Dictionary > Archaea

Archaea

Archaea
n., plural: archeon
[ɑːˈkiːə]
Definition: prokaryotes that live in extreme environmental conditions and are genetically distinct from bacteria, which is another group of prokaryotes

Archaea is a group of prokaryotic life forms distinct from bacteria forming a separate domain of life. They possess pseudo-peptidoglycan cell wall, archaeol plus ether-linked plus highly branched isoprenoid chain lipids in their cell membrane with no nuclei or cell organelles. They have a ubiquitous distribution and are widely known extremophiles.

Let’s gain a deeper understanding of archaea definition, habitats, characteristics,  structure, metabolism, genetics, reproduction, placement in the tree of life, and many more.

Archaea Definition

What are archaea? In biology, the definition of archaea is that they are prokaryotic forms of life sharing some features with bacteria and other features with eukarya. Archaea constitute one major domain of life and comprise only single-celled organisms devoid of nuclei.

Now we know how to define archaea, let’s move ahead and learn more.

Archaea Etymology

Archaea is a modern Latin word derived from the Greek word “arkhaios” meaning ‘primitive’. The singular of archaea is archaeon. Archaea is the plural form of “archaeon“.

Domain Archaea and other Classification Systems

When biological sciences are studied, a variety of different organisms come into the picture. Understanding one organism in relation to the other is very difficult due to the vast diversity.

For ease of studying, classification systems are proposed. In the history of life science, several such methods have been proposed. Look at the table below for a brief summary of the different classification systems over the course of time.

Table 1: Summary of the Different Classification Systems

Year Scientist Systems of classification Groups under the system
1735 Carl Linnaeus 2-kingdom system Primary kingdoms-Vegetabilia & Animalia
1866 Ernst Haeckel 3-kingdom system Plantae, Protista & Animalia
1925 Édouard Chatton 2-empire system Prokaryota & Eukaryota
1938 Herbert Faulkner Copeland 4-kingdom system Monera, Plantae, Protista & Animalia
1969 Robert Harding Whittaker 5-kingdom system Monera, Plantae, Fungi, Protista & Animalia
1990 Carl Richard Woese 3-domain system Domain bacteria, domain archaea, third domain eukarya
1998 Thomas Cavalier-Smith 2 empire, 6 kingdom system Bacteria, Protozoa, Chromista, Plantae, Fungi, & Animalia
2015 Thomas Cavalier-Smith 2 empire, 6 kingdom system Bacteria, Archaea kingdom, Protozoa, Chromista, Plantae, Fungi, & Animalia

Data Source: Dr. Harpreet Narang of Biology Online

Notice the introduction of archaea in 1990 by Carl R. Woese. It was at this time that nucleotide sequences of the small subunit of rRNA (16S ribosomal RNA) were compared from all the cellular life forms from common ancestors. Since this molecule is conserved in all other life forms that are cellular in nature, the genome phylogeny (phylogenetic structures derived from phylogenetic trees upon phylogenetic analyses) derived from this work turned out revolutionary. What was earlier believed to be just “monera” was now split into “bacteria and archaea”. This global phylogeny overturned the existing notions of purely prokaryotic and eukaryotic cell dichotomy. An understanding of the prokaryotic domain deepened from this point. 

Archaea versus Archaebacteria

Since they were earlier placed under the monera kingdom up till the 5-kingdom classification (1969), they are called archaebacteria then. But after the introduction of the 3-domain system (1990) and the identification of the major differences between archaea and bacteria, the term “archaebacteria” has fallen out of use in the scientific community.

Difficulties with Studies of Archaea Group

Although the discovery of this group from the studies of Carl R. Woese and group ignited interest in the subject, there were some legit problems associated with it. Most of the archaeal cells haven’t been discovered or isolated in the lab. They have only been detected in some environmental samples with the aid of gene sequencing.

This has made their classification into different phyla relatively difficult. In recent years, a lot of evolutionary biology-related work has been undertaken to better understand evolutionary relationships between different archaeal species.

Evolutionary relationships and evolutionary history can bring a lot of clarity to the table. Evolutionary histories help in clearly deciphering the origin, evolution, and directions of further changes at molecular levels (molecular evolution). Molecular biology tools help in such work.

tree of life - phylogenetic tree
Figure 1: Eukarya group is in red, the bacteria group is in blue and the archaea group is in green. Notice the close affinity of archaea with eukarya rather than with bacteria. Image Credit: Ciccarelli et al. (2006).

Differences between Archaea and Bacteria

Look at the table of comparison below to learn about the major differences between these 2 domains of life; archaea vs bacteria. Both of these domains have been found to be evolutionarily distinct as per 16S rRNA phylogeny.

Table 2: Summary of the Differences between Archaea and Bacteria

Characteristics of prokaryotic cells Archaea Bacteria
Membrane constitution Prominence of ether-linked lipids Prominence of ester-linked lipids (like Eukarya)
Peptidoglycan in cell wall Absent Present
Pseudopeptidoglycan in cell wall Present Absent
Types of RNA 3 1
Transcription similar to Eukarya Yes No (Unique)
Number of RNA polymerases Many Only one
Translation similar to Eukarya Yes No (Unique)
Translation initiation codon (for protein synthesis) Methionine Formylmethionine
Major reproductive strategy
  • Binary fission
  • Budding
  • Fragmentation
  • Binary fission
  • Budding
  • Fragmentation
  • Spore formation
Rigid or fragile towards harsh environmental conditions Very rigid Relatively fragile
Major metabolic activity
  • Diazotrophy
  • Chemotrophy
  • Methanogenesis (a form of anaerobic respiration that is unique to this group)
Genetic similarity to Eukarya More Less
Sensitivity to diphtheria toxin Sensitive Resistant
Example Halobacterium spp. Escherichia coli

Data Source: Dr. Harpreet Narang of Biology Online

RNA polymerase structures - bacteria, archaea, Eukaryote
Figure 2: Notice the differences in the structure of RNAP (RNA polymerase) required for the transcription process. Archaeal lineage RNAP shares similarities with eukaryotic RNAP II, while the RNAP of bacteria is different from both groups. Image Credit: Applied Microbiology and Biotechnology.

 

Archaeal phospholipid vs bactreial and eukaryotic phospholipid in cell membrane
Figure 3: Archaeal membrane is formed by lipids containing ether links. Contrastingly, bacterial membranes are formed by lipids containing ester links. Image Credit: Tortora, G.J.

Watch this vid about archaea:

Biology definition:
Archaea are unicellular prokaryotes that comprise the domain of the same name, Archaea. These microorganisms physically resemble the bacteria but are genetically distinct from the latter. Archaea are typically found inhabiting and thriving in extreme environmental conditions. They include halophiles (archaea inhabiting extremely salty environments), methanogens (archaea producing methane), and thermophiles (archaea that thrive in scorching environments).
Characteristics:
Archaea or archaebacteria evolved separately from eubacteria and eukaryotes. They are similar to eubacteria in being prokaryotes and lacking a distinct nucleus. However, they differ in terms of ribosomal structure, the presence of introns (in some archaeal species), and membrane structure or composition. They are similar to eukaryotes in ways that archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably, the enzymes involved in transcription and translation. They are regarded to be living fossils and survivors of an ancient group of organisms that bridged the gap in evolution between eubacteria and eukaryotes.
Etymology: The term archaea (ar-KAY-ə) (singular: archeon) came from Greek arkhaion, arkhaios, meaning “ancient”. Synonyms: archaebacteria.
Compare: eubacteria
See also: prokaryote, eukaryote

 Habitats of the Archaea

Archaea were first identified from extreme environments like volcanoes, hydrothermal vents, etc. But as the sequencing technology became more widely available, the archaeal presence was found to be ubiquitous. Now they are known to inhabit a vast range of natural environments and habitats. Besides constituting a major part of the ecosystem, they play an instrumental role in its functioning, too. They inhabit both terrestrial and aquatic ecosystems.

Where do archaebacteria live? To answer that, here’s the list of some of their major habitats:

  • Deeps seas and oceans (archaea form nearly 20% of microbial diversity of the oceans)
  • Geysers
  • Hot water springs
  • Hydrothermal vents
  • Volcanoes
  • Black smokers
  • Mines and oil wells
  • Very cold habitats like ice sheaths of tundra
  • Highly saline lakes
  • Highly acidic places
  • Highly alkaline waters
  • Swamps, wetlands, and marshlands
  • Sewage
  • Intestinal tracts of humans and animals
  • Highly degraded soils, anoxic muds (archaea in soil)

Archaeal Groups Inhabiting Different Extreme Habitats

Archaea examples
Figure 4: Archaea examples- Both thermophilic and extreme thermophilic species. Image Credit: Carolina Andrade.

Since archaea inhabit extreme habitats, they are called extremophiles. Within extremophiles, there are different physiological categories or types of archaea like:

  1. Halophiles (live in extreme salt conditions like salt lakes, and brackish waters)
    Example: Halobacterium spp.
  2. Thermophiles (live in extremely high temperatures like hot springs and vents)
    Example: Methanopyrus kandleri
  3. Alkaliphiles (live in extreme alkaline conditions like marine hydrothermal systems)
    Example: Thermococcus alcaliphilus is a marine archaea.
  4. Acidophiles (live in extremely acidic conditions like dry hot soil and volcanic sites)
    Example: Picrophilus torridus

An archaeon doesn’t necessarily come under only one of these categories. In fact, many archaea are a combination of two or more of these features.

archea habitat - Great Salt Lake of Utah USA
Figure 4: The Great Salt Lake of Utah in the United States is home to halophilic archaea species. They inhabit the salt crust (shown in [a]). Figure [b] shows them growing in lab conditions on salt agar. Figure [c] shows the pinkish tinge that these halophilic archaea impart to the Utah lake. Image Credit: Daniel L. Jones.
Picrophilus torridus
Figure 6: Picrophilus torridus is an acidophilic archaeon whose membrane integrity is disturbed at pH above 4.00. It was isolated for the 1st time from dry hot soil samples from Hokkaido in Japan. Image Credit: Alchetron.

Characteristics of the Archaea

So, read the archaea characteristics in this section and get an answer to what is special about archaea.

  • Energy sources used by archaea

    • Relatively diverse group sources than eukaryotic organisms, like sugars, ammonia, metal ions, and hydrogen gas
    • Based on their preference of source for deriving energy, they are divided into different nutritional groups. Some of them are:
      • Phototrophic Archaea: Some species of archaea are known to utilize energy from the sun. Hence they are called phototrophic archaea. Although they can utilize sunlight like the plants, they can’t fix atmospheric carbon. So, the answer to the query “if archaea photosynthesize” is NO. They can be “PHOTOTROPHIC” and “NOT PHOTOSYNTHETIC”.Example: Haloarchaea or Halobacterium.
Haloarchaea in Lonar Lake India
Figure 7: This is a picture of a lake in India, Lonar lake that recently turned color to pinkish red. A probe led by the scientists from CSIR-NEERI lab brought to light the presence of salt-tolerant Haloarchaea populations in the lake. The photo pigment (for phototropism) of these archaea organisms is called ‘bacteriorhodopsin’ which is opaque to long wavelengths (red) and imparts this color to the lake. Image Credit: Mohammad Iqbal.
      • Lithotrophic Archaea: Some species of archaea are known to utilize inorganic compounds (chemical energy) to take care of their energy needs like metal ions, hydrogen, ammonia, etc.Examples: Pyrolobus, Ferroglobus, Methanobacteria, ammonia oxidizing archaea, sulfate reducing archaea.
Ferroglobus placidus
Figure 8: Ferroglobus placidus is a lithotrophic archaea. It is an extremophile and can grow at temperatures up to 113°C. Image Credit: GI Genome Portal.
      • Organotrophic Archaea: Some species of archaea are known to utilize organic compounds to take care of their energy needs like pyruvate, starch, maltose, etc.Examples: Methanosarcinales, Pyrococcus, Sulfolobus
Pyrococcus furiosus
Figure 9: Pyrococcus furiosus is an extreme thermophilic organotrophic archaeon that can grow at temperatures up to 100°C. The main metabolic pathway in this organism is anaerobic oxidation/ respiration as it’s an anaerobic archaeon. This metabolism makes it a suitable candidate for microbial fuel cell (MFC) development. MFCs are biological cells that can generate power at temperatures close to boiling point. As can be seen in the picture, the main source of energy is the organic compound “malt-short form of maltose”. Image Credit: Narendran Sekar.
  • Extremophiles

Most of the members of the archaeal phylum are extremophilic in nature growing in vents, springs, salt lakes and ditches, volcanoes, marshlands, and deep surfaces of seas and oceans. In fact, archaea were first discovered in such habitats.

  • Reproduction

Asexual reproduction is the only way for archaea. They reproduce asexually via binary fission, budding, or fragmentation. No archaeal member has been reported to undergo endospore formation.

  • Roles in Earth’s biomes functioning

Archaea play a multitude of ecological roles ranging from that in the nitrogen cycle to the maintenance of microbial symbiotic communities. Most of the known archaea either build mutualistic or commensalistic relationships. Their pathogenic or parasitic representatives haven’t been observed yet.

Example of mutualistic archaea: Methanogenic archaea inhabiting the GIT of humans and other organisms like ruminating animals like cows, buffalo, etc. Archaea in the gut help in the facilitation of digestion.

archaea inhabiting the human gastrointestinal tract
Figure 10: A number of examples of the archaea inhabiting the human gastrointestinal tracts (archaea in humans). Image Credit: Nadia Gaci.
methanogenic genera found in the biogas plant
Figure 11: The different methanogenic genera found in the biogas plant in a study by I. Bergmann et al. in 2010. The figure also shows their relative abundances as qPCR %. Methanomicrobiales showed the highest abundance here (84%). Image Credit: I.Bergmann.
  • Archaea in biogas production

Because of their methanogenic and extremophilic activity, archaea are extensively used in the commercial production of biogas and also in sewage treatment plants. Biotechnological advancements enable the exploitation of archaeal enzymes from these extremophilic species. Since processes including high temperatures, pressures, and usage of organic solvents are mainstream in biogas production and sewage treatment; these hydrogenotrophic species widen the scope.

Example: Methanoculleus sp., Methanobrevibacter sp., etc.

Structure, Composition Development, and Operation

Archaea, although different from bacteria, share many common features with bacteria too. Both of them being prokaryotic life forms lack nuclei and membrane-bound cell organelles.

  • Size range: 0.1-15 micrometers
  • Shape range: Spherical, rod-like, spiral, plates, irregularly shaped, lobed, needle-like filamentous, rectangular rods, flat square shape.
archaeal cell structure
Figure 12: Structure of archaeal cells. Image Credit: ucmp.berkeley.edu.
  • Cell wall and archaella (archaeal flagella)

The cell wall is present in most archaea except Thermoplasma and Ferroplasma. The surface-layer proteins encoded constitute the cell wall or S-layer. The role of the S-layer or cell wall in archaea is for physical and chemical protection. While bacterial cell walls are made up of peptidoglycan, archaea cell walls lack it. They rather possess pseudo-peptidoglycan like in Methanobacteriales.

Pseudopeptidoglycan is similar to bacterial peptidoglycan (morphologically, functionally) but is chemically distinct (no D-amino acids & N-acetylmuramic acid). Rather, they have N-Acetyltalosaminuronic acid.

The name for archaeal flagella is archaella. It functions similar to bacterial flagella.

pseudopeptidoglycans in the archaeal cell walls
Figure 13: Notice the presence of pseudopeptidoglycans in the archaeal cell walls. Image Credit: Erin E. Gill.
  • Membranes

While bacterial and eukarya cell membranes have ester-linked lipids, archaea cell membranes have ether-linked lipids. Bacterial and eukarya cells have D-glycerols in their membranes but archaeal membranes have L-glycerols.

The bacterial and eukarya backbone is built on “sn-glycerol-3-phosphate” whereas the archaeal phospholipid backbone is built on “sn-glycerol-1-phosphate”.

The enzymes used by archaea for their membrane synthesis are different from those used by bacteria and eukarya.

Archaeal membrane lipid tails possess multiple side branches whereas the bacterial and eukarya membranes lipid tails are devoid of side branches or rings.

Isoprenoids find their distinct usage in the archaeal membrane phospholipids. Other microbes/organisms have isoprenoids in their bodies but not in membrane phospholipids.

Archaea also have archaeols, a type of core membrane lipids. These are often used as “archaeal biomarkers” associated with methanogens.

archaeol in archaeal cell membrane
Figure 14: Notice the presence of archaeol, ether-links and branched isoprene chains in the archaeal membrane. Contrastingly, bacterial membranes lack archaeol and possess unbranched fatty acids with ester links. Archaea cell structure is distinct in a number of ways. Image Credit: K. Gottlieb.

 

archaeol synthesis diagram
Figure 15: Archaeols are unique core membrane lipids synthesized by the archaea group. The process of archaeol synthesis is carried out via an ‘alternate MVA pathway’. For the synthesis of the isoprenoid chains constituting archaeol, a total of 3 unique steps have been identified. Image Credit: Dhoenngg.

FAQs on  Archaea


  • Are archaea prokaryotes? Answer: Yes
  • Do archaea have cell walls? Answer: Yes (of pseudo-peptidoglycan and not peptidoglycan)
  • Are archaea unicellular or multicellular? Answer: Unicellular
  • Which are the most culturable species of archaea? Answer: Crenarchaeota and Euryarchaeota. Crenarchaeota and korarchaeota were included in a superphylum in 2011 and are closely related to the evolution of eukarya.
  • Is Thermus aquaticus archaea? Answer: No, it’s a bacterium.
  • What are asgard archaea? Answer: They are a supergroup that have been speculated to be “a connecting link between prokaryotic and eukaryotic life”)
  • Do archaea have circular or linear chromosomes? Answer: One circular chromosome.

Metabolism

Archaeal metabolism displays a range of biochemical reactions. Some of these are common to all archaeal species; others are specific to certain taxa.

Chemical structure of methanofuran
Figure 16: Chemical structure of methanofuran, a unique coenzyme possessed by methanogenic archaea. Image Credit: PubChem.
  1. As discussed in previous sections, there are 3 major nutritional groups namely phototrophic, lithotrophic and organotrophic. Lithotrophic and organotrophic are sometimes placed under a broader category called chemotrophic. They, as chemotrophs, play vivid roles like:
    • Nitrifiers
    • Methanogens
    • Anaerobic methane oxidizers (main inhabitants of anaerobic environments)
  2. Phototrophic archaea carry out the chemiosmosis process without fixing atmospheric carbon.
  3. Archaea also carry out aerobic and anaerobic respiration. The process of glycolysis occurring in the archaea is a modified form of the one happening in eukarya and bacteria.
  4. Archaea carry out citric cycles; complete or partial.
  5. Archaea residing in anaerobic conditions are often methanogenic (produce methane). Studies have found that this metabolic reaction would have evolved very early on, probably signaling the methanogenic nature of the 1st free-living organisms on this planet.
  6. Archaea are in possession of a unique set of coenzymes for methanogenesis activity. Example: Methanofuran and coenzyme M.

Genetics

Let’s briefly discuss archaeal genomes and genetic material.

  • Number and nature of chromosome: 1 and circular
  • The largest known genome for archaea: Methanosarcina acetivorans (5,751,492 bp)
  • The smallest known genome for archaea: Nanoarchaeum equitans (490,885 bp)
  • The presence of plasmids is also noted in archaea just like in bacteria. And their inter-cell transfer is also similar via conjugation-like processes. Both archaea and bacterial conjugation aid plasmid transfer.
  • Genetically quite different from bacteria and eukarya.
  • Transcription: Close resemblance to eukaryotic transcription (archaeal RNAP is also similar to that of eukaryotes RNAP II).
  • Some of the archaeal transcription factors (TFs) have a resemblance with those of bacteria.
  • Post-transcriptional modification (PTMs): Closely resemble those of eukaryotes.

Gene transfer and genetic exchange

Gene transfer, exchange, and horizontal gene transfer/ lateral gene transfer happen via inter-cell cytoplasmic bridges.

cytoplasmic bridge between Haloferax volcanii cells
Figure 17: The illustration shows the “cytoplasmic bridge” formation between 2 Haloferax volcanii cells. These are extreme halophilic archaeal species. Image Credit: Shamphavi Sivabalasarma.

Cellular aggregations are also known for genetic exchange and recombinations in archaeal species. These aggregations are induced by physical agents (UV, pH, temperature) or chemical agents (mitomycin C, bleomycin). These homologous recombinations serve as the repair mechanisms for the DNA damage caused due to different agents. Some scientists have also speculated this as an alternative type of sexual reproduction in primitive archaeal species.

Cellular aggregation
Figure 18: “Cellular aggregation” has been studied in hyperthermophilic archaeal species Sulfolobus solfataricus.
Pic A: Cellular aggregation after different UV doses.
Pic B: Light micrographs of Sulfolobus solfataricus cell aggregates at different UV doses.
Pic C: A cell aggregate at 75 J/m2 UV dose.
Image Credit: Sabrina Fröls.

Archaeal viruses

A number of viruses target archaea; some are archaea-specific while some are cosmopolitan. In contrast to bacterial viruses which either conduct lytic or lysogenic pathways or display a mixed version of both, archaeal viruses usually maintain stable, lysogenic-like pathways.

Archaea Reproduction

Archaea reproduction strategies encompass:

  • Binary fission
  • Multiple fission
  • Fragmentation
  • Budding

There is no endospores formation of archaea as in bacteria and some eukarya.

Featuring … the Archeon “Haloquadratum walsbyi”


Haloquadratum walsbyi is a unique species of archaea with “typically flat, square-shaped cells”. This taxon was discovered in a brine pool by British microbiologist, Dr. A.E. Walsby in Egypt in 1980. Hence the species was named after him. This is a halophilic archaeon that survives highly saline conditions rich in sodium chloride (NaCl) and magnesium chloride (MgCl2). This species is also phototrophic in nature.

Haloquadratum walsbyi is a unique archaeon because the members possess unique square-shaped cells. Image Credit: Alchetron.

 

Haloquadratum walsbyi infographic
An infographic related to Haloquadratum walsbyi. Image Credit: UST Microbiology Society.


Answer the quiz below to check what you have learned so far about archaea.

Quiz

Choose the best answer. 

1. With distinct nucleus
2. Prokaryotic organisms
3. Reproduce by binary fission
4. Carry out methanogenesis
5. Cell wall is made up of pseudopeptidoglycan

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References

  • Howland JL (2000). The Surprising Archaea: Discovering Another Domain of Life. Oxford: Oxford University Press. pp. 25–30. ISBN 978-0-19-511183-5.
  • Woese CR, Fox GE (November 1977). “Phylogenetic structure of the prokaryotic domain: the primary kingdoms”. Proceedings of the National Academy of Sciences of the United States of America. 74 (11): 5088–90. Bibcode:1977PNAS…74.5088W. doi:10.1073/pnas.74.11.5088. PMC 432104. PMID 270744
  • Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (March 2006). “Toward automatic reconstruction of a highly resolved tree of life”. Science. 311 (5765): 1283–87.
  • Bibcode:2006Sci…311.1283C. CiteSeerX 10.1.1.381.9514. doi:10.1126/science.1123061. PMID 16513982. S2CID 1615592
  • Tortora, G.J., Funke, B.R., Case, C.L. and Johnson, T.R., 2004. Microbiology: an introduction (Vol. 9). San Francisco, CA: Benjamin Cummings.
  • Gaci, N., Borrel, G., Tottey, W., O’Toole, P. W., & Brugère, J. F. (2014). Archaea and the human gut: new beginning of an old story. World journal of gastroenterology, 20(43), 16062–16078. https://doi.org/10.3748/wjg.v20.i43.16062
  • I.BergmannI. Bergmann, E.NettmannE. Nettmann, K.MundtK. Mundt, and M.KlockeM. Klocke. Determination of methanogenic Archaea abundance in a mesophilic biogas plant based on 16S rRNA gene sequence analysis. Canadian Journal of Microbiology. 56(5): 440-444. https://doi.org/10.1139/W10-021
  • Wagner, A., Whitaker, R., Krause, D. et al. Mechanisms of gene flow in archaea. Nat Rev Microbiol 15, 492–501 (2017). https://doi.org/10.1038/nrmicro.2017.41
  • Fröls, S., Ajon, M., Wagner, M., Teichmann, D., Zolghadr, B., Folea, M., Boekema, E. J., Driessen, A. J., Schleper, C., & Albers, S. V. (2008). UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation. Molecular microbiology, 70(4), 938–952. https://doi.org/10.1111/j.1365-2958.2008.06459.x
  • Pace, N. R. (May 2006). “Time for a change”. Nature. 441 (7091): 289. doi:10.1038/441289a

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