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Archaea

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Part of the Encyclopedia of Earth Sciences Series book series (EESS)

Synonym

Archaebacteria

Definition

Archaea constitute one of the three domains of life, as phylogenetically distinct from the domains Bacteria and Eukarya (Woese and Fox, 1977; Woese et al., 1990).

Etymology

Archaea (singular: archaeon) are derived from Greek ἀρχαῖος – ancient, primitive.

The term was coined to reflect the apparent antiquity of traits in archaeal species and their aptness to inhabit environments like those presumed for early Earth.

Phylogeny

On the phylogenetic tree of organisms, Archaea form one of the three fundamental branches called domains (Woese et al., 1990). Further branching within the archaeal domain is largely based on ribosomal RNA sequences, but also relies on evidence from comparative analysis of protein sequences. Typical markers in archaeal phylogeny are ribosomal proteins, histones, and components of the transcription system and the cell division apparatus (Brochier-Armanet et al., 2011). In addition to the initially recognized phyla Crenarchaeota and...

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Bibliography

  • Amend, J. P., and Shock, E. L., 2001. Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. FEMS Microbiology Reviews, 25, 175–243.

    Google Scholar 

  • Beal, E. J., House, C. H., and Orphan, V. J., 2009. Manganese- and iron-dependent marine methane oxidation. Science, 325, 184–187.

    Google Scholar 

  • Bernhard, A. E., and Bollmann, A., 2010. Estuarine nitrifiers: new players, patterns and processes. Estuarine, Coastal and Shelf Science, 88, 1–11.

    Google Scholar 

  • Bini, E., 2010. Archaeal transformation of metals in the environment. FEMS Microbiology Ecology, 73, 1–16.

    Google Scholar 

  • Bowers, K. J., and Wiegel, J., 2011. Temperature and pH optima of extremely halophilic archaea: a mini-review. Extremophiles, 15, 119–128.

    Google Scholar 

  • Brochier-Armanet, C., Forterre, P., and Gribaldo, S., 2011. Phylogeny and evolution of the Archaea: one hundred genomes later. Current Opinion in Microbiology, 14, 274–281.

    Google Scholar 

  • Cabello, P., Roldán, M. D., and Moreno-Vivián, C., 2004. Nitrate reduction and the nitrogen cycle in archaea. Microbiology, 150, 3527–3546.

    Google Scholar 

  • Conrad, R., 2009. The global methane cycle: recent advances in understanding the microbial processes involved. Environmental Microbiology Reports, 1, 285–292.

    Google Scholar 

  • Erguder, T. H., Boon, N., Wittebolle, L., Marzorati, M., and Verstraete, W., 2009. Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. FEMS Microbiology Reviews, 33, 855–869.

    Google Scholar 

  • Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E., and Oakley, B. B., 2005. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proceedings of the National Academy of Sciences of the United States of America, 102, 14683–14688.

    Google Scholar 

  • Genomes Online database. www.genomesonline.org.

  • Hatzenpichler, R., 2012. Diversity, physiology, and niche differentiation of ammonia-oxidizing Archaea. Applied and Environmental Microbiology, 78, 7501–7510.

    Google Scholar 

  • Knittel, K., and Boetius, A., 2009. Anaerobic oxidation of methane: progress with an unknown process. Annual Review of Microbiology, 63, 311–334.

    Google Scholar 

  • Lipp, J. S., Morono, Y., Inagaki, F., and Hinrichs, K.-U., 2008. Significant contribution of Archaea to extant biomass in marine subsurface sediments. Nature, 454, 991–994.

    Google Scholar 

  • Liu, Y., and Whitman, W. B., 2008. Metabolic, phylogenetic, and ecological diversity of the methanogenic Archaea. Annals of the New York Academy of Sciences, 1125, 171–189.

    Google Scholar 

  • Marraffini, L. A., and Sontheimer, E. J., 2010. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nature Reviews Genetics, 11, 181–190.

    Google Scholar 

  • Martens-Habbena, W., Berube, P. M., Urakawa, H., de la Torre, J. R., and Stahl, D. A., 2009. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature, 461, 976–979.

    Google Scholar 

  • Milucka, J., Ferdelman, T. G., Polerecky, L., Franzke, D., Wegener, G., Schmid, M., Lieberwirth, I., Wagner, M., Widdel, F., and Kuypers, M. M. M., 2012. Zero-valent sulphur is a key intermediate in marine methane oxidation. Nature, 491, 541–546.

    Google Scholar 

  • Moissl-Eichinger, C., and Huber, H., 2011. Archaeal symbionts and parasites. Current Opinion in Microbiology, 14, 364–370.

    Google Scholar 

  • Oelgeschläger, E., and Rother, M., 2008. Carbon monoxide-dependent energy metabolism in anaerobic bacteria and archaea. Archives of Microbiology, 190, 257–269.

    Google Scholar 

  • Pester, M., Schleper, C., and Wagner, M., 2011. The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Current Opinion in Microbiology, 14, 300–306.

    Google Scholar 

  • Philippot, L., 2002. Denitrifying genes in bacterial and archaeal genomes. Biochimica et Biophysica Acta, 1577, 355–376.

    Google Scholar 

  • Pina, M., Bize, A., Forterre, P., and Prangishvili, D., 2011. The archeoviruses. FEMS Microbiology Reviews, 35, 1035–1054.

    Google Scholar 

  • Prosser, J. I., and Nicol, G. W., 2008. Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environmental Microbiology, 10, 2931–2941.

    Google Scholar 

  • Sorek, R., Kunin, V., and Hugenholtz, P., 2008. CRISPR – a widespread system that provides acquired resistance against phages in bacteria and archaea. Nature Reviews Microbiology, 6, 181–186.

    Google Scholar 

  • Stahl, D. A., and de la Torre, J. R., 2012. Physiology and diversity of ammonia-oxidizing Archaea. Annual Review of Microbiology, 66, 83–101.

    Google Scholar 

  • Stolz, J. A., Basu, P., Santini, J. M., and Oremland, R. S., 2006. Arsenic and selenium in microbial metabolism. Annual Review of Microbiology, 60, 107–130.

    Google Scholar 

  • Takai, K., and Nakamura, K., 2011. Archaeal diversity and community development in deep-sea hydrothermal vents. Current Opinion in Microbiology, 14, 282–291.

    Google Scholar 

  • Torres-Alvarado, M. R., Fernández, F. J., Ramírez Vives, F., and Varona-Cordero, F., 2013. Dynamics of the methanogenic Archaea in tropical estuarine sediments. Archaea, 0, 582646.

    Google Scholar 

  • Valentine, D. L., 2007. Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nature Reviews Microbiology, 5, 316–323.

    Google Scholar 

  • Woese, C. R., and Fox, G. E., 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences of the United States of America, 74, 5088–5090.

    Google Scholar 

  • Woese, C. R., Kandler, O., and Wheelis, M. L., 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eukarya. Proceedings of the National Academy of Sciences of the United States of America, 87, 4576–4579.

    Google Scholar 

  • Wrede, C., Dreier, A., Kokoschka, S., and Hoppert, M., 2012. Archaea in symbioses. Archaea, 0, 596846.

    Google Scholar 

  • Zumft, W. G., 1997. Cell biology and molecular basis of denitrification. Microbiology and Molecular Biology Reviews, 61, 533–616.

    Google Scholar 

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Correspondence to Antje Rusch .

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Rusch, A. (2016). Archaea. In: Kennish, M.J. (eds) Encyclopedia of Estuaries. Encyclopedia of Earth Sciences Series. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-8801-4_287

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