Archaea

You have probably seen images of the colorful hot springs in Yellowstone National Park. The orange, yellow, pink, or red coloration is given by the microorganisms that live in these extremely hot and acidic environments. Most of these microorganisms are archaea, single-cell organisms that resemble bacteria but are actually more related to you! We describe the archaea traits that allow them to live in these harsh environments and make them unique, the similarities with bacteria and eukaryotes, and why they are important to understand our own origins.

Archaea Archaea

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Contents
Table of contents

    Prokaryotes: Archaea and Bacteria

    Despite the great diversity of life forms on earth and the enormous number of species, we currently classify all of them into two major groups based on the type of cell that forms an organism: the prokaryotes and the eukaryotes.

    • Prokaryotes consist mostly of single-cell organisms formed by relatively simple prokaryotic cells,
    • while eukaryotes include single-cell, colonial, and multicellular organisms formed by more complex eukaryotic cells.

    Prokaryotes, in turn, are divided into two domains, Bacteria and Archaea.

    Thus, archaea have the four features found in all cells: plasma membrane, cytoplasm, ribosomes, and DNA. They also have the general features of prokaryotic cells: DNA organized in a single circular strain of DNA, not enclosed but only concentrated in a region called a nucleoid, absence of organelles surrounded by a membrane, and they can have a cell wall externally surrounding the cell membrane. They can also have appendices that serve in locomotion.

    Archaea definition

    Until the 1970s archaea were thought to be bacteria, due to the similarities in general structure and appearance and because they were much less studied than bacteria. Then in 1977, Woese and Fox used the 16s ribosomal RNA (rRNA) gene, a molecular marker that helps to determine evolutionary relationships among organisms, and found that several of these “bacterial microorganisms” were actually more closely related to eukaryotes than to bacteria. Later studies revealed that archaea do share some traits with bacteria and others with eukaryotes, while also having unique characteristics.

    This led to giving these microorganisms a domain of their own, the Archaea.

    Archaea Micrograph of archaea StudySmarter

    Fig. 1: Scanning electron microscopic image of Metanohalophilus mahii strain SLP.

    Archaea are prokaryotic single-cell organisms (they do not have a nucleus, or membrane-bound organelles, and have a single circular chromosome) more closely related to eukaryotes than to bacteria.

    Before the development of genomic sequencing techniques, most microscopic life could only be studied through laboratory cultures, but it is really hard to get the right conditions to culture most organisms. Now, any environmental sample, like a soil or water sample, can be processed to sequence different DNA regions of all the genetic material found on it (called metagenomics).

    For the Archaea domain, this meant the expansion of the known diversity from 2 phyla at the moment of archaea discovery to about 30 phyla (and approximately 20,000 species). New archaea groups and species are being constantly described, thus Archaea phylogeny, metabolism, and ecology are continuously being updated1.

    Archaea characteristics

    Prior to being classified as Archaea, one of the characteristics that initially led to putting these organisms as a different type of bacteria was the observation that many archaea are extremophiles.

    (from the Greek philos = lovers, the lovers of the extreme)

    They live in environments with extreme conditions. While some bacteria can also live in extreme environments, archaea are most commonly found under these conditions and are the only ones found in the most extreme habitats.

    Archaea structure and composition

    Cell membrane: archaeal membranes have a similar structure to bacterial and eukaryote ones but have important differences in composition:

    • Archaea membranes can be composed of a phospholipid bilayer (two layers of lipid molecules, like bacteria and eukaryotes) or have monolayers, only one layer of lipids (the tails of opposing phospholipids are fused). The monolayer might be a key to survival at high temperatures and/or extremely low acidity2.

    • They have isoprene chains as the side chains in membrane phospholipids instead of fatty acids.

    • The isoprene chains are linked to the glycerol molecule by an ether linkage (it has only one oxygen atom, bound to the glycerol) instead of an ester linkage (it has two oxygen atoms attached, one bound to the glycerol, one sticking out from the molecule).

    • Some of the isoprene chains have side branches, that enable the main chain to curl upon itself and form a ring, or to join with another main chain. It is thought that these rings give more stability to membranes, especially in extreme environments. Fatty acids do not form side branches.

    • Archaea can have one or more appendages similar to flagella for movement. However, they are structurally different from bacterial and eukaryotic flagella.

    Archaea Cell membrane structure and composition StudySmarter

    Fig. 2: Archaeal membrane structure and composition. Top: archaeal membrane: 1-isoprene sidechain, 2-ether linkage, 3-L-glycerol, 4-phosphate molecule. Medium: bacterial and eukaryotic membrane: 5-fatty acid, 6-ester linkage, 7-D-glycerol, 8-phosphate molecule. Bottom: 9-lipid bilayer in bacteria, eukarya and most archaea, 10-lipid monolayer in some archaea.

    Cell wall: there are four types of archaeal cell walls, but unlike bacteria, none have peptidoglycan. They can be composed of:

    • pseudopeptidoglycan (similar to peptidoglycan but with different sugars in the polysaccharide chains),
    • polysaccharides,
    • glycoproteins,
    • or only protein.

    Archaea nutritional modes

    Archaea can use a wide variety of energy and carbon sources, as prokaryotes in general do. They can be photoheterotrophs (use light as an energy source and break down organic molecules to obtain carbon), chemoautotrophs, or chemoheterotrophs (both use chemical sources of energy, but the autotrophs use inorganic sources for carbon, like CO2, and heterotrophs break down organic molecules).

    You can learn more about nutritional modes and trophic levels in our Food Chains and Food Webs article.

    Although a few archaea (Halobacteria) can use light as an energy source, it seems to be an alternative and not an obligate energy source. These archaea are phototrophs but are not photosynthetic, as they do not fix carbon to synthesize biomolecules as part of the process (they are photoheterotrophs).

    Moreover, a metabolic pathway unique to archaea is methanogenesis, methanogens are organisms that release methane as a by-product of energy production. They are obligate anaerobes and survive through the conversion of several substrates (for example from H2 + CO2, methanol, acetate) to methane as the final product.

    Archaea distribution

    Although many archaea are lovers of extreme conditions, it was later found that the group is actually widely distributed and is also found in more normal environments (like soil, lake sediments, sewage, and the open ocean) as well as associated with a host. While some archaea are just really good for tolerating these conditions, the more extreme ones have a specific cell composition that can only function properly in these extreme conditions. Archaea can live in extreme environments such as habitats with high salinity (hyperhalophiles or extreme halophiles), temperature (hyperthermophiles or extreme thermophiles), acidity (acidophiles), or a mix of these conditions.

    Archaea Hotspring coloration by archaea and bacteria StudySmarter

    Fig. 3: Aerial view of Grand Prismatic Spring, Yellowstone National Park. The brilliant orange color in the border is given by microorganisms including bacteria and archaea.

    Methanogens are anaerobes found in extreme environments like under kilometers of ice, or in more common habitats like swamps and marshes, and even animal guts.

    They are part of the microbial community (which includes bacteria, fungi, and protists) that live in animal guts, especially in herbivores (cattle, termites, and others), but have also been found in humans.

    During food decomposition by bacteria in animal intestines, a normal waste product is H2. Methanogens archaea are an important part of H2 metabolism (producing methane as the final product) avoiding its accumulation in high quantities.

    Archaea examples

    Let's see some examples of archaeal species and their main traits2,3,4:

    Table 1: Examples of archaeal organisms and description of some of their traits.

    Example archaea

    Description

    Halobacterium marismortui

    Hyperhalophile, obligate aerobe, chemoheterotrophic (Halobacteria can be phototrophic). Lives in environments with a salt concentration of at least 12% (concentration 3.4 to 3.9 M). Originally isolated from the Dead Sea.

    Sulfolobus solfataricus

    Thermoacidophile, chemoautotroph and chemoheterotroph. Lives in sulfur-rich volcanic springs (75 - 80°C, pH 2 - 4), using sulfur as a source of energy.

    Pyrococcus furiosus

    Hyperthermophilic, anaerobe, chemoheterotroph that uses organic compounds as energy source. Lives in marine sediments heated by geothermal energy (optimal growth at 100°C and pH 7)

    Methanobrevibacter smithii, Methanosphaera stadtmanae, Methanomethylophilaceae (1)

    Methanogens found in herbivores and human guts. Chemoautotrophs

    Nanoarchaeum equitans and its host Ignicoccus hospitalis

    N. equitans is a very small archaean with a reduced genome, it lives attached to the surface of I. hospitalis (autotroph) in hyperthermophilic conditions.

    Source: Schäfer, 1999; Bräsen et al. 2014, and Kim, 2020.

    Importance of Archaea

    Archaea, like bacteria, are a vital part of the carbon and nitrogen cycles. As chemoautotrophs, they convert these inorganic compounds to ways readily available for other organisms that would not be able to reuse them otherwise. Methane is also a key compound in the biogeochemical cycle of carbon and, as mentioned earlier, the only organisms capable of producing methane are methanogenic archaea.

    Archaea are also being subject of numerous evolutionary studies, as it is an important key in the origin of eukaryotes. The most accepted hypothesis (the endosymbiosis theory) indicates that eukaryotes originated from the fusion of an ancestral Archaean organism (or closely related to archaea) and an ancestral bacterium that eventually evolved into the organelle mitochondrion.

    You have learned that all organisms are classified into three domains: Bacteria, Archaea, and Eukarya. When the archaea domain was proposed it was placed as a sister lineage to Eukarya. Now that more Archaean groups are being described, the most recent phylogenomic studies place the Eukarya not as a separate sister branch to Archaea but within the Archaea lineage. The Eukarya lineage seems to be more closely related to a group called the Asgard archaea. A new tree of life of only two domains is being proposed5, and this would mean eukaryotes are actually part of the Archaea domain!

    Archaea vs Bacteria vs Eukaryotes

    We summarize the main similarities and differences between Archaea and the two other domains of life in table 26,7. As mentioned, Archaea share many prokaryotic traits with Bacteria. However, note how the machinery for genetic information processing (replication, transcription, and translation), represented here by tRNA and RNA polymerase types and ribosome composition, is more closely related to Eukarya.

    Table 2: Similarities and differences between the three domains of life.

    Characteristic

    Bacteria

    Archaea

    Eukarya

    Organism type

    Unicellular (can form filaments)

    unicellular

    Unicellular, colonial, multicellular

    Nucleus

    no

    no

    yes

    Membrane-bound organelles

    no

    no

    yes

    Cell wall with peptidoglycan

    yes

    no

    no

    Layers in cell membrane

    Bilayer

    Bilayer and monolayer in some species

    Bilayer

    Membrane lipids

    Fatty acids, unbranched, ester bonds

    Isoprene, some chains branched, ether bonds

    Fatty acids, unbranched, ester bonds

    RNA polymerase kinds

    single

    multiple

    multiple

    Protein synthesis initiator (tRNA)

    Formyl-methionine

    Methionine

    Methionine

    DNA associated with histone proteins

    no

    Some species

    yes

    Chromosomes

    Single, circular

    Single, circular

    Several, linear

    Response to streptomycin (related to ribosome composition)

    sensitive

    Not sensitive

    Not sensitive

    Methane production

    no

    yes

    no

    Photosynthesis

    some groups

    no

    Some groups (plants and algae)

    Source: Urry et al., 2021 and Mary Ann Clark, 2022.

    Archaea - Key takeaways

      • Archaea are single-cell organisms composed of prokaryotic cells but compose a different domain than Bacteria, moreover, they are more closely related to Eukarya.
      • The main distinctive characteristics of archaea are the phospholipids (isoprenoid chains with ether links) in their cell membranes and their cell wall composition.
      • Archaea are widely distributed (soil, lake sediments, sewage, the open ocean, animal guts) but many are extremophiles living in conditions with high salinity, temperature, and/or acidity.
      • A variety of nutritional modes are found among archaea, and although a few are phototrophic none perform photosynthesis.
      • A metabolic pathway unique to archaea is methanogenesis.

    References

    1. Guillaume Tahon, et al., Expanding Archaeal Diversity and Phylogeny: Past, Present, and Future, Annual Review of Microbiology, 2021.
    2. Günter Schäfer, et al., Bioenergetics of the Archaea, Microbiology and Molecular Biology Reviews, Sept 1999.
    3. Christopher Bräsen, et al., Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation. Microbiology and Molecular Biology Reviews, Mar 2014.
    4. Joon Yong Kim, et al., The human gut archaeome: identification of diverse haloarchaea in Korean subjects. Microbiome, 4 Aug. 2020.
    5. Tom A. Williams, et al. Phylogenomics provides robust support for a two-domains tree of life. Nat Ecol Evol, 9 Dec. 2020.
    6. Lisa Urry et al., Biology, 12th edition, 2021.
    7. Mary Ann Clark et al., Biology 2e, Openstax web version 2022
    8. Fig. 1: Scanning electron microscopic image of Metanohalophilus mahii strain SLP (https://commons.wikimedia.org/wiki/File:Methanohalophilus_mahii_SLP.jpg) by Spring, S.; Scheuner, C.; Lapidus, A.; Lucas, S.; Rio, T. G. D.; Tice, H.; Copeland, A.; Cheng, J.; Chen, F. (https://www.hindawi.com/journals/archaea/2010/690737/) is Licensed by CC BY 4.0 (https://creativecommons.org/licenses/by/4.0).
    9. Fig. 3: Grand prismatic spring (https://www.nps.gov/features/yell/slidefile/thermalfeatures/hotspringsterraces/midwaylower/Images/17708.jpg) by Jim Peaco, National Park Service, Public Domain.
    Frequently Asked Questions about Archaea

    Are archaea stationary or mobile? 

    Archaea are mobile, like bacteria they have flagella for cell motility and although they resemble in appearance, the archaeal flagellum seem to have a different origin. 

    What are archaea? 

    Archaea are prokaryotic single-cell organisms (they do not have a nucleus, membrane-bound organelles, and have a single circular chromosome) more closely related to eukaryotes than to bacteria. 

    Do archaea have a nucleus? 

    No, archaea do not have a nucleus are they are prokaryotic. 

    Are archaea autotroph or heterotroph? 

    Some archaea are autotroph, and some are heterotroph. 

    Are archaea prokaryotes? 

    Yes, archaea are prokaryotes, but form a different domain than bacteria and are phylogenetically more closely related to eukaryotes.

    Test your knowledge with multiple choice flashcards

    Archaea are more closely related to bacteria than to eukaryotes. 

    Archaea and bacteria have the following similarities: 

    H2S, NH3, or Fe2+ are examples of ___ sources while CO2 and HCO3 are ___ sources. 

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