Archaea

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. with no nuclei or cell organelles. They have
a ubiquitous distribution and are widely known extremophiles.

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.

Archaea Etymology

Archaea is a modern Latin word derived from the Greek word “arkhaios” meaning ‘primitive’.
The singular of archaea is 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 Groups under the system

classification

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 4-kingdom system Monera, Plantae, Protista & Animalia
Copeland

1969 Robert Harding 5-kingdom system Monera, Plantae, Fungi, Protista &
Whittaker Animalia

1990 Carl Richard 3-domain system Domain bacteria, domain archaea, third
Woese domain eukarya

1998 Thomas 2 empire, 6 Bacteria, Protozoa, Chromista, Plantae,

Cavalier-Smith kingdom system Fungi, & Animalia

2015 Thomas 2 empire, 6 Bacteria, Archaea kingdom, Protozoa,

Cavalier-Smith kingdom system Chromista, Plantae, Fungi, & Animalia
Data Source: Dr. Harpreet Narang of Biology Online

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.

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.
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 Archaea Bacteria

prokaryotic cells

Peptidoglycan in cell wall Absent Present

Pseudopeptidoglycan in Present Absent

cell wall
 Types of RNA 3 1

Transcription similar to Yes No (Unique)

Eukarya

Number of RNA Many Only one

polymerases

Translation similar to Yes No (Unique)

Eukarya

Translation initiation Methionine Formylmethionine

codon (for protein
synthesis)

Major reproductive  Binary fission  Binary fission

strategy  Budding  Budding
 Fragmentation  Fragmentation
 Spore
formation

Rigid or fragile towards Very rigid Relatively fragile

harsh environmental
conditions

Major metabolic activity  Diazotrophy  Photosynthesis

 Chemotrophy
 Methanogenesis (a form of  Respiration
anaerobic respiration that  Autotrophy
is unique to this group)  Fermentation
 Diazotrophy

Genetic similarity to More Less

Eukarya

Sensitivity to diphtheria Sensitive Resistant

toxin

Example Halobacterium spp. Escherichia coli

/Methanobacteria
Data Source: Dr. Harpreet Narang of Biology Online
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)

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.

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.
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

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:
o 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.
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.

o
 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. / Methane-Butane

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.
  Organotr
ophic

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

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.
Figure 10: A number of examples of the archaea inhabiting the human gastrointestinal tracts
(archaea in humans). Image Credit: Nadia Gaci.

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/ Bacteria – 1-10 micrometers/ 10-300 nanometers
 Shape range: Spherical, rod-like, spiral, plates, irregularly shaped, lobed, needle-like
filamentous, rectangular rods, flat square shape.

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.

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.
  Are archaea prokaryotes? Answer:
 Do archaea have cell walls?What is it? Answer:
 Are archaea unicellular or multicellular? Answer:
 Which are the most culturable species of archaea? Answer:
 Is Thermus aquaticus archaea? Answer:

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:

o Nitrifiers
o Methanogens
o Anaerobic methane oxidizers (main inhabitants of anaerobic environments)

Phototrophic archaea carry out the chemiosmosis process without fixing atmospheric
carbon.

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.

Archaea carry out citric cycles; complete or partial.

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.

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.
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 (MgCl 2). This
species is also phototrophic in nature.

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

VIRUS

DNA virus- 14
RNA virus- 7
Draw its structure-
Size- nm