT ONLY FOR RESEARCH INTO LIGHT-HARVESTING PROTEINS

(BACTERIORHODOPSIN), BUT ALSO FOR STRUCTURAL BIOLOGY STUDIES OF PROTEINS THAT CONTAIN MULTIPLE TRANSMEMBRANE DOMAINS. Article  CAS  PubMed  Google Scholar  * Spudich, J. L. & Bogomolni,

R. A. Mechanism of colour discrimination by a bacterial sensory rhodopsin. _Nature_ 312, 509–513 (1984). Article  CAS  PubMed  PubMed Central  Google Scholar  * Lanyi, J. K.

Bacteriorhodopsin as a model for proton pumps. _Nature_ 375, 461–463 (1995). Article  CAS  PubMed  Google Scholar  * Kolbe, M., Besir, H., Essen, L. O. & Oesterhelt, D. Structure of the

light-driven chloride pump halorhodopsin at 1.8 Å resolution. _Science_ 288, 1390–1396 (2000). Article  CAS  PubMed  Google Scholar  * Spudich, J. L., Yang, C. S., Jung, K. H. & Spudich,

E. N. Retinylidene proteins: structures and functions from Archaea to humans. _Annu. Rev. Cell. Dev. Biol._ 16, 365–392 (2000). Article  CAS  PubMed  Google Scholar  * Rasmussen, S. G. et

al. Crystal structure of the human β2 adrenergic G-protein-coupled receptor. _Nature_ 450, 383–387 (2007). Article  CAS  PubMed  Google Scholar  * Overington, J. P., Al-Lazikani, B. &

Hopkins, A. L. How many drug targets are there? _Nature Rev. Drug Discov._ 5, 993–936 (2006). Article  CAS  Google Scholar  * Béjà, O. et al. Bacterial rhodopsin: evidence for a new type of

phototrophy in the sea. _Science_ 289, 1902–1906 (2000). AN IMPORTANT STUDY DESCRIBING A PREVIOUSLY UNKNOWN PHOTOTROPHIC SYSTEM FOR MARINE HETEROTROPHS. Article  PubMed  Google Scholar  *

Béjà, O., Spudich, E. N., Spudich, J. L., Leclerc, M. & DeLong, E. F. Proteorhodopsin phototrophy in the ocean. _Nature_ 411, 786–789 (2001). Article  PubMed  Google Scholar  * Venter,

J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. _Science_ 304, 66–74 (2004). Article  PubMed  Google Scholar  * Frigaard, N. U., Martinez, A., Mincer, T. J. &

DeLong, E. F. Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. _Nature_ 439, 847–850 (2006). Article  CAS  PubMed  Google Scholar  * Moran, M. A. &

Miller, W. L. Resourceful heterotrophs make the most of light in the coastal ocean. _Nature Rev. Microbiol._ 5, 792–800 (2007). Article  CAS  Google Scholar  * Gómez-Consarnau, L. et al.

Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation. _PLoS Biol._ 8, e1000358 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  * DeLong, E. F.

& Béjà, O. The light-driven proton pump proteorhodopsin enhances bacterial survival during tough times. _PLoS Biol._ 8, e1000359 (2010). Article  CAS  PubMed  PubMed Central  Google

Scholar  * Torsvik, T. & Dundas, I. D. Bacteriophage of _Halobacterium salinarium_. _Nature_ 248, 680–681 (1974). Article  CAS  PubMed  Google Scholar  * Dyall-Smith, M., Tang, S-L.

& Bath, C. Haloarchaeal viruses: how diverse are they? _Res. Microbiol._ 154, 309–313 (2003). Article  PubMed  Google Scholar  * Prangishvili, D., Forterre, P. & Garrett, R. A.

Viruses of the Archaea: a unifying view. _Nature Rev. Microbiol._ 4, 837–848 (2006). Article  CAS  Google Scholar  * Ortmann, A. C., Wiedenheft, B., Douglas, T. & Young, M. Hot

crenarchaeal viruses reveal deep evolutionary connections. _Nature Rev. Microbiol._ 4, 520–528 (2006). THIS ARTICLE, ALONG WITH REFERENCE 99, REVEALS THE DIVERSITY AND EXTENT OF ARCHAEAL

VIRUSES. Article  CAS  Google Scholar  * Sapienza, C. & Doolittle, W. F. Unusual physical organization of the _Halobacterium_ genome. _Nature_ 295, 384–389 (1982). EARLY INSIGHT INTO

GENOME REARRANGEMENT THAT LED TO THEORIES ABOUT THE ROLE OF LGT IN EVOLUTION. Article  CAS  PubMed  Google Scholar  * Ng, W. V. et al. Genome sequence of _Halobacterium species_ NRC-1.

_Proc. Natl Acad. Sci. USA_ 97, 12176–12181 (2000). Article  CAS  PubMed  PubMed Central  Google Scholar  * Papke, R. T., Koenig, J. E., Rodríguez-Valera, F. & Doolittle, W. F. Frequent

recombination in a saltern population of _Halorubrum_. _Science_ 306, 1928–1929 (2004). CAS  PubMed  Google Scholar  * Papke, R. T. et al. Searching for species in haloarchaea. _Proc. Natl

Acad. Sci. USA_ 104, 14092–14097 (2007). Article  CAS  PubMed  PubMed Central  Google Scholar  * Rodriguez-Valera, F. et al. Explaining microbial population genomics through phage predation.

_Nature Rev. Microbiol._ 7, 828–836 (2009). Article  CAS  Google Scholar  * Baliga, N. S. et al. Coordinate regulation of energy transduction modules in _Halobacterium_ sp. analyzed by a

global systems approach. _Proc. Natl Acad. Sci. USA_ 99, 14913–14918 (2002). Article  CAS  PubMed  PubMed Central  Google Scholar  * Facciotti, M. T. General transcription factor specified

global gene regulation in archaea _Proc. Natl Acad. Sci. USA_ 104, 4630–4635 (2007). Article  CAS  PubMed  PubMed Central  Google Scholar  * Koide, T. et al. Prevalence of transcription

promoters within archaeal operons and coding sequences. _Mol. Syst. Biol._ 5, 285 (2009). Article  CAS  PubMed  PubMed Central  Google Scholar  * Bonneau, R. et al. A predictive model for

transcriptional control of physiology in a free living cell. _Cell_ 131, 1354–1365 (2007). Article  CAS  PubMed  Google Scholar  * Bare, J. C., Koide, T., Reiss, D. J., Tenenbaum, D. &

Baliga, N. S. Integration and visualization of systems biology data in context of the genome. _BMC Bioinformatics_ 11, 382 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Rosenshine, I., Tchelet, R. & Mevarech, M. The mechanism of DNA transfer in the mating system of an archaebacterium. _Science_ 245, 1387–1389 (1989). Article  CAS  PubMed  Google Scholar

  * Humbard, M. A. et al. Ubiquitin-like small archaeal modifier proteins (SAMPs) in _Haloferax volcanii_. _Nature_ 463, 54–60 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Grogan, D. W. Exchange of genetic markers at extremely high temperatures in the archaeon _Sulfolobus acidocaldarius_. _J. Bacteriol._ 178, 3207–3211 (1996). Article  CAS  PubMed  PubMed

Central  Google Scholar  * Bertani, G. & Baresi, L. Genetic transformation in the methanogen _Methanococcus voltae_ PS. _J. Bacteriol._ 169, 2730–2738 (1987). Article  CAS  PubMed 

PubMed Central  Google Scholar  * Sato, T., Fukui, T., Atomi, H. & Imanaka, T. Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon _Thermococcus

kodakaraensis_ KOD1. _J. Bacteriol._ 185, 210–220 (2003). Article  CAS  PubMed  PubMed Central  Google Scholar  * Charlebois, R. L., Lam, W. L., Cline, S. W. & Doolittle, W. F.

Characterization of pHV2 from _Halobacterium volcanii_ and its use in demonstrating transformation of an archaebacterium. _Proc. Natl Acad. Sci. USA_ 84, 8530–8534 (1987). Article  CAS 

PubMed  PubMed Central  Google Scholar  * Metcalf, W. W., Zhang, J. K., Apolinario, E., Sowers, K. R. & Wolfe, R. S. A genetic system for Archaea of the genus _Methanosarcina_:

liposome-mediated transformation and construction of shuttle vectors. _Proc. Natl Acad. Sci. USA_ 94, 2626–2631 (1997). A STRIKING EXAMPLE OF THE DEVELOPMENT OF A NOVEL, HIGH-EFFICIENCY GENE

TRANSFER SYSTEM. Article  CAS  PubMed  PubMed Central  Google Scholar  * Schleper, C., Kubo, K. & Zillig, W. The particle SSV1 from the extremely thermophilic archaeon _Sulfolobus_ is a

virus: demonstration of infectivity and of transfection with viral DNA. _Proc. Natl Acad. Sci. USA_ 89, 7645–7649 (1992). Article  CAS  PubMed  PubMed Central  Google Scholar  * Allers, T.

& Mevarech, M. Archaeal genetics — the third way. _Nature Rev. Genet._ 6, 58–73 (2005). A GOOD SUMMARY OF THE GENETIC SYSTEMS THAT HAVE BEEN DEVELOPED FOR ARCHAEA. Article  CAS  PubMed 

Google Scholar  * Sowers, K. & Anderson, K. in _Archaea: Molecular and Cellular Biology_ (ed. Cavicchioli, R.) 463–477 (American Society for Microbiology Press, Washington DC, 2007).

Book  Google Scholar  * Seghal, S. N., Kates, M. & Gibbons, N. E. Lipids of _Halobacterium cutirubrum_. _Can. J. Biochem. Physiol._ 40, 69–81 (1962). Article  Google Scholar  * Darland,

G., Brock, T. D., Samsonoff, W. & Conti, S. F. A thermophilic, acidophilic mycoplasma isolated from a coal refuse pile. _Science_ 170, 1416–1418 (1970). THE DISCOVERY OF AN UNUSUAL

ARCHAEON BEFORE THE KNOWLEDGE THAT A THIRD DOMAIN EXISTED. Article  CAS  PubMed  Google Scholar  * Langworthy, T. A., Smith, M. E. & Mayberry, W. R. A new class of lipopolysaccharide

from _Thermoplasma acidophilum_. _J. Bacteriol._ 119, 106–116 (1974). CAS  PubMed  PubMed Central  Google Scholar  * Brock, T. D., Brock, K. M., Belly, R. T. & Weiss, R. L. _Sulfolobus_:

a new genus of sulphur oxidizing bacteria living at low pH and high temperature. _Arch. Microbiol._ 84, 54–68 (1972). CAS  Google Scholar  * Langworthy, T. A., Smith, M. E. & Mayberry,

W. R. Long-chain glycerol diether and polyol dialkyl glycerol triether lipids of _Sulfolobus acidocaldarius_. _J. Bacteriol._ 112, 1193–1200 (1972). CAS  PubMed  PubMed Central  Google

Scholar  * Stetter, K. O. History of discovery of the first hyperthermophiles. _Extremophiles_ 10, 357–262 (2006). A BRIEF, BUT INFORMATIVE, REVIEW DESCRIBING HOW ARCHAEAL HYPERTHERMOPHILES

WERE DISCOVERED. Article  PubMed  Google Scholar  * Stetter, K. O. Hyperthermophiles in the history of life. _Philos. Trans. R. Soc. Lond. B. Biol. Sci._ 361, 1837–1842 (2006). Article  CAS

  PubMed  PubMed Central  Google Scholar  * Waters, E. et al. The genome of _Nanoarchaeum equitans_: insights into early archaeal evolution and derived parasitism. _Proc. Natl Acad. Sci.

USA_ 100, 12984–12988 (2003). Article  CAS  PubMed  PubMed Central  Google Scholar  * Podar, M. et al. A genomic analysis of the archaeal system _Ignicoccus hospitalis-Nanoarchaeum

equitans_. _Genome_ _Biol._ 9, R158 (2008). Google Scholar  * Küper, U., Meyer, C., Müller, V., Rachel, R. & Huber, H. Energized outer membrane and spatial separation of metabolic

processes in the hyperthermophilic Archaeon _Ignicoccus hospitalis_. _Proc. Natl Acad. Sci. USA_ 107, 3152–3126 (2010). INSIGHT INTO THE UNUSUAL RELATIONSHIP BETWEEN AN ARCHAEAL HOST AND

ARCHAEAL SYMBIONT OR PARASITE, WITH POSSIBLE IMPLICATIONS FOR THE EVOLUTION OF A EUKARYOTE-LIKE CELL TYPE. Article  PubMed  PubMed Central  Google Scholar  * van Ooij, C. A road to

eukaryotes? _Nature Rev. Microbiol._ 8, 246–247 (2010). Article  CAS  Google Scholar  * Fuhrman, J. A., McCallum, K. & Davis, A. A. Novel major archaebacterial group from marine

plankton. _Nature_ 356, 148–149 (1992). Article  CAS  PubMed  Google Scholar  * DeLong, E. F. Archaea in coastal marine environments. _Proc. Natl Acad. Sci. USA_ 89, 5685–5689 (1992). ALONG

WITH REFERENCE 132, THIS PAPER DESCRIBES THE NEW INSIGHT THAT ARCHAEA ARE IMPORTANT MEMBERS OF MARINE ENVIRONMENTS. Article  CAS  PubMed  PubMed Central  Google Scholar  * Karner, M. B.,

DeLong, E. F. & Karl, D. M. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. _Nature_ 409, 507–510 (2001). THE SHEER ABUNDANCE OF ARCHAEA IN THE MARINE BIOSPHERE IS

DESCRIBED. Article  CAS  PubMed  Google Scholar  * Cavicchioli, R. Cold adapted Archaea. _Nature Rev. Microbiol._ 4, 331–343 (2006). INSIGHT INTO THE DIVERSITY, FUNCTIONAL ROLES AND ADAPTIVE

MECHANISMS OF ARCHAEA IN THE COLD BIOSPHERE. Article  CAS  Google Scholar  * Franzmann, P. D. et al. _Halobacterium lacusprofundi_ sp. nov., a halophilic bacterium isolated from Deep Lake,

Antarctica. _Syst. Appl. Microbiol._ 11, 20–27 (1988). Article  CAS  Google Scholar  * Franzmann, P. D., Stringer, N., Ludwig, W., Conway de Macario, E. & Rohde, M. A methanogenic

archaeon from Ace Lake, Antarctica: _Methanococcoides burtonii_ sp. nov. _System. Appl. Microbiol._ 15, 573–581 (1992). Article  Google Scholar  * Franzmann, P. D. et al. _Methanogenium

frigidum_ sp. nov., a psychrophilic, H2-using methanogen from Ace Lake, Antarctica. _Int. J. Syst. Bacteriol._ 47, 1068–1072 (1997). Article  CAS  PubMed  Google Scholar  * Allen, M. et al.

The genome sequence of the psychrophilic archaeon, _Methanococcoides burtonii_: the role of genome evolution in cold-adaptation. _ISME J._ 3, 1012–1035 (2009). Article  CAS  PubMed  Google

Scholar  * Takai, K. et al. Cell proliferation at 122 °C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation. _Proc. Natl Acad. Sci. USA_

105, 10949–10954 (2008). Article  PubMed  PubMed Central  Google Scholar  * Schleper, C. et al. Genomic analysis reveals chromosomal variation in natural populations of the uncultured

psychrophilic archaeon _Cenarchaeum symbiosum_. _J. Bacteriol._ 180, 5003–5009 (1998). CAS  PubMed  PubMed Central  Google Scholar  * Schleper, C., Jurgens, G. & Jonuscheit, M. Genomic

studies of uncultivated archaea. _Nature Rev. Microbiol._ 3, 479–488 (2005). Article  CAS  Google Scholar  * Könneke, M. et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon.

_Nature_ 437, 543–546 (2005). REVEALING INSIGHT INTO AN ELUSIVE PHYLOGENETIC AND PHENOTYPIC TYPE OF ARCHAEA: CHEMOLITHOAUTROPHIC AMMONIA OXIDIZERS. Article  CAS  PubMed  Google Scholar  *

Walker, C. B. et al. _Nitrosopumilus maritimus_ genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine _Crenarchaea_. _Proc. Natl Acad. Sci. USA_

107, 8818–8823 (2010). Article  PubMed  PubMed Central  Google Scholar  * Berg, I. A. et al. Autotrophic carbon fixation in archaea. _Nature Rev. Microbiol._ 8, 447–460 (2008). Article  CAS

  Google Scholar  * Buckley, D. H., Graber, J. R. & Schmidt, T. M. Phylogenetic analysis of nonthermophilic members of the kingdom _Crenarchaeota_ and their diversity and abundance in

soils. _Appl. Environ. Microbiol._ 64, 4333–4339 (1998). CAS  PubMed  PubMed Central  Google Scholar  * Leininger, S. et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils.

_Nature_ 442, 806–809 (2006). Article  CAS  PubMed  Google Scholar  * Erguder, T. H., Boon, N., Wittebolle, L., Marzorati, M. & Verstraete, W. Environmental factors shaping the

ecological niches of ammonia-oxidizing archaea. _FEMS Microbiol. Rev._ 33, 855–869 (2009). Article  CAS  PubMed  Google Scholar  * Hirata, A., Klein, B. J. & Murakami, K. S. The X-ray

crystal structure of RNA polymerase from Archaea. _Nature_ 451, 851–854 (2008). A STRIKING EXAMPLE OF HOW VISUALLY AND FUNCTIONALLY SIMILAR KEY COMPONENTS OF THE INFORMATION PROCESSING

SYSTEMS ARE IN THE ARCHAEA AND EUKARYA. Article  CAS  PubMed  PubMed Central  Google Scholar  * Cavicchioli, R., Siddiqui, K. S., Andrews, D. & Sowers, K. R. Low-temperature

extremophiles and their applications. _Curr. Opin. Biotech._ 13, 253–261 (2002). Article  CAS  PubMed  Google Scholar  * Schiraldi, C., Giuliano, M. & De Rosa, M. Perspectives on

biotechnological applications of archaea. _Archaea_ 1, 75–86 (2002). Article  CAS  PubMed  PubMed Central  Google Scholar  * Auernik, K. S., Cooper, C. R. & Kelly, R. M. Life in hot

acid: pathway analyses in extremely thermoacidophilic archaea. _Curr. Opin. Biotechnol._ 19, 445–453 (2008). Article  CAS  PubMed  PubMed Central  Google Scholar  * Krishnan, L. &

Sprott, G. D. Archaeosome adjuvants: immunological capabilities and mechanism(s) of action. _Vaccine_ 26, 2043–2055 (2008). Article  CAS  PubMed  Google Scholar  * Cavicchioli, R.

Extremophiles and the search for extra-terrestrial life. _Astrobiology_ 2, 281–292 (2002). Article  CAS  PubMed  Google Scholar  * Tung, H. C., Bramall, N. E. & Price, P. B. Microbial

origin of excess methane in glacial ice and implications for life on Mars. _Proc. Natl Acad. Sci. USA_ 102, 18292–18296 (2005). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Oremland, R. S. & Voytek, M. A. Acetylene as fast food: implications for development of life on anoxic primordial Earth and in the outer solar system. _Astrobiology_ 8, 45–58 (2008).

Article  CAS  PubMed  Google Scholar  * Oremland, R. S. NO connection with methane. _Nature_ 464, 500–501 (2010). Article  CAS  PubMed  Google Scholar  * Stetter, K. O. Hyperthermophilic

procaryotes. _FEMS Microbiol. Rev._ 18, 149–158 (1996). Article  CAS  Google Scholar  * Koonin, E. V. & Martin, W. On the origin of genomes and cells within inorganic compartments.

_Trends Genet._ 21, 647–654 (2005). Article  CAS  PubMed  PubMed Central  Google Scholar  * Brazelton, W. J. et al. Archaea and bacteria with surprising microdiversity show shifts in

dominance over 1,000-year time scales in hydrothermal chimneys. _Proc. Natl Acad. Sci. USA_ 107, 1612–1617 (2010). Article  PubMed  PubMed Central  Google Scholar  * Glansdorff, N., Xu, Y.

& Labedan, B. The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner. _Biol. Direct_ 3, 29 (2008). Article  CAS  PubMed  PubMed Central 

Google Scholar  * (No authors listed). A sequence of changes. _Nature Rev. Microbiol._ 8, 85 (2010). * Delsuc, F., Brinkmann, H. & Philippe, H. Phylogenomics and the reconstruction of

the tree of life. _Nature Rev. Genet._ 6, 361–375 (2005). Article  CAS  PubMed  Google Scholar  * Doolittle, W. F. & Zhaxybayeva, O. On the origin of prokaryotic species. _Genome Res._

19, 744–756 (2009). Article  CAS  PubMed  Google Scholar  * Theobald, D. L. A formal test of the theory of universal common ancestry. _Nature_ 465, 219–222 (2010). Article  CAS  PubMed 

Google Scholar  * Pace, N. R. Time for a change. _Nature_ 441, 289 (2006). AN IMPORTANT AND AXIOMATIC ESSAY ABOUT LEARNING FROM WHAT WE HAVE LEARNED. Article  CAS  PubMed  Google Scholar  *

Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. _Nucleic Acids Res._ 35, 7188–7196 (2007). Article

  CAS  PubMed  PubMed Central  Google Scholar  * Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. _Bioinformatics_ 22,

2688–2690 (2006). Article  CAS  PubMed  Google Scholar  Download references 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. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * School of Biotechnology and

Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia Ricardo Cavicchioli Authors * Ricardo Cavicchioli View author publications You can also search for this

author inPubMed Google Scholar ETHICS DECLARATIONS COMPETING INTERESTS The author declares no competing financial interests. RELATED LINKS RELATED LINKS FURTHER INFORMATION Ricardo

Cavicchioli's homepage NCBI Taxonomy Datbase PubMed 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. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Cavicchioli, R. Archaea — timeline of the

third domain. _Nat Rev Microbiol_ 9, 51–61 (2011). https://doi.org/10.1038/nrmicro2482 Download citation * Published: 06 December 2010 * Issue Date: January 2011 * DOI:

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