ARCHAEBACTERIA

#414A4C BY
BIBASWAN
PRITAM
SRISTY
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).

ETYMOLOGY

The term archaea (ar-KAY-ə) (singular: archeon) came from Greek arkhaion, arkhaios,
meaning “ancient”.
DIFFICULTIES WITH THE STUDY OF THE ARCHEA 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.
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.

Source: Ciccarelli et al. (2006)

ARCHAE VS 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.

Characteristics of prokaryotic Archaea Bacteria

cells
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)

Characteristics of prokaryotic Archaea Bacteria
cells
Translation initiation codon (for Methionine Formylmethionine
protein synthesis)

Major reproductive strategy •Binary fission •Binary fission

•Budding •Budding
•Fragmentation •Fragmentation
•Spore formation

Rigid or fragile towards harsh Very rigid Relatively fragile

environmental conditions

Major metabolic activity •Diazotrophy •Photosynthesis

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

Genetic similarity to Eukarya More Less

Sensitivity to diphtheria toxin Sensitive Resistant

Example Halobacterium spp. Escherichia coli

CHARACTERISTICS OF ARCHAEBACTERIA

1. They evolved separately from eubacteria and eukaryotes.

2. They are similar to eubacteria in being prokaryotes and lacking a distinct nucleus.

3. They differ in terms of ribosomal structure, the presence of introns (in some archaeal species),
and membrane structure or composition.

4. Archaea possess genes and several metabolic pathways that are more closely related to those of
eukaryotes, notably, the enzymes involved in transcription and translation.

5. 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.
STRUCTURE,DEVELOPMENT AND COMPOSITION OF ARCHAEABACTERIA

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.

• 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.
 CELL AND THE CELL WALL OF ARCHAEBACTERIA

GENERAL STRUCTURE OF ARCHAEAL CELLS ARCHAEAL CELL WALL

STRUCTURE OF MEMBRANES IN ARCHAEABACTERIA

• 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”.

• 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.
IN-DEPTH DIVE INTO THE ARCHAEAL MEMBRANE SYSTEM
WHERE DO ARCHAEBACTERIA LIVE?

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.

Archaebacteria are mostly found in these major habitats namely:

Deeps seas and oceans (archaea form nearly 20% of microbial diversity of the oceans),geysers, hot
water springs, hydrothermal springs, hydrothermal and oil wells, cold habitats like ice sheaths of
tundra, saline lakes, highly acidic places, highly alkaline waters, swamps, wetlands, and waters,
swamps tracts of humans and animals, highly degraded soils, anoxic muds etc.
CLASSIFICATION OF ARCHEABACTERIA

Based on the type of habitat they are found in:

• Halophiles
• Thermophiles
• Alkaliphiles
• Acidophiles

Based on energy sources used by the bacteria:

• Phototrophic Archaea
• Lithotrophic Archaea
• Organotrophic Archaea
BASED ON HABITATS

HALOPHILES

• Halophiles are bacteria that can survive in environments with

high salt concentrations. The name "halophile" comes from
the Greek word for "salt-loving".
• Halophiles have adapted to exclude salts from their cytoplasm
to avoid protein aggregation.
• Halophiles can tolerate up to 5 M NaCl.
• Halophiles can grow under aerobic or anaerobic conditions.
• Halophiles can adapt to high temperatures and solar
radiation.

• Example: Halobacterium spp.

THERMOPHILES

• Thermophiles can survive at high temperatures, while other

bacteria or archaea would be damaged or killed. They are
industrially valuable because they secrete bioenzymes and
biofuels.
• Thermophiles have heat shock proteins (Hsps) that help them
manage instability of the plasma membrane, inactivation of
enzymes, and instability of DNA.
• Thermophiles have more ion pairs than mesophilic proteins,
which may help preserve their protein structure.

• Example:Methanopyrus kandleri
ALKALIPHILES

• These are microorganisms that can survive in alkaline

environments with a pH of 8.5–11. They grow best at a pH of
10. Alkaliphiles are anaerobic and grow on organic substrates
like yeast extract, casein, and peptone. They can grow
between 56–93°C, but their optimum temperature is 85°C.

Alkaliphiles adapt to high pH values by:

• Maintaining cytoplasmic pH homeostasis

• Uptaking H+ using electrogenic, secondary cation/proton
antiporters

• Example:Thermococcus alcaliphilus
ACIDOPHILES

• Acidophiles are organisms that can survive in environments

with pH values as low as 0.
• Acidophiles use proton pumps to balance a neutral pH.
• Acidophiles have highly impermeable cell membranes. They
also reverse their membrane potential, making the inside of
the cell positive compared to the outside.
• Genes for organic acid degradation: Acidophiles have genes
for organic acid degradation.

• Example:Picrophilus torridus
BASED ON ENERGY SOURCES USED

PHOTOTROPIC 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.

• It is to be noted that these archaebacteria are phototropic

and not photosynthetic.

• Example: Haloarchaea or Halobacterium.

• The Lonar Lake turned pinkish due to the the

photopigment of these bacteria called bacteriorhodopsin
which is opaque to long wavelengths (red) and imparts pink
color to the lake.
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 is a lithotrophic archaea. It is

an extremophile and can grow at temperatures up to
113°C. It was the first hyperthermophile discovered
to grow anaerobically by oxidizing aromatic
compounds such as benzoate coupled to the
reduction of ferric iron (Fe3+) to ferrous iron
(Fe2+).
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 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.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.
METABOLISM OF ARCHAEBACTERIA

• 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)
• Phototrophic archaea carry out the chemiosmosis process without fixing atmospheric
carbon.
• Archaea also carry out aerobic and anaerobic respiration.
• Archaea carry out citric cycles; complete or partial.
• Archaea residing in anaerobic conditions are often methanogenic. 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.
ARCHAEAL GENETICS

• Number of chromosome: 1

• Nature of chromosome: Circular

• 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.

• 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 GENE EXCHANGE

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

The illustration shows the

“cytoplasmic bridge” formation
between 2 Haloferax volcanii
cells(extreme halophilic archaeal
species)
GENE TRANSFER AND GENE
EXCHANGE

Cellular aggregations are also known for

genetic exchange and recombination in
archaeal species. These aggregations are
induced by physical agents (UV, pH,
temperature) or chemical agents (mitomycin
C, bleomycin). These homologous
recombination 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 “Cellular aggregation” has been studied in
sexual reproduction in primitive archaeal hyperthermophilic archaeal species Sulfolobus
species. 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.
REPRODUCTION

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

ROLES PLAYED BY ARCHAEBACTERIA

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. which help in the facilitation
of digestion.