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 (contd)
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 m) 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 > 100C

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 140150C

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