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The Archaea
CHAPTER OVERVIEW
This chapter summarizes the properties of a diverse group of organisms known as the Archaea. These
organisms are very different from bacteria and from eukaryotes, but also share many qualities. The chapter
describes some of the major characteristics associated with each of the major groups of Archaea.
CHAPTER OBJECTIVES
After reading this chapter you should be able to:
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discuss the morphological and physiological diversity of the Archaea
describe the membrane lipid composition and cell walls of the Archaea
discuss the general genetic, molecular, and metabolic characteristics of the Archaea
discuss the habitats that are typical for the Archaea
discuss the classification scheme for the Archaea used in Bergey’s Manual
discuss the unique cofactors used by methanogenic and sulfate-reducing archaea
describe the structural, chemical, and metabolic adaptations that allow the Archaea to grow in extreme
environments
CHAPTER OUTLINE
I.
Overview of the Archaea
A. Archaea are quite diverse in morphology and physiology
1. May be spherical, rod-shaped, spiral, lobed, plate-shaped, irregularly shaped, or pleomorphic;
may exist as single cells, aggregates, or filaments
2. May multiply by binary fission, budding, fragmentation, or other mechanisms
3. May be aerobic, facultatively anaerobic, or strictly anaerobic; nutritionally range from
chemolithoautotrophs to organotrophs
B. Ecology
1. Often found in extreme aquatic and terrestrial habitats; commonly considered extremophiles
2. Some are mesophiles, while others are hyperthermophiles that can grow above 100°C; some
grow in freshwater, while others grow in concentrated brines
3. Some are symbionts in animal digestive systems
C. Archaeal taxonomy
1. Bergey’s Manual divides the archaea into two phyla: Euryarchaeota and Crenarchaeota
2. Euryarchaeota are metabolically and ecologically diverse and include methanogens,
halophiles, and thermophiles
3. Crenarchaeota are considered a more ancient lineage, rich in thermophiles and
hyperthermophiles; Thaumarchaeota is a provisional taxon of mesophilic crenarchaeota
D. Archaeal cell walls and membranes
1. Archaeal cell walls are quite diverse and do not contain bacterial peptidoglycan (no muramic
acid or D-amino acids); may contain pseudomurein, chondroitin sulfate-like polysaccharides,
or protein walls; a protein S-layer is a common archaeal cell envelope; archaeal flagella
resemble bacterial pili
2. The membrane lipids of archaea differ from those of other organisms in having ether linkages
(rather than esters), long tetraethers, and pentacyclic rings (crenarchaeol lipids)
E. Genetics and molecular biology
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1.
The archaeal chromosomes consist of a single, closed DNA circle as seen in bacteria; Archaea
may have plasmids; genotypically diverse; some archaeal genomes have histone proteins like
those in eukaryotes
2. Archaeal DNA replication combines features of both bacteria and eukaryotes; it is usually
bidirectional like bacteria; uses mainly eukaryotic-like replication enzymes
3. Transcription in archaea uses an RNA polymerase very much like that of eukaryotes and
promoter recognition is dependent on eukaryotic-like transcription factors; transcriptional
regulators often resemble bacterial proteins
4. Archaeal mRNAs have features from bacteria and eukaryotes like that of bacteria; they may be
polygenic with bacterial ribosome binding sequences, but often lack a leader sequence and
sometimes have introns like eukaryotes
5. Archaeal tRNAs have modified bases not found in the other domains; the initiator tRNA
carries methionine like eukaryotes; ribosomal structure appears to be unique but has antibiotic
sensitivities similar to eukaryotes; unique protein amino acids (selenocysteine and pyrrolysine)
are included in the genetic code
6. Archaea use a Sec-dependent pathway for protein secretion that relies on binding to signal
peptides like bacteria, but some of the protein machinery resembles that of eukaryotes
F. Metabolism
1. Carbohydrate metabolism is best understood
a. Archaea use a modified Embden-Meyerhof pathway for glucose catabolism and two
modified forms of the Entner-Doudoroff pathway
b. Some (halophiles and extreme thermophiles) have a complete TCA cycle while others
(methanogens) do not
2. Archaeal biosynthetic pathways appear to be similar to those of other organisms
3. Autotrophy is widespread; the reductive TCA cycle and the reductive acetyl-CoA cycle are
used for carbon fixation
G. Thermostability
1. Proteins are made more rigid by increasing core hydrophobicity, packing density, and
hydrogen bonds
2. DNA is protected from denaturation with increased supercoiling
II. Phylum Crenarchaeota—consists of one class divided into four orders (Thermoproteales, Sulfolobales,
Desulfurococcales, and Caldisphaerales)
A. Many are extremely thermophilic (hyperthermophiles), acidophilic, and sulfur-dependent, although
there is molecular evidence that Crenarchaeota may be widespread in mesophilic environments
1. Sulfur may be used as an electron acceptor in anaerobic respiration, or as an electron source by
lithotrophs; almost all are strict anaerobes; Some are organotrophic; others are lithotrophic
2. Found in geothermally heated water or soils (solfatara) that contain elemental sulfur; some can
grow well above the boiling point of water
3. There are 25 genera; two of the better-studied genera are Sulfolobus and Thermoproteus
B. Genus Sulfolobus
1. Irregularly lobed, spherical cells; cell walls lack peptidoglycan, stain gram negative, and
contain lipoproteins and carbohydrates
2. Thermoacidophiles; oxidize sulfur to sulfuric acid; oxygen is the normal electron acceptor, but
ferric iron can also be used; sugars and amino acids may serve as carbon and energy sources
C. Genus Thermoproteus
1. Long, thin, bent or branched rods; cell wall is composed of glycoprotein
2. Found in hot springs and other hot aquatic habitats that contain elemental sulfur; have
temperature optima from 70–97˚C and pH optima from 2.5 to 6.5
3. Carry out anaerobic respiration using organic molecules as electron donors and elemental
sulfur as the electron acceptor; can also grow lithotrophically using H2 and S0 as electron
donors and CO or CO2 as the sole carbon source
III. Phylum Euryarchaeota
A. Methanogens
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1.
B.
C.
D.
E.
Strict anaerobes that obtain energy by converting CO2, H2, formate, methanol, acetate, and
other compounds to either methane or to methane and CO2; can be autotrophic
2. Consists of five orders and 26 genera; great diversity in shape, 16S rRNA sequence, cell walls,
and membrane lipids
3. Methanogenesis is an unusual metabolic process and methanogens contain several unusual
cofactors; many do not have cytochromes
4. They are of great potential importance because methane is a clean-burning fuel and an
excellent energy source
5. May be an ecological concern; methane is a greenhouse gas that contributes to global warming
Halobacteria
1. Halobacteriales consists of 17 genera of extreme halophiles
2. Aerobic chemoheterotrophs with respiratory metabolism; nonmotile or motile; found in many
different cell shapes including cubes and pyramids
3. Require at least 1.5 M NaCl to maintain cell structure and have growth optima near 3–4 M
NaCl; cells accumulate organic or inorganic (K+) compatible solutes to balance osmolarity
with brine
4. Involved in production and spoilage of salted foods
5. Halobacterium salinarum uses four different light-utilizing rhodopsin molecules
a. Bacteriorhodopsin uses light energy to drive outward proton transport for ATP synthesis;
thus they carry out a type of photosynthesis that does not involve chlorophyll
b. Halorhodopsin uses light energy to transport chloride ions into the cell to maintain a 4–5
M intracellular KCl concentration
c. Two sensory rhodopsins act as photoreceptors that control flagellar activity to position
the bacterium in the water column at a location of high light intensity, but one in which
the UV light is not sufficiently intense to be lethal
d. A type of rhodopsin called proteorhodopsin appears to be widespread among bacteria
Thermoplasms
1. The class Thermoplasmata consists of three genera of thermoacidophiles that lack cell walls
2. Genus Thermoplasma
a. Irregular filament or cocci found in hot acidic coal mine refuse; optimum growth
temperature is 55–59˚C and optimum pH is ≤2; may be flagellated
b. Cell membrane strengthened by diglycerol tetraethers, lipopolysaccharides, and
glycoproteins; histonelike proteins stabilize DNA forming particles resembling
eukaryotic nucleosomes
3. Genus Picrophilus
a. Isolated from hot solfataric fields; can grow at 65°C and near pH 0;
aerobic
b. Irregularly shaped cocci ; contains S-layer
Extremely thermophilic S0 metabolizers—class Thermococci, consists of three genera
1. Strictly anaerobic, reduce sulfur to sulfide; flagellated
2. Optimum growth temperatures of 88–100˚C
Sulfate-reducing Euryarchaeota—Class Archaeoglobi, consisting of one major genus,
Archaeoglobus, and two others
1. Gram-negative, irregular coccoid cells with glycoprotein walls
2. Use a variety of electron donors and reduce sulfite, sulfate, or thiosulfate to sulfide
3. Extremely thermophilic; found near marine hydrothermal vents
TERMS AND DEFINITIONS
Place the letter of each term in the space next to the definition or description that best matches it.
____ 1.
A peptidoglycan-like polymer in the cell walls of some
methanogenic archaea
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____ 2.
A strict anaerobe that
obtains energy by
converting CO2, H2,
formate, methanol, acetate, and other compounds to
methane
____ 3. An organism that requires at least 1.5 M NaCl in order
to grow
____ 4. A modified cell membrane that carries out
photosynthesis in the absence of chlorophyll
____ 5. A protein that mediates photosynthesis without
chlorophyll in archaea
____ 6. An organism with a temperature growth optimum
around 80°C and a pH growth optimum from 1.0 to 6.5
____ 7. Photoreceptor that controls flagellar activity to
position Halobacterium in the water column
____ 8. Thermoacidophilic bacteria that lack cell walls and
grow in refuse piles of coal mines
____ 9. Organic molecules accumulated by archaeal cells to
balance the osmotica of hypersaline environments
____ 10. A type of lipid found in archaea that includes
cyclopentane rings
____ 11. A protein found in bacteria that is closely related to the
photosynthetic protein in archaeal purple membranes
____ 12. A cell wall envelope found in archaea that is made of
protein
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a.
b.
c.
d.
e.
f.
g.
h.
i.
j.
k.
l.
bacteriorhodopsin
compatible solutes
crenarchaeol
extreme halophile
methanogen
proteorhodopsin
pseudomurein
purple membrane
sensory rhodopsin
S-layer
thermoacidophile
thermoplasma
ARCHAEAL TAXONOMY
Complete the following table.
Phylum
Crenarchaeota
Representative Genera
Important Characteristics (structural,
physiological, ecological)
Euryarchaeota
Methanogens
(Classes Methanobacteria,
Methanococci and Methanopyri)
Halobacteria
(Class Halobacteria)
Thermoplasms
(Class Thermoplasmata)
Extremely thermophilic S0
metabolizers
(Class Thermococci)
Sulfate reducers
(Class Archaeoglobi)
FILL IN THE BLANK
1.
2.
3.
Living organisms can be divided into three domains; Eucarya, Bacteria, and
. The latter
have many distinguishing characteristics. For instance, they lack peptidoglycan in their cell walls;
instead, some have a peptidoglycan-like component called
.
The
and extreme thermophiles have a complete TCA cycle, but
do not.
Many members of the phylum Crenarchaeota (e.g., genus Solfolobus) grow in geothermally heated
waters having a low pH. Such organisms are called
.
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4.
5.
6.
Under certain environmental conditions, some strains of Halobacterium synthesize a modified cell
membrane called the
membrane, which contains the protein
. This
protein drives outward proton transport, creating a proton gradient that can be used to synthesize ATP.
The metabolically and ecologically diverse ________________ includes methanogens, _____________
and ________________, while the more ancient lineage, ___________________, are almost entirely
___________________ and ____________________.
Archaeal proteins are known to contain amino acids coded in the DNA that are not included in the typical
20 protein amino acids, namely,
and
.
TRUE/FALSE
____
____
____
____
____
____
____
1.
2.
3.
4.
5.
6.
7.
____ 8.
____ 9.
Archaea are all strict anaerobes.
Thermoproteus is found in hot aquatic habitats that contain elemental sulfur.
Halorhodopsin uses light energy to pump protons for ATP synthesis.
The chromosomal DNA of some archaea is smaller than the chromosomal DNA of bacteria.
Archaeoglobus uses elemental sulfur as an electron acceptor.
Recently, archaea have been found in cold environments such as Antarctic surface waters.
The genome of Methanococcus jannaschii has been completely sequenced and has been
found to be genotypically indistinct from the bacteria.
Picrophilus has a pH optimum below 1 and can even grow at or near pH 0.
Autotrophic archaea use the reductive TCA cycle and the acetyl-CoA cycle to fix carbon.
MULTIPLE CHOICE
For each of the questions below select the one best answer.
1.
2.
3.
4.
Which of the following is used by archaea as
a mechanism for reproduction?
a. binary fission
b. budding
c. fragmentation
d. All of the above are correct.
Which of the following is true about archaeal
ribosomes?
a. They are 70S, like bacterial ribosomes.
b. Their shape differs from both bacterial
and eukaryotic ribosomes.
c. They have antibiotic sensitivities
similar to those of eukaryotic
ribosomes.
d. All of the above are true.
Which of the following groups does not have
a functional TCA cycle?
a. methanogens
b. extreme halophiles
c. extreme thermophiles
d. All of the above have a functional TCA
cycle.
Which is the largest group of cultured
archaea?
a. the methanogens
b. the halobacteria
c. the thermoplasms
d. the thermococci
5.
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Which of the following is NOT true about
methanogens?
a. They are potentially of great importance
because methane is an even-burning
fuel and an excellent energy source.
b. They may contribute to the greenhouse
effect and global warming.
c. They may cause corrosion in iron pipes.
d. All of the above are true about
methanogens.
6.
7.
What happens to the cell wall of
Halobacterium if the NaCl concentration
drops to about 1.5 M?
a. The cell wall becomes more rigid.
b. The cell wall loses permeability.
c. The cell wall disintegrates.
d. All of the above are correct.
Which of the following is true about
Sulfolobus?
a. Oxygen is the normal electron acceptor.
b. Ferric ion can be used as an electron
acceptor.
c. Both (a) and (b) are correct.
d. Neither (a) nor (b) is correct.
8.
9.
Which of the following is true about the
genus Thermoplasma?
a. They are spherical at temperatures
below 59°C.
b. They are filamentous at temperatures at
or above 59°C.
c. Both (a) and (b) are correct.
d. Neither (a) nor (b) is correct.
Which of the following do not have cell
walls?
a. halobacteria
b. thermoplasms
c. thermococci
d. None of the above have cell
walls.
CRITICAL THINKING
1.
In the future, certain members of the archaea may provide a pollution-free source of energy. Explain.
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ANSWER KEY
Terms and Definitions
1. g, 2. e, 3. d, 4. h, 5. a, 6. k, 7. i, 8. l, 9. b, 10. c, 11. f, 12. j
Fill in the Blank
1. Archaea; pseudomurein 2. halophiles; methanogens 3. thermoacidophiles 4. purple; bacteriorhodopsin 5.
Euryarchaeota; halophiles; thermophiles; Crenarchaeota; thermophiles; hyperthermophiles 6. selenocysteine;
pyrrolysine
True/False
1. F, 2. T, 3. F, 4. T, 5. F, 6. T, 7. F, 8. T, 9.T
Multiple Choice
1. d, 2. d, 3. a, 4. a, 5. c, 6. c, 7. c, 8. c, 9. b
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