Archaea were discovered during research that aimed to understand the fundamental evolutionary relationships of all extant life. Bacteria have been studied since the 17th century and, until relatively recently, taxonomy was based on characterizing morphological and physiological properties of organisms grown in laboratory culture. The advent of molecular biology led to new approaches for defining taxonomic and evolutionary relationships. In the late 1970s, Carl Woese and George Fox discovered, through the comparison of gene sequences encoding ribosomal RNA (rRNA), that all "bacteria" were placed within two distinct groups, rather than one: the Eubacteria (including most prokaryotic species grown in the laboratory) and the Archaebacteria, later termed "Archaea" to reflect their distinct evolutionary history from (Eu)Bacteria. At the time, an important feature of cultivated archaea was that they were generally found in environments that were considered to represent extremes of temperature, salinity, pH or oxygen availability at which life could be sustained. Although this view was maintained for around fifteen years following the discovery of Archaea, the application of molecular techniques in microbial ecology in the 1990s revolutionized scientists' understanding of archaeal diversity. Molecular signatures of archaea (16S rRNA genes) were found in all "non-extreme" environments, including soils, sediments, marine, and freshwater habitats. During the past twenty years, scientists have come to recognize that Archaea represent a major proportion of microbial biomass on the planet and make unique and essential contributions to biogeochemical cycles.
The discovery of Archaea and subsequent analyses of archaeal diversity and ecology were based on the discovery of the three domains of life. After the discovery of Archaebacteria in the late 1970s, Woese, et al. 1990 proposed the term "Archaea" (replacing "Archaebacteria") to reflect the distinct nature of the archaeal domain and to highlight its distinction from (Eu)Bacteria. The dramatic history of the discovery of archaea is reviewed in articles by Albers, et al. 2013 and Cavicchioli 2011. Archaea make major contributions to global biogeochemical cycles and Offre, et al. 2013 presents an excellent overview of the diverse range of physiologies that contribute to ecological functioning. Madigan, et al. 2015 is perhaps the best-known general microbiology textbook, but it also has a strong ecological focus. Garrett and Klenk 2006 has a greater focus on the biochemistry and genetics of Archaea that define their ecological functions.
Albers, Sonja-Verena, Patrick Forterre, David Prangishvili, and Christa Schleper. 2013. The legacy of Carl Woese and Wolfram Zillig: From phylogeny to landmark discoveries. Nature Reviews Microbiology 11:713–719.
This short essay celebrates the work of two pioneers of archaeal research and provides an overview of the major discoveries during the thirty years following the discovery of archaea in the late 1970s.
Cavicchioli, Ricardo. 2011. Archaea—Timeline of the third domain. Nature Reviews Microbiology 9:51–61.
A comprehensive review of the historical development of research on the phylogeny, cell biology, physiology, and ecology of archaea, focusing on unique characteristics that distinguish them from bacteria.
Garrett, Roger A., and Hans-Peter Klenk, eds. 2006. Archaea: Evolution, physiology, and molecular biology. Oxford: Blackwell.
An important textbook providing detailed information on biochemistry and genetics as well as the evolution of archaea and individual phyla that have more direct ecological relevance.
Madigan, Michael T., John M. Martinko, Kelly S. Bender, Daniel H. Buckley, and David A. Stahl, eds. 2015. Brock biology of microorganisms. 14th ed. Boston: Prentice Hall.
An excellent standard microbiology textbook with a strong focus on ecology. While covering all aspects of microbiology, it has very good coverage of archaeal physiology, diversity, and ecology.
Offre, Pierre, Anja Spang, and Christa Schleper. 2013. Archaea in biogeochemical cycles. Annual Review of Microbiology 67:437–457.
An excellent overview of archaeal ecology that emphasizes the roles of archaea in the biogeochemical cycles (i.e., carbon, nitrogen, sulphur, etc.), in contrast to other reviews that focus on phylogeny and taxonomy.
Woese, Carl R., Otto Kandler, and Mark L. Wheelis. 1990. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences of the United States of America 87:4576–4579.
This paper introduced and proposed the term "Archaea" (replacing "Archaebacteria") for one of the three domains of life, the other two being Bacteria and Eucarya. It precedes the development of cultivation-independent techniques for characterizing natural communities of archaea, but provides an interesting overview of the ecology of cultivated, "extremophilic" archaea.