This document provides information about the archaea domain. It begins with an introduction to the six kingdoms of life and explains how archaea were recognized as a distinct domain separate from bacteria and eukaryotes based on rRNA studies. It then discusses the characteristics of archaea including their cell structure, unusual lipids, ability to thrive in extreme environments, and classification into five phyla. Examples are provided of notable archaea genera from each phylum like Sulfolobus, Halobacterium, Methanococcus, and Methanopyrus.

1. SU BMIT T E D T O - SU BMIT T E D BY -
MRS.JAY A MAT HU R AD IT I BAGD I
ASSIST AN T PRO F E SSO R AT MSBT 1S T SE M.
L AC HO O ME MO RIAL C O L L E GE BIO T E C HN O L O GY
O F SC IE N C E AN D T E C HN O L O GY .
LACHOO MEMORIAL COLLEGE OF
SCIENCE AND TECHNOLOGY

2. THE ARCHAEBACTERIA

3. CONTENTS-
 Introduction
 The domain archaea
 Evolutionary relationship between three domains
 Some basic facts
 Kingdom archaebacteria
 Characteristics of archaebacteria
 Morphological features of Archaebacteria
 Archaeal Cell wall
 Archaeal plasma membrane
 Classification
I. Crenarchaeota
II. Euryarchaeota
III. Korarchaeota
IV. Thaumarchaeota
 Importance of archaebacteria

4. INTRODUCTION-
 Biologists have organised living things into large groups called KINGDOMS.
 There are six of them-
i. Archaebacteria
ii. Eubacteria
iii. Protista
iv. Fungi
v. Plantae
vi. Animalia

5. THE DOMAIN ARCHAEA-
 In 1996, scientists decided to split Monera
into two groups of bacteria: Archaebacteria
and Eubacteria.
 Because these two groups of bacteria were
different in many ways scientists created a
new level of classification called a
DOMAIN.
 Now we have 3 domains
1. Bacteria
2. Archaea
3. Eukarya

7. Evolutionary relationship between three domains-
 There are many similarities and differences between the three domains. Bacteria
and Archaea differ in how they gain energy. Bacteria gain energy either by being
phototrophs, lithotrophs or organotrophs.
 One similarity between domain Archaea and domain Bacteria is that they both
contain only prokaryotes while domain Eukarya only contains eukaryotes.
Domain Archaea is the only domain that is sensitive to antibiotics.
 Another similarity between domain Bacteria and domain Eukarya is that
Methionine is the first amino acid seen during protein synthesis while in domain
Archaea, the first amino acid is Formylmethionine.
 The last major similarity between domain Archaea and domain Bacteria is that
they do not contain any organelles while domain Eukarya does. A difference
between all three domains is what their cell walls contain.
 A cell wall in domain Archaea has peptidoglycan. The organisms that have a cell
wall in domain Eukarya, will have a cell wall made up of polysaccharides. A cell
wall in domain Bacteria contains neither peptidoglycan or polysaccharides .

10. Some basic facts-
 Carl Woese was an American Microbiologist and
Biophysicist.
 Archaebacteria were not recognized as a distinct
form of life from bacteria until 1977,when Carl
Woese and George Fox determined this through
RNA studies.
 Dr. Carl Woese spearheaded a study of
evolutionary relationships among prokaryotes.
 Instead of physical characters, he relied on rRNA
sequences to determine how closely related these
microbes were.

11. KINGDOM ARCHAEBACTERIA-
 Archae means Ancient.
 The word Archae came from the Greek word Arkhaion which means ancient.
 Archae is also the Latin name for Prokaryotic cells.
 Any of a large group of primitive bacteria having unusual cell walls, membrane lipids,
ribosomes, and RNA sequences, and having the ability to produce methane and to live in
anaerobic, extremely hot, salty, or acidic conditions. They live in extreme environments
(like hot springs or salty lakes) and normal environments (like soil and ocean water).
 All are unicellular (each individual is only one cell).
 No peptidoglycan in their cell wall.
 Some have a flagella that aids in their locomotion.
 Most don't need oxygen to survive. They can produce ATP (energy) from sunlight.
 They can survive enormous temperature extremes.
 They can survive under rocks and in ocean floor vents deep below the ocean's surface.
 They can tolerate huge pressure differences.

12. The hot springs of Yellowstone National Park, USA, were among the first places
Archaea were discovered. At left is Octopus Spring, and at right is Obsidian Pool.
Each pool has slightly different mineral content, temperature, salinity, etc., so
different pools may contain different communities of archaeans and other microbes.
The biologists pictured above are immersing microscope slides in the boiling pool
onto which some archaeans might be captured for study.

13. Detailedphylogenetic treeofthe Archaeabased on comparisonsof ribosomalproteinsfrom sequenced
genomes.Each of the five archaealphyla is indicatedin a differentcolour.The Korarchaeotaand
Nanoarchaeotaare each representedby only a single known species.

14. Characteristics of Archaebacteria-

15. MORPHOLOGICAL FEATURES OF ARCHAEA-
❑ Size
 Archaea are slightly less than 1 micron long.
 A micron is 1/1,000 of a millimeter.
 In order to see their cellular features, scientists use powerful electron
microscopes.
❑ Shape
 Shapes can be spherical or ball shaped and are called coccus,
 Others are rod shaped, long and thin, and labelled bacillus.
 Variations of cells have been discovered in square and bacillus, coccus and
spirillum.

16. Basic archealshapes-
Basic Archaeal Shapes : At far left, Methanococcus janaschii, a coccus form with
numerous flagella attached to one side. At left centre, Methanosarcina barkeri, a
lobed coccus form lacking flagella. At right centre, Methanothermus fervidus, a short
bacillus form without flagella. At far right, Methanobacterium
thermoautotrophicum, an elongate bacillus form.

17. STRUCTURE-
❑ Locomotion
 Some archaea have flagella, hair-like structures that assist in movement.
 There can be one or many attached to the cell's outer membrane. Protein
networks can also be found on the cell membrane, which allow cells to attach
themselves in groups.
❑ Cell Features
 Within the cell membrane, the archaea cell contains cytoplasm and DNA, which
are in single-looped forms called plasmids.
 Most archaeal cells also have a semi-rigid cell wall that helps it to maintain its
shape and chemical balance.
 This protects the cytoplasm, which is the semi-liquid gel that fills the cell and
enables the various parts to function

18. ARCHAEAL CELL WALL-
 Archael cellwall lacks peptidoglycan and exhibit
considerable variety in terms of their chemical make
up.
 The most common type of archaeal cell wall is an S-
layer composed of either protein or glycoprotein
the layer may be as thick as 20 to 40 nm.
 Eg; methanococcus, halobacterium
 Other archaea have additional layers of material
outside the S-layer
 Methanospirillum has a protein sheath external to
the s-layer
 Methanosarcina has a layer of chondroitin- like
material, this material is called methanochondroitin

19. ▪In some archaea S-layer is the outer most layer and seperated from the
plasma membrane by pseudomurein.
▪pseudomurein is a peptidogycan-like molecule
differs from pepidoglycan in that it has N acetyltalosaminuronic acid
instead of N acetylmuramic acid ,and beta (1, 3) glycosidic linkage
instead of beta (1, 4) glycosidic linkage.
eg- Methanobacterium, Methanothermus and Methanopyrus
▪ The last type of archael cell wall does not include an s-layer .these
archaea have a wall with a single, homogenous layer resembling in
gram-positive bacteria.

21. Substitutes for N
Acetylmuramic
Acid (NAM)
of peptidoglycan
Pseudomurein

22. ARCHEAL PLASMA MEMBRANE-
 Archaeal membranes are composed primarily of lipids
that differ from bacterial and eukaryotic in two ways.
1. They contain hydrocarbons derived from isoprene
units(five carbon, branched).
2. Hydrocarbons attached to glycerol by ether linkage
rather than ester links.

23. Archaeal phospholipids differ from those found in Bacteria and Eukarya in two ways.
First, they have branched phytanyl side chains instead of linear ones. Second, an ether
bond instead of an ester bond connects the lipid to the glycerol.

24. CLASSIFICATION-
Five Phylum's-
 Crenarchaeota
 Euryarchaeota
 Korarchaeota
 Thuamarchaeota
 Nanoarchaeota

26. PHYLUM CRENARCHAEOTA-
 The name Crenarchaeota means "scalloped archaea." they are often irregular in shape.
 All crenarchaeota synthesize distinctive tetraether lipid, called crenarchaeol.
Originally containing thermophylic & hyperthermophilic sulphur metabolizing
archaea. Recently discovered Crenarchaeota are inhibited by sulphur & grow at lower
temperatures.
 These organisms stain Gram negative & are morphologically diverse having rod,
cocci, filamentous & oddly shaped cells.
 Divided into one class – Thermoprotrei & three orders :
Thermoproteales
Sulfolobales
Desulfurococcales
 Contain 69 genera – two of the better studied genera are Thermoproteus & Sulfolobus

27. Example s:
• One of the best characterized members of the Crenarcheota is Sulfolobus
solfataricus isolated from geothermally heated sulphuric springs in Italy &
grows at 80 °C & pH of 2-4Othwer examples are Pyrolobus fumarii
• Sulfolobus solfataricus and Sulfolobus acidocaldarius.
Sulfolobus solfataricus

28. ➢SULFOLOBUS-
 Gram –ve, aerobic, irregularly lobed spherical
archaeons
 Optimum temp.– 70 to 80 0C & optimum pH 2 –
3 hence also referred to as thermoacidophiles
 Cell wall – lipoprotein & CH, lacks peptidoglycan
 Grow lithotrophically on S granules in hot S
springs oxidizing S to Sulphuric acid
 Oxygen Is the normal electron acceptor, Fe+3 may
be used.
 Sugars & amino acids (glutamate) also serve as C
& energy sources

29. ➢THERMOPROTEUS-
 Gram –ve, strictly anaerobic, hyperthermophilic
long thin rod, can be bent or branched.
 Cell wall consists of glycoprotein
 Grows at temp. from 70 - 97 0C & pH 2.5 – 6.5
 Found in hot springs & other hot aquatic habitats
rich in sulfur.
 Can grow organotrophically & oxidize glucose,
amino acids, alcohols & organic acids with S.
 Grows chemolithtrophically using Hydrogen & S0
 CO & CO2 can serve as the sole C source An aquatic spring in Japan
with Thermoproteus growth

30. PHYLUM EURYARCHAEOTA-
 Very diverse with 7 classes
 Methanococcus,Methanobacteria,. Halobacteria,Thermoplasmata,
Thermococci,Archaeglobi& Methanopyri
 Consists of 9 orders & 15 families.
 On the basis of habitat they are divided into the followings. methanogens,
Extreme halophiles,Sulphate reducers & many extreme thermophileswith S
dependentmetabolism.
 Examples-Methanopyrus kandleri,Methanocaldococcusjannaschii.

31. ➢Extremely halophilic Archaea-
 Halo = salt, phil = loving
 The halophilic organisms require salty environment
for survival. Such salty habitats are called
hypersaline.
 Occurrence :-they are found in salts lakes & areas
where evaporation of séa water occurs such as the
Great Salt Lake in the U.S. and the Dead Sea.
 Can live in water with salt concentrations 12-23%
 The ocean's concentration is roughly 4%
 Example: Halobacterium which includes several
species, found in salt lakes & high saline ocean
environments. Halobacterium salinarum, H.
denitrificans &H. halobium

32. ➢Methanogenic Archaea-
 Methanogensare microorganismsthat producemethaneas a metabolic
byproductin anoxicconditions.
 This is the largestgroup of archaeawith 5 orders( Methanobacteriales,
methanococcales,methanomicrobiales,and methanopyrales).
 They are strictly anaerobicorganisms& are killed when exposedto O2.
They reduce CO using H, & releaseCH4, in swamps& marshesthat is
calledmarsh gas.
 Occurrence:-Manylive in mud at the becauseit lacksoxygenbottomof
lakesand swamps.
 They are also found in the gut of some herbivoreslike cows, humans
dead & decayingmatter.
 They are addedto biogasreactorsfor productionof CHA gasfor cooking
& sewagetreatmentplants.
 Examples:- Methanofollis aquaemaris,M. ethanolicus,M. formosanus,
M. liminatans.
Methanobrevib
acter smithii

33. ➢Thermoplasmatales-
 A phylogenetically distinct line of Archaea contains Thermophilic and
extremely acidophilic genera: Thermoplasma, Ferroplasma, and
Picrophilus.
 These prokaryotes are among the most acidophilic of all known
microorganisms, with Picrophilus being capable of growth even below
pH 0. Most are thermophilic as well.
 These genera also form their own taxonomic order within the
Euryarchaeota, the Thermoplasmatales. They resemble the
mycoplasmas.

34. ➢Thermococcus and Pyrococcus-
 Thermococcus is an obligately anaerobic chemoorganotroph that metabolizes
proteins and other complex organic mixtures (including some sugars) with
elemental sulfur (S0) as electron acceptor at temperatures from 55 to 95°C.
Pyrococcus is morphologically similar to Thermococcus
 Pyrococcus differs from Thermococcus primarily by its higher temperature
requirements; Pyrococcus grows between 70 and 106°C with an optimum of
100°C.
 Thermococcus and Pyrococcus are also metabolically quite similar. Proteins,
starch, or maltose are oxidized as electron donors,and (S0) is the terminal electron
acceptor and is reduced to hydrogen sulfide (H2S).Both Thermococcus and
Pyrococcus form H2S when (S0) is present, but form H2 when S0 is absent.

35. Spherical hyperthermophilic Euryarchaeota from submarine volcanic
areas.
(a) Thermococcus celer. Electron micrograph of shadowed cells (note tuft of
flagella).
(b) Dividing cell of Pyrococcus furiosus. Electron micrograph of thin section.
Cells of both organisms are about 0.8 μm in diameter.

36. ➢Methanopyrus-
Methanopyrusgrows optimally
at 100°C and
can make CH4 only from CO2 +
H2. (a) Electron micrograph of
a cell of Methanopyrus
kandleri, the most thermophilic
of all known organisms (upper
temperaturelimit,122°C).This
cell measures 0.5 × 8 μm. (b)
Structure of the novel lipid of
M. kandleri. This is the normal
ether-linkedlipidof the
Archaea except that the side
chains are an unsaturated form
of phytanyl (geranylgeraniol).
• Methanopyrus is a rod-shaped hyperthermophilic
methanogen. Methanopyrus was isolated from hot
sediments near submarine hydrothermal vents and from
the walls of “black smoker” hydrothermal vent chimneys.
• Methanopyrus shares phenotypic properties with both
the hyperthermophiles and the methanogens.
Methanopyrus produces CH4 only from H2 + CO2 and
grows rapidly for an autotrophic organism (generation
time <1 h at 100°C).
•In special pressurized vessels, growth of one strain of
Methanopyrus has been recorded at 122°C, the highest
temperature yet shown to support microbial growth.
• Methanopyrus is also unusual because it contains
membrane lipids found in no other known organism.

37. ➢Archaeoglobales-
 Hyperthermophilic Crenarchaeota catalyze anaerobic respirations in
which elemental sulfurb(S0) is used as an electron acceptor, being
reduced to H 2 S. One hyperthermophilic euryarchaeote, Archaeoglobus,
can reduce sulfate (SO4 2− ) and form phylogenetically distinct lineage
within the Euryarchaeota . Eg: Archaeoglobus, Ferroglobus

38. PHYLUM KORARCHEOTA-
 The nameis derivedfrom the Greek noun korosorkore, meaning
"youngman" or "youngwoman," and the Greek adjectivearchaios
which means"ancient."
 They are also knownas Xenarchaeota.The Korarchaeotahaveonly
been found in high temperaturehydrothermalenvironments.
 In Obsidian Poolin YellowstoneNationalPark(YNP), Korarchaeota
were most abundantin springs with a pH rangeof 5.7 to 7.0
 The Korarchaeotawereoriginally discoveredby microbial
communityanalysisof ribosomalRNA genesfrom environmental
samplesof a hot spring in YellowstoneNationalPark.
 K. cryptofilum whose name means“the crypticfilamentof youth” is
the only characterisedspeciesin the phlym korarcheota.
Korarchaeum
cryptofilum

39. Each of these hot springs in Kamchatka was found to contain
Korarchaeota. (Yelowstone National Park, USA)

40. PHYLUM THAUMARCHAEOTA-
 The Thaumarchaeota (fromthe Greek 'thaumas', meaning
wonder) are proposed in 2008 after the genome of
C.symbiosum was sequenced and found to thus far
identified are chemolithoautotrophic ammonia-oxidizers
and maydiffer significantly from other members of
phylum Crenarchaeota. All organisms of this lineage play
important roles in biogeochemical cycles, such as the
nitrogen cycle and the carbon cycle.
 It was proposed on basis of phylogenetic data, such as
the sequences of these organisms' ribosomal RNA genes,
and the presence of a form of type I topoisomerase that
was previously thought to be unique to the eukaryotes.
 Examples- Nitrosopumilus maritimus, Nitrososphaera
viennensis
Nitrososphaera
veinnensis

41. PHYLUM NANOARCHAEOTA-
 In taxonomy, the Nanoarchaeota from Greek meaning"old
dwarf“.
 They inhabit high-temperature environments with an
optimal growth of 90 C, and are highly unusual because
they and divide on the surface of another archaea,
Ignicoccus. Nanoarchaea, which were discovered in 2002,
contain both the smallest known living cell (1/100th the
size of Escherichia coli) and the smallest known genome
(480 kilobases [1 kilobase = 1,000 base pairs of DNA).
 Members of this phyla have not been detected in pure
culture.
 Cells of Nanoarchaeum are about 0.4 um in diameter and
replicate only when attached to the surface of Ignicoccus.
 Example- Nanoarchaeum equitans

42. Recently detected species of archaea. Archaeal Richmond Mine
acidophilic (ARMAN), which were discovered in 2006.

43. IMPORTANCE OF ARCHAEBACTERIA-
Extremophiles as a source of novel enzymes for industrial application
 Extremophilic microorganisms are adapted to survive in ecological niches:
high temperatures,
extremes of pH,
high salt concentrations
high pressure.
 These microorganisms produce unique biocatalysts which operate under extreme
conditions
 Selected extracellular-polymer-degrading enzymes and other enzymes could be used
in food, chemical and pharmaceutical industries and in environmental biotechnology.
(amylases, pullulanases, cyclodextrin glycosyltransferases, cellulases, xylanases,
chitinases, proteinases, esterases, glucose isomerases, alcohol dehydrogenases and
DNAmodifyingenzymes )

44. Biotechnological applications of archaeal biomasses
• Biological methanogenesis is applied to the anaerobic treatment of
▪sewage sludge,
▪ agricultural, municipal and industrial wastes
• Methanogens are a group of microorganisms that obtain energy for
growth from the reaction leading to methane production.
• Many bioreactor configurations have been exploited to increase the
efficiency of anaerobic digestion, such as,
▪the rotating biological contactor,
▪the anaerobic baffle reactor
▪the upflow anaerobic sludge blanket reactor,
▪several large-scale plants are in operation

45. Archaeal enzymes of biotechnological interest
• Natural and modified archaeal enzymes present huge possibilities for industrial
applications
• Many archaeal enzymes involved in carbohydrate metabolism - special interest to
the industrial biotechnology sector.
• The starch processing industry can profit from the exploitation of thermostable
enzymes.
• Another promising application of hyperthermophilic archaeal enzymes is in
trehalose production.
• Several other polymer-degrading enzymes isolated from archaea could play
important roles in the chemical, pharmaceutical, paper, pulp or waste treatment
industries. (xylanases and cellulases)
• Some archaeal metabolites have potential industrial applications.
(proteins, osmotically active substances, exopolysaccharides and special lipids )
• Archaeal lipids have been proposed as monomers for bioelectronics

46. References-
 Prescott, Lansing M.; Harley, John P. and Klein, Donald A.,2003. Microbiology,
5 edition. McGraw Hill, a business unit of The McGraw- Hill Companies.
 Madigan, MT, Martinko, Blender, Buckley & Stahl,2014, Brock Biology of
Microorganisms, 14th Edition, Pearson Prentice Hall, USA.
 www.euarch.blogspot.com
 www.filebox.vt.edu
 www.nature.com/ntmicroljournal/v5/n4
 www.fib_tab/nrmicro1619_F3.html
 www.microbewiki.kenyon.edu/
 http://www.ncbi.nlm.nih.gov/pubmed/11250034 (2016.04.15)