Chapter 19 Archaea

I. Diversity 19.1 Phylogenetic and Metabolic Diversity of Archaea © 2012 Pearson Education, Inc.

19.1 Phylogenetic and Metabolic Diversity of Archaea Archaea share many characteristics with both Bacteria and Eukarya Archaea are split into two major groups (Figure 19.1) Crenarchaeota Euryarchaeota © 2012 Pearson Education, Inc.

Euryarchaeota Crenarchaeota Figure 19.1 Extreme halophiles Marine Euryarchaeota Marine Crenarchaeota Euryarchaeota Halobacterium Halococcus Archaeoglobus Extreme halophiles Natronococcus Methanobacterium Methanocaldococcus Crenarchaeota Halophilic methanogen Methanothermus Sulfolobus Pyrodictium Methanosarcina Thermococcus/ Pyrococcus Methanospirillum Nanoarchaeum Thermoproteus Hyperthermophiles Thermoplasma Methanopyrus Figure 19.1 Detailed phylogenetic tree of the Archaea based on 16S rRNA gene sequence comparisons. Desulfurococcus Picrophilus Ferroplasma Extreme acidophiles © 2012 Pearson Education, Inc.

19.1 Phylogenetic and Metabolic Diversity of Archaea Bioenergetics and intermediary metabolism of Archaea are similar to those found in Bacteria Except some Archaea use methanogenesis Autotrophy via several different pathways is widespread in Archaea © 2012 Pearson Education, Inc.

II. Euryarchaeota 19.2 Extremely Halophilic Archaea 19.3 Methanogenic Archaea 19.4 Thermoplasmatales 19.5 Thermococcales and Methanopyrus 19.6 Archaeoglobales 19.7 Nanoarchaeum and Aciduliprofundum © 2012 Pearson Education, Inc.

II. Euryarchaeota Euryarchaeota Physiologically diverse group of Archaea Many inhabit extreme environments Examples: high temperature, high salt, high acid © 2012 Pearson Education, Inc.

19.2 Extremely Halophilic Archaea Haloarchaea Key genera: Halobacterium, Haloferax, Natronobacterium Extremely halophilic Archaea Have a requirement for high salt concentrations Typically require at least 1.5 M (~9%) NaCl for growth Found in artificial saline habitats (e.g., salted foods), solar salt evaporation ponds, and salt lakes (Figure 19.2) © 2012 Pearson Education, Inc.

Figure 19.2 Figure 19.2 Hypersaline habitats for halophilic Archaea. © 2012 Pearson Education, Inc.

19.2 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 © 2012 Pearson Education, Inc.

19.2 Extremely Halophilic Archaea 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 Cell wall is composed of glycoprotein and stabilized by Na+ (Figure 19.3) © 2012 Pearson Education, Inc.

Figure 19.3 Nucleoids Figure 19.3 Electron micrographs of thin sections of the extreme halophile Halobacterium salinarum. © 2012 Pearson Education, Inc.

19.2 Extremely Halophilic Archaea Water Balance in Extreme Halophiles Halophiles need to maintain osmotic balance This is usually achieved by accumulation or synthesis of 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 © 2012 Pearson Education, Inc.

19.2 Extremely Halophilic Archaea Proteins of halophiles Are highly acidic Contain fewer hydrophobic amino acids and lysine residues © 2012 Pearson Education, Inc.

19.2 Extremely Halophilic Archaea Some haloarchaea are capable of light-driven synthesis of ATP (Figure 19.4) Bacteriorhodopsin Cytoplasmic membrane proteins that can absorb light energy and pump protons across the membrane Animation: Bacteriorhodopsin and Light Mediated ATP Synthesis © 2012 Pearson Education, Inc.

Out In Membrane Bacteriorhodopsin ATPase Figure 19.4 Figure 19.4 Model for the mechanism of bacteriorhodopsin. ATPase © 2012 Pearson Education, Inc.

19.2 Extremely Halophilic Archaea Other rhodopsins can be present in Archaea Halorhodopsin Light-driven pump that pumps Cl into cell as an anion for K+ Sensory rhodopsins Control phototaxis © 2012 Pearson Education, Inc.

19.3 Methanogenic Archaea Methanogens (Figure 19.5) Key genera: Methanobacterium, Methanocaldococcus, Methanosarcina Microbes that produce CH4 Found in many diverse environments Taxonomy based on phenotypic and phylogenetic features Process of methanogenesis first demonstrated over 200 years ago by Alessandro Volta © 2012 Pearson Education, Inc.

Figure 19.5 Figure 19.5 Scanning electron micrographs of cells of diverse species of methanogenic Archaea. © 2012 Pearson Education, Inc.

19.3 Methanogenic Archaea Diversity of Methanogens Demonstrate diversity of cell wall chemistries (Figure 19.6 and Figure 19.7) Pseudomurein (e.g., Methanobacterium) Methanochondroitin (e.g., Methanosarcina) Protein or glycoprotein (e.g., Methanocaldococcus) S-layers (e.g., Methanospirillum) © 2012 Pearson Education, Inc.

Figure 19.6 Figure 19.6 Transmission electron micrographs of thin sections of methanogenic Archaea. © 2012 Pearson Education, Inc.

Figure 19.7 Figure 19.7 Hyperthermophilic and thermophilic methanogens. © 2012 Pearson Education, Inc.

19.3 Methanogenic Archaea 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 © 2012 Pearson Education, Inc.

19.4 Thermoplasmatales Thermoplasmatales Key genera: Thermoplasma, Ferroplasma, Picrophilus Taxonomic order within the Euryarchaeota Thermophilic and/or extremely acidophilic Thermoplasma and Ferroplasma lack cell walls © 2012 Pearson Education, Inc.

19.4 Thermoplasmatales Thermoplasma (Figure 19.8) Chemoorganotrophs Facultative aerobes via sulfur respiration Thermophilic Acidophilic Found in self-heating coal piles (Figure 19.9) © 2012 Pearson Education, Inc.

Figure 19.8 Figure 19.8 Thermoplasma species. © 2012 Pearson Education, Inc.

Figure 19.9 Figure 19.9 A typical self-heating coal refuse pile, habitat of Thermoplasma. © 2012 Pearson Education, Inc.

19.4 Thermoplasmatales Thermoplasma (cont’d) Evolved unique cytoplasmic membrane structure to maintain positive osmotic pressure and tolerate high temperatures and low pH levels Membrane contains lipopolysaccharide-like material (lipoglycan) consisting of tetraether lipid monolayer membrane with mannose and glucose (Figure 19.10) Membrane contains glycoproteins but not sterols © 2012 Pearson Education, Inc.

R  Man (1  2) Man (1  4) Man (1  3) Figure 19.10 Ether linkage Figure 19.10 Structure of the tetraether lipoglycan of Thermoplasma acidophilum. R  Man (1  2) Man (1  4) Man (1  3) © 2012 Pearson Education, Inc.

19.4 Thermoplasmatales Ferroplasma Chemolithotrophic Acidophilic Oxidizes Fe2+ to Fe3+, generating acid Grows in mine tailings containing pyrite (FeS2) © 2012 Pearson Education, Inc.

19.4 Thermoplasmatales Picrophilus Extreme acidophiles Grow optimally at pH 0.7 Model microbe for extreme acid tolerance © 2012 Pearson Education, Inc.

19.5 Thermococcales and Methanopyrus Three phylogenetically related genera of hyperthermophilic Euryarchaeota: Thermococcus Pyrococcus Methanopyrus Comprise a branch near root of archaeal tree © 2012 Pearson Education, Inc.

19.5 Thermococcales and Methanopyrus Distinct order that contains Thermococcus and Pyrococcus (Figure 19.11) Indigenous to anoxic thermal waters Highly motile © 2012 Pearson Education, Inc.

Figure 19.11 Figure 19.11 Spherical hyperthermophilic Euryarchaeota from submarine volcanic areas. © 2012 Pearson Education, Inc.

19.5 Thermococcales and Methanopyrus Methanopyrus (Figure 19.12) Methanogenic Contains unique membrane lipids © 2012 Pearson Education, Inc.

Ether linkage Figure 19.12 Figure 19.12 Methanopyrus. © 2012 Pearson Education, Inc.

19.6 Archaeoglobales Archaeoglobales (Figure 19.13) Key genera: Archaeoglobus, Ferroglobus Hyperthermophilic Couple oxidation of H2, lactate, pyruvate, glucose, or complex organic compounds to the reduction of SO42 to H2S © 2012 Pearson Education, Inc.

Figure 19.13 Figure 19.13 Archaeoglobales. © 2012 Pearson Education, Inc.

19.7 Nanoarchaeum and Aciduliprofundum Nanoarchaeum equitans (Figure 19.14) One of the smallest cellular organisms (~0.4 µm) Obligate symbiont of the crenarchaeote Ignicoccus Contains one of the smallest genomes known Lacks genes for all but core molecular processes Depends upon host for most of its cellular needs © 2012 Pearson Education, Inc.

Figure 19.14 Figure 19.14 Nanoarchaeum equitans. © 2012 Pearson Education, Inc.

III. Crenarchaeota 19.8 Habitats and Energy Metabolism 19.9 Crenarchaeota from Terrestrial Volcanic Habitats 19.10 Crenarchaeota from Submarine Volcanic Habitats 19.11 Crenarchaeota from Nonthermal Habitats and Nitrification in Archaea © 2012 Pearson Education, Inc.

19.8 Habitats and Energy Metabolism Crenarchaeota Inhabit temperature extremes Most cultured representatives are hyperthermophiles Found in extreme heat environments (Figure 19.16) Other representatives found in extreme cold environments © 2012 Pearson Education, Inc.

Figure 19.16 Figure 19.16 Terrestrial habitats of hyperthermophilic Archaea: Yellowstone National Park (Wyoming, USA). © 2012 Pearson Education, Inc.

19.8 Habitats and Energy Metabolism Hyperthermophilic Crenarchaeota Most are obligate anaerobes Chemoorganotrophs or chemolithotrophs with diverse electron donors and acceptors © 2012 Pearson Education, Inc.

19.9 Crenarchaeota from Terrestrial Volcanic Habitats Sulfolobales Key genera: Sulfolobus and Acidianus (Figure 19.17) Sulfolobus Grows in sulfur-rich acidic hot springs Aerobic chemolithotrophs that oxidize reduced sulfur or iron Acidianus Also lives in acidic sulfur hot springs Uses elemental sulfur both aerobically and anaerobically © 2012 Pearson Education, Inc.

Figure 19.17 Figure 19.17 Acidophilic hyperthermophilic Archaea, the Sulfolobales. © 2012 Pearson Education, Inc.

19.9 Crenarchaeota from Terrestrial Volcanic Habitats Thermoproteales Key genera: Thermoproteus, Thermofilum, and Pyrobaculum (Figure 19.18) Inhabit neutral or slightly acidic hot springs or hydrothermal vents © 2012 Pearson Education, Inc.

Figure 19.18 Figure 19.18 Rod-shaped hyperthermophilic Archaea, the Thermoproteales. © 2012 Pearson Education, Inc.

19.10 Crenarchaeota from Submarine Volcanic Habitats Shallow-water thermal springs and deep-sea hydrothermal vents harbor the most thermophilic of all known Archaea Pyrodictium and Pyrolobus Desulfurococcus and Ignicoccus Staphylothermus © 2012 Pearson Education, Inc.

19.10 Crenarchaeota from Submarine Volcanic Habitats Pyrodictium and Pyrolobus (Figure 19.19) Optimum growth temperature above 100C Pyrolobus fumarii is one of the most thermophilic Strain 121 can grow up to 121C © 2012 Pearson Education, Inc.

Figure 19.19 Figure 19.19 Desulfurococcales with growth temperature optima 100°C. © 2012 Pearson Education, Inc.

19.10 Crenarchaeota from Submarine Volcanic Habitats Desulfurococcus and Ignicoccus (Figure 19.20) Desulfurococcus is a strictly anaerobic S0-reducing organism Ignicoccus grows optimally at 90Cand its metabolism is H2/S0 based Ignicoccus contains an outer membrane similar to that of gram-negative Bacteria © 2012 Pearson Education, Inc.

Figure 19.20 Figure 19.20 Desulfurococcales with growth temperature optima 100°C. © 2012 Pearson Education, Inc.

19.10 Crenarchaeota from Submarine Volcanic Habitats Staphylothermus (Figure 19.21) Spherical cells About 1 mm in diameter Forms aggregates of up to 100 cells Chemoorganotroph that grows optimally at 92C © 2012 Pearson Education, Inc.

Figure 19.21 Figure 19.21 The hyperthermophile Staphylothermus marinus. © 2012 Pearson Education, Inc.

19.11 Crenarchaeota from Nonthermal Habitats Nonthermophilic Crenarchaeota have been identified in cool or cold marine waters and terrestrial environments by culture-independent studies (Figure 19.22) Abundant in deep ocean waters Appear to be capable of nitrification (Figure 19.23) © 2012 Pearson Education, Inc.

Figure 19.22 Figure 19.22 Cold-dwelling Crenarchaeota. © 2012 Pearson Education, Inc.

Figure 19.23 Figure 19.23 Nitrosopumilus maritimus, a nitrifying species of Archaea. © 2012 Pearson Education, Inc.

IV. Evolution and Life at High Temperatures 19.12 An Upper Temperature Limit for Microbial Life 19.13 Molecular Adaptations to Life at High Temperature 19.14 Hyperthermophilic Archaea, H2, and Microbial Evolution © 2012 Pearson Education, Inc.

19.12 An Upper Temperature Limit for Microbial Life What are the upper temperature limits for life? New species of thermophiles and hyperthermophiles being discovered (Figure 19.25) Laboratory experiments with biomolecules suggest 140–150C © 2012 Pearson Education, Inc.

Methanopyrus kandleri Archaea 120 Strain 121 Pyrolobus fumarii Figure 19.25 130 Bacteria Methanopyrus kandleri Archaea 120 Strain 121 Pyrolobus fumarii 110 Pyrodictium occultum 100 Thermoproteus tenax Aquifex pyrophilus Maximum growth temperature (°C) 90 Sulfolobus acidocaldarius 80 Thermus aquaticus Figure 19.25 Thermophilic and hyperthermophilic prokaryotes. 70 60 Geobacillus stearothermophilus 50  1960 1970 1980 1990 2000 2010 Year © 2012 Pearson Education, Inc.

19.13 Molecular Adaptations to Life at High Temperature Stability of Monomers Protective effect of high concentration of cytoplasmic solutes Use of more heat-stable molecules For example, use of nonheme iron proteins instead of proteins that use NAD and NADH © 2012 Pearson Education, Inc.

19.13 Molecular Adaptations to Life at High Temperature 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 © 2012 Pearson Education, Inc.

19.13 Molecular Adaptations to Life at High Temperature Chaperonins Class of proteins that refold partially denatured proteins Thermosome A major chaperonin protein complex in Pyrodictium © 2012 Pearson Education, Inc.

19.13 Molecular Adaptations to Life at High Temperature DNA Stability High intracellular solute levels stabilize DNA Reverse DNA gyrase Introduces positive supercoils into DNA Stabilizes DNA Found only in hyperthermophiles High intracellular levels of polyamines (e.g., putrescine, spermidine) stabilize DNA and RNA DNA-binding proteins (histones) compact DNA into nucleosome-like structures (Figure 19.27) © 2012 Pearson Education, Inc.

Figure 19.27 Figure 19.27 Archaeal histones and nucleosomes. © 2012 Pearson Education, Inc.

19.13 Molecular Adaptations to Life at High Temperature Lipid Stability Possess dibiphytanyl tetraether type lipids; form a lipid monolayer membrane structure SSU rRNA Stability Higher GC content © 2012 Pearson Education, Inc.

19.14 Hyperthermophilic Archaea, H2, and Microbial 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 (Figure 19.28) © 2012 Pearson Education, Inc.

S0 or Fe2 H2 ? Figure 19.28 Thermophilic Chemolithotrophy 95° 113° 122° Thermophilic Chemoorganotrophy 110° Thermophilic Phototrophy 73 40 50 60 70 80 90 100 110 120 130 140 Figure 19.28 Upper temperature limits for energy metabolism. Temperature (C) © 2012 Pearson Education, Inc.