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

Figure 17.2a

Great Salt Lake, Utah

Figure 17.2b

Seawater Evaporating Ponds Near San Francisco Bay, California

Figure 17.2c

Pigmented Haloalkaliphiles Growing in pH 10 Soda Lake in Egypt

Figure 17.2d

SEM of Halophilic Bacteria

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

Figure 17.3

Dividing cell

Glycoprotein subunit structure

on the cell wall

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

Figure 17.6a

Methanobrevibacterruminantium

Micrographs of Cells of Methanogenic Archaea

Figure 17.6b

Methanobrevibacter arboriphilus

Micrographs of Cells of Methanogenic Archaea

Figure 17.6c

Methanospirillum hungatei

Micrographs of Cells of Methanogenic Archaea

Figure 17.6d

Methanosarcina barkeri

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

Figure 17.7a

Methanobrevibacter ruminantium

Methanosarcina barkeri

Hyperthermophilic and Thermophilic Methanogens

Figure 17.8a

Methanocaldococcus jannaschii

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

Figure 17.9a

Thermoplasma acidophilum

Thermoplasma Species

Figure 17.9b

Thermoplasma volcaniumIsolated from Hot Springs

A Self-Heating Coal Refuse Pile, Habitat of Thermoplasma

Figure 17.10

Self-heats from microbial metabolism.

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

Figure 17.12a

Shadowed cells of Thermococcus celer

Figure 17.12b

Dividing cell of Pyrococcus furiosus

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

Figure 17.13a

Electron Micrograph of a cell of Methanopyrus Kandleri

Methanopyrus

Figure 17.13b

Structure of novel lipid of M. kandleri

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

Figure 17.14a

TEM of Archaeoglobus fulgidus

Figure 17.14b

Freeze-etched Electron Micrograph of Ferroglobus placidus

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

Figure 17.15a

Fluorescence micrographof cells of Nanoarchaeum

Ignicoccus

Nanoarchaeum

Figure 17.15b

TEM of a thin section of a cell of Nanoarchaeum

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

Figure 17.16a

A typical Solfatara in Yellowstone National Park

Figure 17.16b

Sulfur-rich hot spring

Figure 17.16c

A typical boiling spring of neutral pH in Yellowstone Park; Imperial Geyser

Figure 17.16d

An acidic iron-rich geothermal spring

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

Figure 17.17a

Sulfolobus acidocaldarius

Figure 17.17b

Acidianus infernus

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

Figure 17.18a

Thermoproteus neutrophilus

Figure 17.18b

Thermofilum librum

Figure 17.18c

Pyrobaculum aerophilum

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

Figure 17.19a

Pyrodictium occultum Thin-section electron micrograph of P. occultum

Figure 17.19c

Thin section of a cell of Pyrolobus fumarii

Figure 17.19d

Negative stain of a cell of strain 121,the most heat-loving of all known

Desulfurococcales with Temperature Optima Below Boiling

Figure 17.20a

Thin section of a cell of Desulfurococcus saccharovorans

Figure 17.20b

Thin section of a cell of Ignicoccus islandicus

Extremely large periplasm

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

Figure 17.22

Photo of the Antarctic peninsulaFlouresence photomicrograph of seawater treated with FISH probe

DAPI (diamidino-2-phenylindole) stained

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 energy-

yielding metabolism

Upper Temperature Limits for Energy Metabolism

Figure 17.26