20 The Archaea Copyright © McGraw-Hill Global Education Holdings, LLC. Permission required for reproduction or display.

20.1 Overview of the Archaea List some common habitats in which archaea reside Describe the debate that surrounds archaeal taxonomy Compare at least three key metabolic pathways that are central to archaeal physiology with those used by bacteria

Archaea Many features in common with Eukarya genes encoding protein: replication, transcription, translation Features in common with Bacteria genes for metabolism Other elements are unique to Archaea unique rRNA gene structure capable of methanogenesis

Archaea 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

Archaeal Taxonomy Five major physiological and morphological groups

Archaeal Taxonomy Two phyla based on Bergey’s Manual Euryarchaeota Crenarchaeota 16S rRNA and SSU rRNA analysis also shows Group I are Thaumarchaeota Group II are Korachaeota

Archaeal Metabolism Great variation among the different archaeal groups Organotrophy, autotrophy, and phototrophy have been observed Differ from other groups in glucose catabolism, pathways for CO2 fixation, and the ability of some to synthesize methane

Archaeal Metabolism Carbon fixation pathways include Reductive acetyl-CoA pathway 3-hydroxyproprionate/4-hydroxybutyrate (HP/HB) cycle Dicarboxylate/4-hydroxybutyrate (DC/HB) cycle

Archaeal Metabolism 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

Archaeal Metabolism 3-hydroxyproprionate/ 4-hydroxybutyrate (HP/HB) cycle Requires more energy input (9 ATP/ pyruvate synthesized) Can be operated under aerobic conditions Has less of a demand for metal cofactors

Archaeal Metabolism Dicarboxylate/4- hydroxybutyrate (DC/HB) cycle Consumes 5 ATP/pyruvate formed Some of its enzymes are sensitive to oxygen Steps are similar to a reversal of the TCA cycle

Carbohydrate Metabolism Similarities in eukaryotes and bacteria 3 pathways unique to Archaea modified Embden- Meyerhof 2 modified Entner- Duodoroff

Carbohydrate Metabolism Similarities in eukaryotes and bacteria 3 pathways unique to Archaea modified Embden- Meyerhof 2 modified Entner- Duodoroff

20.2 Phylum Crenarchaeota List the major physiological types among crenarchaea Evaluate the importance of crenarchaeol in the discovery of new crenarchaeotes Discuss hyperthermophilic and thermoacidophilic growth

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

Crenarchaeota… Include organotrophs and lithotrophs (sulfur- oxidizing and hydrogen-oxidizing) Contains 25 genera two best studied are Sulfolobus and Thermoproteus

Genus Thermoproteus Long thin rod, bent or branched Thermoacidophiles 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

Genus Sulfolobus Irregularly lobed, spherical shaped Thermoacidophiles 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

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)

20.3 Phylum Euryarchaeota Outline the process of methanogenesis and discuss its importance in the flow of carbon through the biosphere as well as in the production of energy Discuss the physiology and ecology of anaerobic methane oxidation Explain the strategies halophiles have evolved to cope with osmotic stress and why these strategies are needed Outline rhodopsin-based phototrophy as used by halophiles Describe the habitats in which methanogens and halophiles reside List one unique feature for Thermoplasma, Pyrococcus, and Archaeoglobus

Phylum Euryarchaeota Consists of many classes, orders, and families Often divided informally into five major groups methanogens halobacteria thermoplasms extremely thermophilic S0-metabolizers sulfate-reducers

Methanogens All methanogenic microbes are Archaea Methanogenesis called methanogens: produce methane Methanogenesis last step in the degradation of organic compounds occurs in anaerobic environments e.g., animal rumens e.g., anaerobic sludge digesters e.g., within anaerobic protozoa

Methanogens 26 genera, largest group of cultured archaea differ in morphology 16S rRNA cell walls membrane lipids

Methanogens Unique anaerobic production of methane hydrogen, CO2 oxidation coenzymes, cofactors ATP production linked with methanogenesis

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

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

Strategies to Cope with Osmotic Stress Increase cytoplasmic osmolarity use compatible solutes (small organics) “Salt-in” approach use antiporters/symporters to increase concentration of KCl and NaCl to level of external environment Acidic amino acids in proteins

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

Features of Halobacterium Rhodopsins Bacteriorhodopsin chromophore similar to retinal seven membrane spanning domains purple aggregates in membrane Halorhodopsin light energy to transport chloride ions 2 sensory rhodopsins flagellar attached photoreceptors

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

Thermoplasms Class Thermoplasmata Three different genera Thermoplasmataceae Picrophilaceae Ferroplasmataceae Thermoacidophiles Lack cell walls

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, lipopolysaccharides, and glycoproteins nucleosome-like structures formed by association of DNA with histonelike proteins

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

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

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

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