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20 The Archaea 1 Copyright © McGraw-Hill Global Education Holdings, LLC. Permission required for reproduction or display. Outlines • 20.1 What is archaea: an overview • 20.2 Phylum Crenarchaeota 熱泉古菌 • 20.3 Phylum Euryarchaeota 寬廣古菌 2 20.1 Overview of the Archaea 1. Some common habitats of archaea 2. The debate that surrounds archaeal taxonomy 3. Three key metabolic pathways that are central to archaeal physiology 3 Archaea • Many features in common with Eukarya (真核) – genes encoding proteins for replication, transcription, translation • Features in common with Bacteria – genes encoding proteins for metabolism • Other elements are unique to Archaea – unique rRNA gene structure – capable of methanogenesis • Highly diverse with respect to morphology, physiology, reproduction, and ecology • Best known for growth in anaerobic, hypersaline, pH extremes, and high-temperature habitats • Also found in marine arctic temperature and tropical waters 4 Archaeal Taxonomy • 5 major physiological and morphological groups 5 Archaeal Taxonomy • Two phyla based on Bergey’s Manual – Euryarchaeota (寬廣古菌) – Crenarchaeota (熱泉古菌) • Metagenomic analysis reveals additional species (some are not culturable) • 16S rRNA and SSU rRNA analysis also shows – Group I are Thaumarchaeota (奇古菌) – Group II are Korachaeota (初 古菌) 6 7 Archaeal Metabolism • Great variation among the different archaeal groups • Autotrophy, organotrophy, and phototrophy have been observed • Differ from other groups in glucose catabolism, pathways for CO2 fixation, and the ability of some to synthesize methane (甲烷) 8 Archaeal Metabolism: Autotrophy • Carbon fixation pathways include – Reductive acetyl-CoA pathway – 3-hydroxyproprionate/4-hydroxybutyrate (HP/HB) cycle – Dicarboxylate/4-hydroxybutyrate (DC/HB) cycle 9 Archaeal Metabolism: Autotrophy-1 • Reductive acetyl-CoA pathway – Most energy efficient (1 ATP burned/pyruvate formed) – 2 CO2 molecules incorporated into 1 acetyl group – Acetyl group combined with additional CO2 to form pyruvate – Used by methanogens both for carbon fixation and for energy conservation 10 Archaeal Metabolism: Autotrophy-2 & 3 – 5 ATP/pyruvate formed – Found in anaerobic and microaerobic members HP/HB cycle DC/HB cycle – Some of its enzymes are sensitive to oxygen – Steps are similar to a reversal of the TCA cycle – 9 ATP/ pyruvate synthesized – Can be operated under aerobic conditions – Has less of a demand for metal cofactors 11 Acetyl-CoA Assimilation: Glyoxylate (red lines) and Methylaspartate Pathways (black lines) Autotrophic archaea and some haloarchaea use the glyoxylate pathway Haloarchaea lack ICL and use the methylaspartate pathway 12 Archaeal Metabolism Chemoorganotropy-1: modified EmbdenNo net ATP generation on Meyerhof archaea • Similarities in eukaryotes and bacteria • 3 pathways unique to Archaea – modified Embden-Meyerhof pathway – 2 modified Entner-Duodoroff pathways 13 Chemoorganotropy-2: 2 modified Entner-Duodoroff pathways No ATP generation 14 20.2 Phylum Crenarchaeota 1. The major physiological types among crenarchaea 2. The importance of crenarchaeol in the discovery of new crenarchaeotes 3. Hyperthermophilic and thermoacidophilic growth 15 Phylum Crenarchaeota • Most are extremely thermophilic – hyperthermophiles (hydrothermal vents) • Most are strict anaerobes • Some are acidophiles • Many are sulfur-dependent – for some, used as electron acceptor in anaerobic respiration – for some, used as electron source 16 Parasitic Nanoarchaeum attaches to Ignicoccus The outer membrane of Ignicoccus house H2:sulfur oxidoreductase and ATP synthase complex, making it the only micro to have an energized outer membrane. Nanoarchaeum equitans forms tiny cells (350-500 mM) that attach to Ignicoccus. Boiling temperature and rich in sulfur 17 Hyperthermophilic Crenarchaeote • Pyrodiciaceae is hyperthermophilic as it can survive autoclaving for an hour • Strictly anaerobic • Use H2/formate as a electron donor and Fe3+ as an electron acceptor • Under anaerobic condition, Fe(III) is reduced to Fe3O4 18 Crenarchaeota… • Include organotrophs and lithotrophs (sulfuroxidizing and hydrogen-oxidizing) • Contains 25 genera – two best studied are Sulfolobus and Thermoproteus 19 Genus Thermoproteus • Long thin rod, bent or branched – cell walls composed of glycoprotein • Thermoacidophiles – 70–97 °C – pH 2.5–6.5 • Anaerobic metabolism – lithotrophic on sulfur and hydrogen – organotrophic on sugars, amino acids, alcohols, and organic acids using elemental sulfur as electron acceptor • Autotrophic using CO or CO2 as carbon source 20 Genus Sulfolobus • Irregularly lobed, spherical shaped – cell walls contain lipoproteins and carbohydrates • Thermoacidophiles – 70–80°C – pH 2–3 • Metabolism – lithotrophic on sulfur using oxygen (usually) or ferric iron as electron acceptor – organotrophic on sugars and amino acids 21 Genome Construction of Sulfolobus Sulfolobus grows at pH 2-4, but maintains a cytoplasmic pH at approximately 6.5. The pH gradient allows for ATP generation by ATPase and at least 15 secondary transporter for organic solute uptake. 22 Phylum Crenarchaeota • Group I archaea – archaeal unique membrane lipid, crenarchaeol is widespread in nature • marine waters • rice paddies, soil, freshwater • Recent growth of mesophilic archaea – capable of nitrification (ammonia to nitrate) 23 20.3 Phylum Euryarchaeota 1. Methanogenesis: process and its importance in carbon flow and energy production 2. The physiology and ecology of anaerobic methane oxidation 3. How halophiles cope with osmotic stress 4. Rhodopsin-based phototrophy as used by halophiles 5. The habitats of methanogens and halophiles 6. List one unique feature for Thermoplasma, Pyrococcus, and Archaeoglobus 24 Phylum Euryarchaeota • Consists of many classes, orders, and families • Often divided informally into five major groups 1. methanogens 2. halobacteria 3. thermoplasms 4. extremely thermophilic S0-metabolizers 5. sulfate-reducers 25 1. Methanogens • All methanogenic microbes are Archaea – called methanogens: produce methane • Methanogenesis – last step in the degradation of organic compounds – occurs in anaerobic environments (only when O2 and most other electron acceptors are unavailable) • e.g., animal rumens • e.g., anaerobic sludge digesters • e.g., within anaerobic protozoa 26 Methanogens • 26 genera, largest group of cultured archaea – differ in morphology – 16S rRNA – cell walls – membrane lipids 27 28 Methanogens • Unique anaerobic production of methane – hydrogen, CO2 oxidation – coenzymes, cofactors – ATP production linked with methanogenesis • What are the potential mechanisms by which methanogens are thought to couple CO2 reduction to ATP generation? Two mechanisms are hypothesized currently, which are not exclusive. One is that protons are generated on the outside of the membrane in step 5, which would build the proton motive force, in turn allowing ATP synthesis via ATP synthase. The other is that step four drives uptake of Na+ ions, and releasing those back across the membrane could drive either H+ export or ATP synthesis directly. 29 30 Ecological and Practical Importance of Methanogens • Important in wastewater treatment • Can produce significant amounts of methane – can be used as clean burning fuel and energy source – is greenhouse gas and may contribute to global warming • Can oxidize iron – contributes significantly to corrosion of iron pipes • Can form symbiotic relationships with certain bacteria, assisting carbon/sulfur cycling Sulfate-reducing bacteria Methanogens 31 2. Halobacteria • Order Halobacteriales; 17 genera in one family, Halobacteriaceae • Extreme halophiles (halobacteria) – require at least 1.5 M NaCl • cell wall disintegrates if [NaCl] < 1.5 M – growth optima near 3–4 M NaCl • Aerobic, respiratory, chemoheterotrophs with complex nutritional requirements 32 Strategies to Cope with Osmotic Stress • Increase cytoplasmic osmolarity – use compatible solutes (small organics) • “Salt-in” approach – use Na+/H+ antiporters/K+ symporters to increase concentration of KCl and NaCl to level of external environment • Acidic amino acids in proteins – Acidic aa on the surface of the folded protein attract cations, which form a hydrated shell on the protein 33 e.g., Halobacterium salinarium (H. halobium) • Has unique type of photosynthesis – not chlorophyll based – uses modified cell membrane (contains bacteriorhodopsin) – absorption of light by bacteriorhodopsin drives proton transport, creating PMF for ATP synthesis 34 Features of Halobacterium Rhodopsins • Bacteriorhodopsin: light-driven ion pumps – chromophore similar to retinal – seven membrane spanning domains – purple aggregates in membrane • Halorhodopsin: light-driven ion pumps – light energy to transport chloride ions • 2 sensory rhodopsins: photosensory receptors – flagellar attached photoreceptors 35 Genomic Reconstruction of of Halobacterium NRC-1 36 Proteorhodopsin • Now known to be widely distributed among bacteria and archaea – found in marine bacterioplankton using DNA sequence analysis of uncultivated organisms – also found in cyanobacteria 37 3. Thermoplasms • Class Thermoplasmata • Three different genera – Thermoplasmataceae – Picrophilaceae – Ferroplasmataceae • Thermoacidophiles • Lack cell walls 38 Genus Thermoplasma • Thermoacidophiles; grow in refuse piles of coal mines at 55–59°C, pH 1–2, FeS • Cell structure – shape depends on temperature – may be flagellated and motile – cell membrane strengthened by diglycerol tetraethers (caldarchaeol), lipopolysaccharides, and glycoproteins – nucleosome-like structures formed by association of DNA with histone-like proteins 39 Genus Picrophilus • Irregularly shaped cocci, 1 to 5 M diameter – large cytoplasmic cavities that are not membrane bound – no cell wall – has S-layer outside plasma membrane • Thermoacidophiles – 47–65°C (optimum 60°C) – pH <3.5 (optimum 0.7) • Aerobic 40 4. Extremely Thermophilic S0-Reducers • Class Thermococci; one order, Thermococcales • One family containing three genera, Thermococcus, Paleococcus, Pyrococcus • Motile by flagella • Optimum growth temperatures 88–100°C • Strictly anaerobic • Reduce sulfur to sulfide 41 5. Sulfate-Reducing Euryarchaeota • class Archaeoglobi; order Archaeoglobales; one family with one genus, Archaeoglobus • irregular coccoid cells – cell walls consist of glycoprotein subunits • extremely thermophilic (optimum 83°C) – isolated from marine hydrothermal vents • metabolism – lithotrophic (H2) or organotrophic (lactate/glucose) – use sulfate, sulfite, or thiosulfite as electron acceptor – possess some methanogen coenzymes 42 Aciduliprofundum • Newly characterized thermophilic euryarchaeote – acidophile, requires pH 3.3 to 5.8 – thermophile, 60–75oC for growth – inhabit hydrothermal vents – sulfur- and iron-reducing heterotroph • First thermoacidophile in sulfide rich areas • May be important in iron and sulfur cycling 43 5/9/2017 Homework 1. Define ‘organotrophy’, ‘lithotrophy’, ‘autotrophy’, and ‘phototrophy’. 2. Why do methogens use the reductive acetyl-CoA pathway for carbon fixation (Figure 20.3)? Given that the DC/HB pathway uses far less ATP per pyruvate synthesized than the HP/MB pathway, why do some archaea use the HP/HB pathway instead? Explain why the fixation of CO2 by Thermoproteus spp. using the DC/HB cycle is not photosynthesis (Figure 20.4). 3. Why do haloarchaea use the methylaspartate rather than the glyoxylate cycle for the incorporation of acetate? Why might the production of glutamate as an intermediate be beneficial for some haloarchaea (Figure 20.5)? 4. Discuss the role of external pH on the magnitude of the proton motive force generated by Sulfolobus spp. (Figure 20.11). 5. Define halophiles. How do halophiles cope with osmotic stress? What are the functions of archaerhodopsins and sensory rhodopsins of Halobacterium salinarum? 6. How do thermoplasmas, a group of archaea lacking cell walls, cope with high temperatures and acidic pH? 44