Preface xi Béatrice CLOUET-D'ORVAL, Bruno FRANZETTI and Philippe OGER -- Chapter 1. The Discovery of Archaea 1 Patrick FORTERRE -- 1.1. Introduction -- 1.2. Prokaryotic-eukaryotic dichotomy -- 1.3. Two domains for prokaryotes: archaebacteria and eubacteria -- 1.3.1. Ribosomal RNA as a molecular marker: a historical choice -- 1.3.2. Atypical ribosomal RNA of methanogenic "bacteria" -- 1.3.3. The concept of archaeobacteria -- 1.3.4. The grouping of halophilic and thermo-acidophilic "bacteria" with methanogens within archaeobacteria -- 1.4. The living trilogy -- 1.4.1. The concept of archaeobacteria confirmed by the uniqueness of their membrane phospholipids -- 1.4.2. German biochemists: champions of the archaeobacteria concept -- 1.4.3. The evolutionary link between archaeobacteria and eukaryotes and the introduction of the term archaea -- 1.5. Archaea and high-temperature living -- 1.5.1. The discovery of anaerobic hyperthermophilic archaea -- 1.5.2. The race for the thermophilia record -- 1.5.3. The discovery of viruses in hyperthermophilic archaea -- 1.6. Non-extremophilic archaea discovered by molecular ecology: a new vision of the third domain -- 1.7. Conclusion -- 1.8. References -- Chapter 2. Evolution of Archaea and Their Taxonomy 29 Patrick FORTERRE -- 2.1. Introduction -- 2.2. One domain, three major branches and a few isolated "phyla" -- 2.2.1. One domain, two phyla -- 2.2.2. A first orphaned phylum, the korarchaeota. -- 2.2.3. The first phylogenies based on conserved proteins -- 2.2.4. The special case of Methanopyrus kandleri -- 2.2.5. The special case of Nanoarchaeum equitans -- 2.2.6. Thaumarchaea -- 2.3. From phyla to superphyla -- 2.3.1. Metagenomics and the explosion in the number of archaeal phyla -- 2.3.2. The superphylum TACK -- 2.3.3. The DPANN -- 2.3.4. The Asgard archaea -- 2.3.5. Stygia/Hadarchaeota -- 2.3.6. Hydrothermarchaeota -- 2.4. Euryarchaea. -- 2.4.1. Group I Euryarchaea -- 2.4.2. Group II Euryarchaea. -- 2.5. A new nomenclature for the taxonomy of archaea? -- 2.6. Reconstructing the last common ancestor of archaea: LACA -- 2.6.1. Rooting the archaeal tree. -- 2.6.2. Two opposing visions of LACA: simple or complex -- 2.6.3. The likely hyperthermophilic nature of LACA. -- 2.6.4. The possibility of a methanogenic LACA -- 2.7. Conclusion -- 2.8. References -- Chapter 3. Archaea and the Tree of Life 89 Patrick FORTERRE -- 3.1. Introduction -- 3.2. The progenote concept -- 3.3. Archaea: prokaryotes related to eukaryotes -- 3.4. Rooting the universal tree -- 3.5. The nature of LUCA -- 3.5.1. A simpler LUCA compared to the organisms of the three current domains -- 3.5.2. An RNA genome for LUCA? -- 3.5.3. A presumably mesophilic LUCA -- 3.5.4. LUCA's proteome -- 3.6. The topology of the universal tree under debate -- 3.6.1. Early challenge to the Woese tree: the eocyte hypothesis -- 3.6.2. Searching for the archean ancestor of eukaryotes -- 3.6.3. Discovery of the Asgard archaea: validation of the 2D hypothesis? -- 3.6.4. Controversies over the position of Asgard archaea -- 3.7. The origin of new eukaryotic-like proteins discovered in Asgard archaea -- 3.8. Asgard archaea and the origin of eukaryotes -- 3.8.1. Asgard archaea at the origin of eukaryotes: a new paradigm -- 3.8.2. The inside-out model based on nanotubes discovered in Asgard archaea -- 3.8.3. The two-bacteria 2D model -- 3.8.4. The origin of eukaryotic cell complexity -- 3.9. The biological issues posed by the 2D model -- 3.10. Viruses and the universal tree of life -- 3.11. Conclusion -- 3.12. References -- Chapter 4. Archaea: Habitats and Associated Physiologies 153 Karine ALAIN, Marc COZANNET, Maxime ALLIOUX, Sarah THIROUX and Jordan HARTUNIANS -- 4.1. Introduction -- 4.2. Archaea of extreme habitats: extremophiles -- 4.2.1. Psychrophiles -- 4.2.2. Thermophiles/hyperthermophiles -- 4.2.3. Acidophiles -- 4.2.4. Alkalophiles -- 4.2.5. Halophiles -- 4.2.6. Piezophiles -- 4.2.7. Radiotolerant archaea -- 4.2.8. Poly-extremophilic archaea -- 4.2.9. Record-holding archaea -- 4.3. Archaea populating ordinary, non-extreme environments -- 4.3.1. Phytobiomes, rice paddies and peatlands -- 4.3.2. Aquatic habitats: lakes, oceans and estuaries -- 4.3.3. Environments linked to human activities: example of waste treatment and anaerobic digesters (methanizers) -- 4.3.4. Animal microbiomes -- 4.4. Archaea resistant to cultivation efforts -- 4.5. Challenges and success stories -- 4.6. Conclusion -- 4.7. References -- Chapter 5. Methanogenic Archaea 205 Tristan WAGNER, Laurent TOFFIN and Guillaume BORREL -- 5.1. Diversity of methanogens and their environments -- 5.1.1. Methane sources and sinks -- 5.1.2. Taxonomic and metabolic diversity -- 5.1.3. Ecological diversity of methanogens -- 5.2. Interactions of methanogens with their environment -- 5.2.1. Competition for substrates -- 5.2.2. Ecological and syntrophic interactions -- 5.2.3. Human-methanogen association -- 5.3. Bioenergetics and biochemistry of methanogenesis -- 5.3.1. Energy extremophiles -- 5.3.2. Cofactors used in methanogenesis -- 5.3.3. Different types of methanogenesis -- 5.3.4. MCR, the unique enzyme capable of generating biogenic methane -- 5.4. Anaerobic methanotrophs and anaerobic oxidation of multi-carbon alkanes -- 5.5. Evolution of methanogenesis -- 5.5.1. An ancestral metabolism -- 5.5.2. Metabolic adaptations -- 5.6. The impact of methanogens in our modern society -- 5.7. References -- Chapter 6. Hyperthermophilic Archaeal Viruses 247 Diana BAQUERO, Mart KRUPOVIC, Claire GESLIN and David PRANGISHVILI -- 6.1. Introduction -- 6.2. Morphological and structural diversity -- 6.2.1. Viruses with unique morphologies: families Ampullaviridae, Spiraviridae and Guttaviridae -- 6.2.2. Filamentous viruses: families Rudiviridae, Lipothrixviridae, Tristromaviridae and Clavaviridae -- 6.2.3. Spherical and icosahedral viruses: families Globuloviridae, Ovaliviridae, Portogloboviridae and Turriviridae -- 6.2.4. Fusiform viruses: families Fuselloviridae and Bicaudoviridae -- 6.3. Genomic features of hyperthermophilic archaeal viruses -- 6.3.1. Genome content -- 6.3.2. Structural genomics -- 6.4. Virus-host interactions -- 6.4.1. Virus entry -- 6.4.2. Virion egress -- 6.5. Conclusions -- 6.6. References -- List of Authors -- Index.