Download Archaea

Chapter 17
Archaea
I. Phylogeny and General Metabolism
 17.1 Phylogenetic Overview of Archaea
 17.2 Energy Conservation and Autotrophy in Archaea
17.1 Phylogenetic Overview of Archaea
 Archaea share many characteristics with both
Bacteria and Eukarya
 Archaea are split into two major groups
 Crenarchaeota
 Euryarchaeota
Detailed Phylogenetic Tree of the Archaea
Figure 17.1
17.2 Energy Conservation and Autotrophy in Archaea
 Chemoorganotrophy and chemolithotrophy
▪ With the exception of methanogenesis, bioenergetics
and intermediary metabolism of Archaea are similar to
those found in Bacteria
- Glucose metabolism
: EMP or slightly modified Entner-Doudoroff pathway
- Oxidation of acetate to CO2
: TCA cycle or some slight variations of TCA cycle
: Reverse route of acetyl-CoA pathway
- Electron transport chains with a, b, and c-type
cytochromes present in some Archaea
: use O2, S0, or some other electron acceptor (nitrate or
fumarate)
: establish proton motive force
: ATP synthesis through membrane-bound ATPase
- Chemolithotrophy
: H2 as a common electron donor and energy source is well
established
▪ Autotrophy via several different pathways is widespread
in Archaea
▪ acetyl-CoA pathway in methanogens and
most hyperthermophiles
▪ Reverse TCA cycle in some hyperthermophiles
▪ Calvin cycle in Methanococcus jannaschii and a Pyrococcus
species (both are hyperthermophiles)
II. Euryarchaeota
 17.3 Extremely Halophilic Archaea
 17.4 Methane-Producing Archaea: Methanogens
 17.5 Thermoplasmatales
 17.6 Thermococcales and Methanopyrus
 17.7 Archaeoglobales
 17.8 Nanoarchaeum and Aciduliprofundum
II. Euryarchaeota
 Euryarchaeota
 Physiologically diverse group of Archaea
 Many inhabit extreme environments
 E.g., high temperature, high salt, high acid
17.3 Extremely Halophilic Archaea
 Haloarchaea
 Extremely halophilic Archaea
 Have a requirement for high salt concentrations
 Typically require at least 1.5 M (~9%) NaCl for growth
 Found in solar salt evaporation ponds, salt lakes, and
artificial saline habitats (i.e., salted foods)
Hypersaline Habitats for Halophilic Archaea
Great Salt Lake, Utah
Figure 17.2a
Seawater Evaporating Ponds Near
San Francisco Bay, California
Figure 17.2b
Pigmented Haloalkaliphiles Growing
in pH 10 Soda Lake in Egypt
Figure 17.2c
SEM of Halophilic Bacteria
Figure 17.2d
17.3 Extremely Halophilic Archaea
 Extremely hypersaline environments are rare
 Most found in hot, dry areas of world
 Salt lakes can vary in ionic composition, selecting
for different microbes
 Great Salt Lake similar to concentrated seawater
 Soda lakes are highly alkaline hypersaline environments
Ionic Composition of Some Highly Saline Environments
 Haloarchaea
 Reproduce by binary fission
 Do not form resting stages or spores
 Most are nonmotile
 Most are obligate aerobes
 Possess adaptations to life in highly ionic environments
Some Genera of Extremely Halophilic Archaea
Some Genera of Extremely Halophilic Archaea
Micrographs of the Halophile Halobacterium salinarum
Dividing cell
Glycoprotein subunit structure
on the cell wall
Figure 17.3
 Water balance in extreme halophiles
 Halophiles need to maintain osmotic balance
 This is usually achieved by accumulation or synthesis of
organic compatible solutes
 Halobacterium species instead pump large amounts of
K+ into the cell from the environment
 Intracellular K+ concentration exceeds extracellular Na+
concentration and positive water balance is maintained
Concentration of Ions in Cells of Halobacterium salinarum
 Proteins of halophiles
 Highly acidic
 Contain fewer hydrophobic amino acids and lysine
residues
 Some haloarchaea are capable of light-driven
synthesis of ATP
 Bacteriorhodopsin
 Cytoplasmic membrane proteins that can absorb light
energy and pump protons across the membrane
Model for the Mechanism of Bacteriorhodopsin
Figure 17.4
 Other rhodopsins can be present in Archaea
 Halorhodpsin
 Light-driven pump that pumps Cl- into cell as an anion for
K+
 Sensory rhodopsins
 Control phototaxis
17.4 Methane-Producing Archaea: Methanogens
 Methanogens
 Microbes that produce CH4
 Found in many diverse environments
 Taxonomy based on phenotypic and phylogenetic
features
 Process of methanogensis first demonstrated over
200 years ago by Alessandro Volta
The Volta Experiment
Figure 17.5
Habitats of Methanogens
Micrographs of Cells of Methanogenic Archaea
Methanobrevibacter
ruminantium
Figure 17.6a
Micrographs of Cells of Methanogenic Archaea
Methanobrevibacter
arboriphilus
Figure 17.6b
Micrographs of Cells of Methanogenic Archaea
Methanospirillum
hungatei
Figure 17.6c
Micrographs of Cells of Methanogenic Archaea
Methanosarcina barkeri
Figure 17.6d
Characteristics of Some Methanogenic Archaea
Characteristics of Some Methanogenic Archaea
 Diversity of Methanogens
 Demonstrate diversity of cell wall chemistries
 Pseudomurein (e.g., Methanobacterium,
Methanobrevibacter)
 Methanochondroitin (e.g., Methanosarcina)
- (N-acetylgalactosamine + glucuronic acid)n
 Protein or glycoprotein (e.g., Methanocaldococcus)
 S-layers (e.g., Methanospirillium)
Micrographs of Thin Sections of Methanogenic Archaea
Methanobrevibacter ruminantium
Methanosarcina barkeri
Figure 17.7a
Hyperthermophilic and Thermophilic Methanogens
Methanocaldococcus jannaschii
Figure 17.8a
 Substrates for Methanogens
 Obligate anaerobes
 11 substrates, divided into 3 classes, can be converted
to CH4 by pure cultures of methanogens
 Other compounds (e.g., glucose) can be converted to
methane, but only in cooperative reactions between
methanogens and other anaerobic bacteria
(syntrophic metabolism)
Substrates Converted to Methane by Methanogens
17.5 Thermoplasmatales
 Methanocaldococcus jannaschii as a model
methanogen
 Contains 1.66 mB circular genome with about 1,700
genes
 Genes for central metabolic pathways and cell division
- Similar to those in Bacteria
 Genes encoding transcription and translation
- More closely resemble those of Eukarya
 Over 50% of genes
- Have no counter parts in known genes from Bacteria and
Eukarya
 Thermoplasmatales
 Taxonomic order within the Euryarchaeota
 Contains 3 genera
 Thermoplasma
 Ferroplasma
 Picrophilus
 Thermophilic and/or extremely acidophilic
 Thermoplasma and Ferroplasma lack cell walls
 Thermoplasma
 Chemoorganotrophs
 Facultative aerobes via sulfur respiration
 Thermophilic
 Acidophilic
Thermoplasma Species
Thermoplasma acidophilum
Figure 17.9a
Thermoplasma Species
Thermoplasma volcanium
Isolated from Hot Springs
Figure 17.9b
A Self-Heating Coal Refuse Pile, Habitat of Thermoplasma
Self-heats from microbial metabolism.
Figure 17.10
 Thermoplasma (cont’d)
 Evolved unique cytoplasmic membrane structure to
maintain positive osmotic pressure and tolerate high
temperatures and low pHs
 Membrane contains lipopolysaccharide-like material
(lipoglycan) consisting of tetraether lipid monolayer
membrane with mannose and glucose
 Membrane also contains glycoproteins but not sterols
Structure of the Tetraether Lipoglycan of T. acidophilum
Figure 17.11
 Ferroplasma
 Chemolithotrophic
 Acidophilic
 Oxidizes Fe2+ to Fe3+, uses CO2 as carbon source
 Grows in mine tailings containing pyrite (FeS)
- Generates acid (acid mine drainage)
 Picrophilus
 Extreme acidophiles
 Grow optimally at pH 0.7
 Have an S-layer
 Model microbe for extreme acid tolerance
17.6 Thermococcales and Methanopyrus
 Three phylogenetically related genera of hyperthermophilic
Euryarchaeota
 Thermococcus
 Pyrococcus
 Methanopyrus
 Comprise a branch near root of archaeal tree
Detailed Phylogenetic Tree of the Archaea
Figure 17.1
 Thermococcales
 Distinct order that contains Thermococcus and
Pyrococcus
 Thermococcus: organics + So, 55-95oC
 Pyrococcus: organics + So, opt. 100oC, 70-106oC
** In the absence of So, form H2
 Indigenous to anoxic thermal waters
 Highly motile
Spherical Hyperthermophilic Archaea
Shadowed cells of
Thermococcus celer
Figure 17.12a
Dividing cell of
Pyrococcus furiosus
Figure 17.12b
 Methanopyrus
 Methanogenic (CO2 + H2)
 Isolated from hot sediments near submarine
hydrothermal vents and from walls of “black smoker”
 Opt. temp. 100oC, max. temp. 110oC (the most
thermophilic of all known methangens)
 Contains unique membrane lipids: unsaturated form
 Contains 2,3-diphosphoglycerate in the cytoplasm (> 1 M)
 Functions as thermostabilizing agent
Methanopyrus
Electron Micrograph of a cell of Methanopyrus Kandleri
Figure 17.13a
Methanopyrus
Structure of novel lipid of M. kandleri
Figure 17.13b
17.7 Archaeoglobales
 Archaeoglobales
 Hyperthermophilic
 Couple oxidation of H2, lactate, pyruvate, glucose, or
complex organic compounds to the reduction of SO42- to
H2S
 Archaeoglobus
 Opt. temp. 83oC
 Produce methane, but lacks genes for methyl-CoM
reductase
 Ferroglobus
 Opt. temp. 85oC
 Fe2+ + NO3- → Fe3+ + NO2- + NO
Archaeoglobales
TEM of Archaeoglobus fulgidus
Figure 17.14a
Freeze-etched Electron Micrograph of
Ferroglobus placidus
Figure 17.14b
17.8 Nanoarchaeum and Aciduliprofundum
 Nanorchaeum equitans
 One of the smallest cellular organisms (~0.4 µm)
 Obligate symbiont of the crenarchaeote Ignicoccus
 Contains one of the smallest genomes known
(0.49 mbp)
 Lacks genes for all but core molecular processes
 Depends upon host for most of its cellular needs
Nanoarchaeum
Ignicoccus
Nanoarchaeum
Fluorescence micrograph
of cells of Nanoarchaeum
Figure 17.15a
TEM of a thin section of a
cell of Nanoarchaeum
Figure 17.15b
 Aciduliprofundum
 Thermophilic: 55-75oC
 Acidophile: pH 3.3-5.8, lives in sulfide deposits in
hydrothermal vents
 Oragnics + So or Fe3+
III. Crenarchaeota
 17.9 Habitats and Energy Metabolism of Crenarchaeota
 17.10 Hyperthermophiles from Terrestrial Volcanic Habitats
 17.11 Hyperthermophiles from Submarine Volcanic
Habitats
 17.12 Nonthermophilic Crenarchaeota
17.9 Habitats and Energy Metabolism of Crenarchaeota
 Crenarchaeota
 Inhabit temperature extremes
 Most cultured representatives are hyperthermophiles
 Other representatives found in extreme cold
environments
Habitats of Crenarchaeota
Habitats of Hyperthermophilic Archaea
A typical Solfatara in
Yellowstone National Park
Figure 17.16a
Sulfur-rich hot spring
Figure 17.16b
A typical boiling spring of neutral pH
in Yellowstone Park; Imperial Geyser
Figure 17.16c
An acidic iron-rich
geothermal spring
Figure 17.16d
 Hyperthermophilic Crenarchaeota
 Most are obligate anaerobes
 Chemoorganotrophs or chemolithotrophs with diverse
electron donors and acceptors
Energy-Yielding Reactions of Hyperthermophilic Archaea
Properties of Some Hyperthermophilic Crenarchaeota
17.10 Hyperthermophiles from Terrestrial Volcanos
 Sulfolobales
 An order containing the genera Sulfolobus and Acidianus
 Sulfolobus
 Grows in sulfur-rich acidic hot springs
 Aerobic chemolithotrophs that oxidize reduced sulfur or iron
 Acidianus
 Also lives in acidic sulfur hot springs
 Able to grow using elemental sulfur both aerobically and
anaerobically (as an electron donor and electron acceptor,
respectively)
Acidophilic Hyperthermophilic Archaea, the Sulfolobales
Sulfolobus acidocaldarius
Figure 17.17a
Acidianus infernus
Figure 17.17b
 Thermoproteales
 An order containing the key genera Thermoproteus,
Thermofilum, and Pyrobaculum
 Inhabit neutral or slightly acidic hot springs or
hydrothermal vents
Rod-Shaped Hyperthermophiles, the Thermoproteales
Thermoproteus neutrophilus
Figure 17.18a
Thermofilum librum
Figure 17.18b
Pyrobaculum aerophilum
Figure 17.18c
17.11 Hyperthermophiles from Submarine Volcanos
 Shallow-water thermal springs and deep-sea
hydrothermal vents harbor the most thermophilic of
all known Archaea
 Pyrodictium and Pyrolobus
 Desulfurococcus and Ignicoccus
 Staphylothermus
Desulfurococcales with Temperature Optima > 100°C
Pyrodictium occultum
Thin-section electron
micrograph of P. occultum
Figure 17.19a
Thin section of a cell of
Pyrolobus fumarii
Figure 17.19c
Negative stain of a cell of strain 121,
the most heat-loving of all known
Figure 17.19d
Desulfurococcales with Temperature Optima Below Boiling
Thin section of a cell of
Desulfurococcus saccharovorans
Figure 17.20a
Extremely large
periplasm
Thin section of a cell of
Ignicoccus islandicus
Figure 17.20b
The Hyperthermophile Staphylothermus marinus
Figure 17.21
17.12 Nonthermophilic Crenarchaeota
 Nonthermophilic Crenarchaeota have been
identified in cool or cold marine waters and
terrestrial environments by culture-independent
studies
 Abundant in deep ocean waters
 Appear to be capable of nitrification
Cold-Dwelling Crenarchaeota
DAPI (diamidino-2-phenylindole) stained
Photo of the Antarctic peninsula
Flouresence photomicrograph of
seawater treated with FISH probe
Figure 17.22
IV. Evolution and Life at High Temperatures
 17.13 An Upper Temperature Limit for Microbial Life
 17.14 Adaptations to Life at High Temperature
 17.15 Hyperthermophilic Archaea, H2, and Microbial
Evolution
17.13 An Upper Temperature Limit for Microbial Life
 What are the upper temperature limits for life?
 Laboratory experiments with biomolecules suggest
140–150°C
Thermophilic and Hyperthermophilic Prokaryotes
Figure 17.23
17.14 Adaptations to Life at High Temperature
 Stability of Monomers
 Protective effect of high concentration of cytoplasmic
solutes
 Use of more heat-stable molecules
 e.g., use of nonheme iron proteins instead of proteins that
use NAD and NADH
 Protein Folding and Thermostability
 Amino acid composition similar to that of
nonthermostable proteins
 Structural features improve thermostability
 Highly hydrophobic cores
 Increased ionic interactions on protein surfaces
 Chaperonins
 Class of proteins that refold partially denatured proteins
 Thermosome
 A major chaperonin protein complex in Pyrodictium
 DNA Stability
 High intracellular solute levels stabilize DNA
 Reverse DNA gyrase
 Introduces positive supercoils into DNA, which stabilizes DNA
 Found only in hyperthermophiles
 High intracellular levels of polyamines (e.g., putrescine,
spermidine) stabilize DNA and RNA
 DNA-binding proteins (archaeal histones) compact DNA into
nucleosome-like structures
Archael Histones and Nucleosomes
Figure 17.25
 SSU rRNA Stability
 Higher GC content
 Lipid Stability
 Possess dibiphytanyl tetraether type lipids; form a lipid
monolayer membrane structure
17.15 Hyperthermophilic Archaea, H2, and Evolution
 Hyperthermophiles may be the closest descendants
of ancient microbes
 Hyperthermophilic Archaea and Bacteria are found on
the deepest, shortest branches of the phylogenetic tree
 The oxidation of H2 is common to many
hyperthermophiles and may have been the first energyyielding metabolism
Upper Temperature Limits for Energy Metabolism
Figure 17.26